diff --git a/README.md b/README.md
index 820b2f11d35686b0aef3d8b19adfcfd5a0d2d588..7aa82f45fac9b6e96cb748bd41d823e002872b8e 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,18 @@
-# naked-singularity
+# Singularity
A repository of definition files for building
[Singularity](https://sylabs.io/guides/latest/user-guide) containers
around the software applications, frameworks, and libraries you need to
run on high-performance computing systems.
+Based on [naked-singularity](https://github.com/mkandes/naked-singularity). Thanks M. Kandas
+
## Install Singularity
Install Singularity on your Linux desktop, laptop, or virtual machine.
```bash
-sudo ./naked-singularity.sh install
+sudo ./install-singularity.sh install
```
## Build a Singularity container from a definition file
@@ -21,47 +23,3 @@ available in this repository.
```bash
sudo singularity build ubuntu.sif definition-files/ubuntu/Singularity.ubuntu-18.04
```
-
-## Download an existing Singularity container
-
-A number of pre-built containers from this repository are also now
-hosted at Singularity Hub.
-
-```bash
-singularity pull shub://mkandes/naked-singularity:ubuntu-18.04
-```
-
-IMPORTANT: [Singularity Hub has been archived](https://vsoch.github.io/2021/singularity-hub-archive).
-For the time being, naked-singularity definition files that rely on
-containers that were built and hosted on Singularity Hub prior to it
-being archived will continue to pull in these container dependencies and
-build properly. Note, however, new pre-built containers of the latest
-naked-singularity definition files are currently being updated to be
-hosted via the [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry).
-
-
-## Status
-
-A work in progress.
-
-## Contribute
-
-If you would like to contribute one of your own Singularity container
-definition files for a specific application OR request a modification to
-an existing container definition, then please submit a pull request.
-
-## Author
-
-Marty Kandes, Ph.D.
-Computational & Data Science Research Specialist
-High-Performance Computing User Services Group
-San Diego Supercomputer Center
-University of California, San Diego
-
-## Version
-
-2.0.2
-
-## Last Updated
-
-Sunday, November 7th, 2021
diff --git a/archive/README.md b/archive/README.md
deleted file mode 100644
index fc8155bc982ccbfa161988f916fc71e9129b24f4..0000000000000000000000000000000000000000
--- a/archive/README.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# Archive
-
-This directory archives all of the older, system-specific, Singularity
-2.x-era container definition files that were created as part of the
-naked-singularity project during its first few years of existance. It
-also stores a copy of the original naked-singularity.sh helper script.
-Neither the original helper script, nor the definitions files stored
-within this directory will be updated again. As such, they should not be
-used in any production workloads moving forward, unless absolutely
-necessary. They are stored here simply to serve as a historical
-reference for the time being.
diff --git a/archive/comet/R/R.def b/archive/comet/R/R.def
deleted file mode 100644
index a53d60cd7ff97ee7320227da7d6db8aa7bd5cd84..0000000000000000000000000000000000000000
--- a/archive/comet/R/R.def
+++ /dev/null
@@ -1,202 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME R
- APPLICATION_VERSION 3.4.2
- APPLICATION_URL https://www.r-project.org/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 4096
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190327
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set PATH and LD_LIBRARY_PATH variables
- export LD_LIBRARY_PATH="/opt/openblas-0.2.20/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/R-3.4.2/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/R-3.4.2/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages and libraries from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- apt-get -y install libgmp-dev
- apt-get -y install libmpfr-dev
- apt-get -y install libmpc-dev
- apt-get -y install libisl-dev
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install R dependencies
- apt-get -y install libreadline-dev
- apt-get -y install zlib1g-dev
- apt-get -y install bzip2
- apt-get -y install libbz2-dev
- apt-get -y install xz-utils
- apt-get -y install liblzma-dev
- apt-get -y install libpcre3
- apt-get -y install libpcre3-dev
- apt-get -y install curl
- apt-get -y install libcurl4-gnutls-dev
-
- #cd /tmp
-
- # Download, build, and install OpenBLAS for R
- wget http://github.com/xianyi/OpenBLAS/archive/v0.2.20.tar.gz
- tar -xzvf v0.2.20.tar.gz
- cd OpenBLAS-0.2.20
- make NUM_THREADS=24
- make install PREFIX='/opt/openblas-0.2.20'
-
- export CPPFLAGS="-I/opt/openblas-0.2.20/include ${CPPFLAGS}"
- export LDFLAGS="-L/opt/openblas-0.2.20/lib ${LDFLAGS}"
- export LD_LIBRARY_PATH="/opt/openblas-0.2.20/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install R
- wget https://cran.cnr.berkeley.edu/src/base/R-3/R-3.4.2.tar.gz
- tar -xzvf R-3.4.2.tar.gz
- cd R-3.4.2
- ./configure --prefix="/opt/R-3.4.2" --enable-R-shlib --with-blas --with-lapack --with-x
- make
- make install
-
- export PATH="/opt/R-3.4.2/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/R-3.4.2/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install OpenMPI for Rmpi
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix='/opt/openmpi-1.8.4'
- make all install
-
- export CPPFLAGS="-I/opt/openmpi-1.8.4/include ${CPPFLAGS}"
- export LDFLAGS="-L/opt/openmpi-1.8.4/lib ${LDFLAGS}"
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install Rmpi
- wget https://cran.r-project.org/src/contrib/Rmpi_0.6-7.tar.gz
- R CMD INSTALL Rmpi_0.6-7.tar.gz --configure-args='--with-Rmpi-type=OPENMPI --with-Rmpi-include=/opt/openmpi-1.8.4/include --with-Rmpi-libpath=/opt/openmpi-1.8.4/lib'
-
- # Install MySQL client / libraries to support RMySQL
- apt-get -y install libmariadb-client-lgpl-dev
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/apbs-pdb2pqr-browndye/README.md b/archive/comet/apbs-pdb2pqr-browndye/README.md
deleted file mode 100644
index c8fbaea85c1df74bcd5335fa5c0d2fe22c6dff3e..0000000000000000000000000000000000000000
--- a/archive/comet/apbs-pdb2pqr-browndye/README.md
+++ /dev/null
@@ -1,75 +0,0 @@
-# Singularity container for molecular electrostatic calculations using PDB2PQR/APBS and Brownian dynamics with BrownDye.
-
-This singularity image contains a complete software environment for running [BrownDye (version 1 and 2)](http://browndye.ucsd.edu/) simulations. It also includes [PDB2PQR](http://www.poissonboltzmann.org/) and [APBS](http://www.poissonboltzmann.org/).
-
-Please [register](http://eepurl.com/by4eQr) your use of APBS and PDB2PQR.
-
-## Using the container
-
-Pull the singularity image:
-```
-singularity pull shub://nbcrrolls/electrostatics-singularity
-```
-
-Start bash shell in the container:
-```
-singularity shell nbcrrolls-electrostatics-singularity-master-latest.simg
-```
-
-Now the container is running and we can start a BrownDye2 job (using the Thrombin example):
-
-```
-cp -ai $BD2_PATH/examples/thrombin .
-cd thrombin
-sed -i 's/-PE0//g' *
-make all
-```
-
-And if you want to use BrownDye version 1:
-
-```
-export PATH=$BD1_PATH/bin:$PATH
-cp -ai $BD1_PATH/thrombin-example .
-cd thrombin-example
-sed -i 's/-PE0//g' *
-make all
-bd_top input.xml
-nam_simulation t-m-simulation.xml # this takes about 20min to run
-cat results.xml
-```
-After we are finished we can quit the container:
-
- exit
-
-You can also access individual applications from the electrostatics container.
-
-To list available applications:
-
-```
-$ singularity apps nbcrrolls-electrostatics-singularity-master-latest.simg
-apbs
-make_rxn_pairs
-nam_simulation
-pdb2pqr
-pqr2xml
-we_simulation
-xyz_trajectory
-```
-
-To run, for example, apbs calculation:
-```
-singularity exec nbcrrolls-electrostatics-singularity-master-latest.simg apbs input.in
-```
-
-or
-
-```
-singularity run --app apbs nbcrrolls-electrostatics-singularity-master-latest.simg input.in
-```
-
-
-This Singularity image is hosted on Singularity Hub: [](https://singularity-hub.org/collections/2497)
-
-
-
-###### This project is supported by [NBCR](http://nbcr.ucsd.edu).
diff --git a/archive/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def b/archive/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def
deleted file mode 100644
index b817be1418d62b71ab469234124317821a515aa8..0000000000000000000000000000000000000000
--- a/archive/comet/apbs-pdb2pqr-browndye/apbs-pdb2pqr-browndye.def
+++ /dev/null
@@ -1,231 +0,0 @@
-#################################################################################
-# Singularity Definition File
-#
-# Version: 2.0
-# Software: Molecular electrostatics singularity image
-# Software Version: 2019.3.7
-# Description: Docker image for BrownDye, APBS and PDB2PQR
-# Website: http://browndye.ucsd.edu
-# Tags: Electrostatics|Brownian Dynamics|Solvation
-# Build command: singularity build electrostatics.simg Singularity
-# Pull command: singularity pull shub://nbcrrolls/electrostatics-singularity
-# Run command: singularity shell nbcrrolls-electrostatics-singularity-master-latest.simg
-# Run command: singularity exec [image name] apbs input.in
-# Run command: singularity run --app apbs [image name] arguments
-# Run command: singularity run --app pdb2pqr [image name] arguments
-#
-#################################################################################
-
-Bootstrap: docker
-From: ubuntu:16.04
-
-%labels
-
- APPLICATION_NAME apbs-pdb2pqr-browndye
- APPLICATION_VERSION 1.5 + 2.1.0 + 2.0
- APPLICATION_URL http://www.poissonboltzmann.org + https://browndye.ucsd.edu
-
- SYSTEM_NAME comet
- SYSTEM_SINGULAIRTY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 1024
-
- ORIGINAL_AUTHOR_NAME Robert Konecny
- ORIGINAL_AUTHOR_EMAIL rok@ucsd.edu
- ORIGINAL_DEFINITION_FILE https://github.com/nbcrrolls/electrostatics-singularity/blob/master/Singularity
-
- MODIFYING_AUTHOR_NAME Marty Kandes
- MODIFYING_AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190416
-
-%help
-
- This is a singularity image with molecular electrostatics tools:
- apbs, pdb2pqr and BrownDye. All applications are intalled in /opt
- sub-directories and are in your $PATH.
-
-%runscript
-
- cat << EOF
-
- This container includes the following apps:
-
- APBS v1.5 - http://www.poissonboltzmann.org/
- PDB2PQR v2.1.0 - http://www.poissonboltzmann.org/
- BrownDye v2.0 (26 Feb 2019) - https://browndye.ucsd.edu/
-
- Please register your use of APBS and PDB2PQR at http://eepurl.com/by4eQr
-
- To list all available applications do "singularity apps [image name]"
-
- EOF
-
-%post -c /bin/bash
-
- set -o errexit
- APBS_VERSION=1.5
- PDB2PQR_VERSION=2.1.0
- APBS_URL=https://versaweb.dl.sourceforge.net/project/apbs/apbs/apbs-${APBS_VERSION}
- APBS_PKG=APBS-${APBS_VERSION}-linux64.tar.gz
- PDB2PQR_URL=https://versaweb.dl.sourceforge.net/project/pdb2pqr/pdb2pqr/pdb2pqr-${PDB2PQR_VERSION}
- PDB2PQR_PKG=pdb2pqr-linux-bin64-${PDB2PQR_VERSION}.tar.gz
- BD1_VERSION="1.0-13-Feb_2019"
- BD2_VERSION="2.0-26_Feb_ 2019"
- BD_URL=https://browndye.ucsd.edu
- BD1_PKG=browndye.tar.gz
- BD2_PKG=browndye2.tar.gz
- RL_URL=https://mirrors.edge.kernel.org/ubuntu/pool/main/r/readline6
- RL_PKG=libreadline6_6.3-8ubuntu8_amd64.deb
-
- DEBIAN_FRONTEND=noninteractive
- apt-get update
- apt-get -y install curl
- apt-get -y install make
- apt-get -y install gcc
- apt-get -y install g++
- #apt-get -y install ocaml
- apt-get -y install libexpat-dev
- apt-get -y install nano
- apt-get -y install readline-common
- apt-get -y install libgfortran3
- apt-get -y install wget
- apt-get -y install libboost-dev
- apt-get -y install liblapack-dev
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- cd /tmp
-
- wget http://caml.inria.fr/pub/distrib/ocaml-4.06/ocaml-4.06.0.tar.gz
- tar -xzvf ocaml-4.06.0.tar.gz
- cd ocaml-4.06.0
- ./configure
- make world.opt
- umask 022
- make install
-
- curl -k ${BD_URL}/${BD1_PKG} | tar xzf - -C /opt
- cd /opt/browndye
- curl -k -sO ${BD_URL}/browndye/doc/fixes.html
- make all
-
- curl -k ${BD_URL}/${BD2_PKG} | tar xzf - -C /opt
- cd /opt/browndye2
- curl -k -sO ${BD_URL}/browndye2/doc/fixes.html
- make all
- mkdir lib && cd lib
- curl -k -sO ${BD_URL}/coffdrop.xml.gz
- curl -k -sO ${BD_URL}/connectivity.xml
- curl -k -sO ${BD_URL}/map.xml
- curl -k -sO ${BD_URL}/charges.xml
-
- curl -k ${RL_URL}/${RL_PKG} -o /tmp/${RL_PKG}
- dpkg -i /tmp/${RL_PKG}
-
- apt-get -y purge gcc
- apt-get -y purge g++
- #apt-get -y purge ocaml
- apt-get -y purge libexpat-dev
- apt-get -y purge libboost-dev
- apt-get -y clean
- apt-get -y autoremove
- apt-get -y install ca-certificates
- rm -rf /var/lib/apt/lists/*
-
- # add apbs
- wget -q --no-check-certificate ${APBS_URL}/${APBS_PKG} -O - | tar xzf - -C /opt
- ln -s /opt/APBS-${APBS_VERSION}-linux64 /opt/apbs
-
- # add pdb2pqr
- wget -q --no-check-certificate ${PDB2PQR_URL}/${PDB2PQR_PKG} -O - | tar xzf - -C /opt
- ln -s /opt/pdb2pqr-linux-bin64-${PDB2PQR_VERSION} /opt/pdb2pqr
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set APBS, PDB2PQR, and BrownDye environment variables
- export APBS_VERSION=1.5
- export APBS_PATH=/opt/apbs
-
- export PDB2PQR_VERSION=2.1.0
- export PDB2PQR_PATH=/opt/pdb2pqr
-
- export BD1_VERSION="1.0-13-Feb_2019"
- export BD1_PATH=/opt/browndye
-
- export BD2_VERSION="2.0-26_Feb_ 2019"
- export BD2_PATH=/opt/browndye2
-
- export PATH=${APBS_PATH}/bin:${PDB2PQR_PATH}:${BD2_PATH}/bin:$PATH
- export LD_LIBRARY_PATH=${APBS_PATH}/lib
-
-%apphelp apbs
-
- apbs version 1.5
- For instructions on use see http://www.poissonboltzmann.org/
- apbs is installed in /opt/apbs
-
-%apprun apbs
-
- /opt/apbs/bin/apbs "$@"
-
-%apphelp pdb2pqr
-
- pdb2pqr version 2.1.0
- For instructions on use see http://www.poissonboltzmann.org/
- pdb2pqr is installed in /opt/pdb2pqr
-
-%apprun pdb2pqr
-
- /opt/pdb2pqr/pdb2pqr "$@"
-
-%apphelp nam_simulation
-
- BrownDye version 2.0 (26 Feb 2019)
- For instructions on use see https://browndye.ucsd.edu
- All BrowDye programs are installed in /opt/browndye/bin
-
-%apprun nam_simulation
-
- /opt/browndye2/bin/nam_simulation "$@"
-
-%apphelp pqr2xml
-
- BrownDye version 2.0 (26 Feb 2019)
- For instructions on use see https://browndye.ucsd.edu
-
-%apprun pqr2xml
-
- /opt/browndye2/bin/pqr2xml "$@"
-
-%apphelp make_rxn_pairs
-
- BrownDye version 2.0 (26 Feb 2019)
- For instructions on use see https://browndye.ucsd.edu
-
-%apprun make_rxn_pairs
-
- /opt/browndye2/bin/make_rxn_pairs "$@"
-
-%apphelp we_simulation
-
- BrownDye version 2.0 (26 Feb 2019)
- For instructions on use see https://browndye.ucsd.edu
-
-%apprun we_simulation
-
- /opt/browndye2/bin/we_simulation "$@"
-
-%apphelp xyz_trajectory
-
- BrownDye version 2.0 (26 Feb 2019)
- For instructions on use see https://browndye.ucsd.edu
-
-%apprun xyz_trajectory
-
- /opt/browndye2/bin/xyz_trajectory "$@"
diff --git a/archive/comet/beast/beast-gpu.def b/archive/comet/beast/beast-gpu.def
deleted file mode 100644
index a7a320e9445b6cd4a542a88001a58cbcfb399867..0000000000000000000000000000000000000000
--- a/archive/comet/beast/beast-gpu.def
+++ /dev/null
@@ -1,403 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME beast
- APPLICATION_VERSION 1.10.4
- APPLICATION_URL http://beast.community/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200209
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set LD_LIBRARY_PATH to beagle
- export LD_LIBRARY_PATH="/opt/beagle/lib:${LD_LIBRARY_PATH}"
-
- # Set PATH to beast
- export PATH="/opt/beast/bin:${PATH}"
-
- # Set PATH to tracer
- export PATH="/opt/tracer/bin:${PATH}"
-
- # Set PATH to figtree
- export PATH="/opt/figtree/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/rhel7/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/rhel7/x86_64"
-
- # Install NVIDIA package dependencies
- yum -y install xorg-x11-server-Xorg
- yum -y install xorg-x11-server-common
- yum -y install xorg-x11-apps
- yum -y install xorg-x11-utils
- yum -y install xorg-x11-xauth
- yum -y install xorg-x11-xkb-utils
- yum -y install cmake
- yum -y install make
- yum -y install dkms
- yum -y install kernel-headers
- yum -y install glibc-devel
- yum -y install glibc-headers
- yum -y install glibc-utils
- yum -y install libwayland-client
- yum -y install libwayland-server
- yum -y install pkgconfig
- yum -y install libvdpau
- yum -y install libva-vdpau-driver
- yum -y install atk
- yum -y install atk-devel
- yum -y install cairo
- yum -y install cairo-devel
- yum -y install cairo-gobject
- yum -y install cairo-gobject-devel
- yum -y install cairo-tools
- yum -y install fontconfig
- yum -y install fontconfig-devel
- yum -y install gdk-pixbuf2
- yum -y install gdk-pixbuf2-devel
- yum -y install gtk3
- yum -y install gtk3-devel
- yum -y install gtk2
- yum -y install gtk2-devel
- yum -y install jansson
- yum -y install freeglut
- yum -y install freeglut-devel
- yum -y install libX11
- yum -y install libX11-devel
- yum -y install libX11-common
- yum -y install libXmu
- yum -y install libXmu-devel
- yum -y install libXi
- yum -y install libXi-devel
- yum -y install mesa-libGLU
- yum -y install mesa-libGLU-devel
- yum -y install java-1.8.0-openjdk
- yum -y install java-1.8.0-openjdk-devel
-
- yum -y install grubby
- yum -y install libtirpc
- yum -y install ocl-icd
- yum -y install opencl-filesystem
- yum -y install vulkan-filesystem
-
- # Download NVIDIA driver, libraries, and packages
- wget --wait=10 "https://developer.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm"
- rpm -i cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm
- yum clean all
-
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/dkms-nvidia-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-devel-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-persistenced-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NVML-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-xconfig-418.67-1.el7.x86_64.rpm"
-
- # Download CUDA libraries and packages
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-devel-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1-10.1.168-1.x86_64.rpm"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-devel-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc-1.0.0-1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl-2.5.6-1+cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- # Install NVIDIA drivers, libraries, and packages
- rpm -i nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-libs-418.67-4.el7.x86_64.rpm
- yum -y install dkms-nvidia
- yum -y install nvidia-driver
- rpm -i nvidia-driver-NVML-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-driver-devel-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-modprobe-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-settings-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-xconfig-418.67-1.el7.x86_64.rpm
- yum -y install nvidia-persistenced
- yum -y install nvidia-driver-cuda
-
- rpm -i cuda-compat-10-1-418.67-1.x86_64.rpm
- rpm -i cuda-license-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvcc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprune-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-compiler-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gdb-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprof-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-memcheck-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cupti-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvtx-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i libcublas10-10.2.0.168-1.x86_64.rpm
- rpm -i libcublas-devel-10.2.0.168-1.x86_64.rpm
- rpm -i cuda-cufft-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-samples-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-documentation-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvvp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-toolkit-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-drivers-418.67-1.x86_64.rpm
- rpm -i cuda-runtime-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-10-1-10.1.168-1.x86_64.rpm
-
- rpm -i libcutensor1-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-devel-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-doc-1.0.0-1.x86_64.rpm
-
- rpm -i libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm
- rpm -i libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm
-
- rpm -i libnccl-2.5.6-1+cuda10.1.x86_64.rpm
- rpm -i libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm
-
- rpm -i libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install beast dependencies
- yum -y install java-1.8.0-openjdk
- yum -y install java-1.8.0-openjdk-devel
- yum -y install ant
-
- # Download, build, and install beagle library
- git clone https://github.com/beagle-dev/beagle-lib.git
- cd /tmp/beagle-lib
- git checkout v3.1.2
- ./autogen.sh
- ./configure --prefix=/opt/beagle
- make install
- export LD_LIBRARY_PATH="/opt/beagle/lib:${LD_LIBRARY_PATH}"
- make check
-
- cd /tmp
-
- # Download, build, and install beast
- git clone https://github.com/beast-dev/beast-mcmc.git
- cd /tmp/beast-mcmc
- git checkout v1.10.4
- export JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8
- ant linux
- mv /tmp/beast-mcmc/release/Linux/BEASTv1.10.4 /opt/beast
- cd /opt/beast/bin
- sed -i 's/-Xms64m -Xmx2048m/-Xms256m -Xmx10000m/' beast
-
- # Set PATH to beast
- export PATH="/opt/beast/bin:${PATH}"
-
- cd /tmp
-
- # Download, build, and install tracer
- git clone https://github.com/beast-dev/tracer.git
- cd /tmp/tracer
- git checkout v1.7.1
- ant linux
- mv /tmp/tracer/release/Linux/Tracer_v1.7.1 /opt/tracer
-
- # Set PATH to tracer
- export PATH="/opt/tracer/bin:${PATH}"
-
- cd /tmp
-
- # Download, build, and install figtree
- git clone https://github.com/rambaut/figtree.git
- cd /tmp/figtree
- git checkout v1.4.4
- sed -i 's/linux_unix_Release/linux/g' build.xml
- ant linux
- mv /tmp/figtree/release/Linux/FigTree_v1.4.4 /opt/figtree
- cd /opt/figtree/bin
- sed -i "s/lib/\/opt\/figtree\/lib/g" figtree
- chmod +x figtree
-
- # Set PATH to figtree
- export PATH="/opt/figtree/bin:${PATH}"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/beast2/beast2-gpu.def b/archive/comet/beast2/beast2-gpu.def
deleted file mode 100644
index 16d98494109e9ace54792b083c92e6e073f6f6e2..0000000000000000000000000000000000000000
--- a/archive/comet/beast2/beast2-gpu.def
+++ /dev/null
@@ -1,403 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME beast2
- APPLICATION_VERSION 2.6.1
- APPLICATION_URL http://www.beast2.org
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200208
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set LD_LIBRARY_PATH to beagle
- export LD_LIBRARY_PATH="/opt/beagle/lib:${LD_LIBRARY_PATH}"
-
- # Set PATH to beast2
- export PATH="/opt/beast2/bin:${PATH}"
-
- # Set PATH to tracer
- export PATH="/opt/tracer/bin:${PATH}"
-
- # Set PATH to figtree
- export PATH="/opt/figtree/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/rhel7/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/rhel7/x86_64"
-
- # Install NVIDIA package dependencies
- yum -y install xorg-x11-server-Xorg
- yum -y install xorg-x11-server-common
- yum -y install xorg-x11-apps
- yum -y install xorg-x11-utils
- yum -y install xorg-x11-xauth
- yum -y install xorg-x11-xkb-utils
- yum -y install cmake
- yum -y install make
- yum -y install dkms
- yum -y install kernel-headers
- yum -y install glibc-devel
- yum -y install glibc-headers
- yum -y install glibc-utils
- yum -y install libwayland-client
- yum -y install libwayland-server
- yum -y install pkgconfig
- yum -y install libvdpau
- yum -y install libva-vdpau-driver
- yum -y install atk
- yum -y install atk-devel
- yum -y install cairo
- yum -y install cairo-devel
- yum -y install cairo-gobject
- yum -y install cairo-gobject-devel
- yum -y install cairo-tools
- yum -y install fontconfig
- yum -y install fontconfig-devel
- yum -y install gdk-pixbuf2
- yum -y install gdk-pixbuf2-devel
- yum -y install gtk3
- yum -y install gtk3-devel
- yum -y install gtk2
- yum -y install gtk2-devel
- yum -y install jansson
- yum -y install freeglut
- yum -y install freeglut-devel
- yum -y install libX11
- yum -y install libX11-devel
- yum -y install libX11-common
- yum -y install libXmu
- yum -y install libXmu-devel
- yum -y install libXi
- yum -y install libXi-devel
- yum -y install mesa-libGLU
- yum -y install mesa-libGLU-devel
- yum -y install java-1.8.0-openjdk
- yum -y install java-1.8.0-openjdk-devel
-
- yum -y install grubby
- yum -y install libtirpc
- yum -y install ocl-icd
- yum -y install opencl-filesystem
- yum -y install vulkan-filesystem
-
- # Download NVIDIA driver, libraries, and packages
- wget --wait=10 "https://developer.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm"
- rpm -i cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm
- yum clean all
-
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/dkms-nvidia-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-devel-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-persistenced-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NVML-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-xconfig-418.67-1.el7.x86_64.rpm"
-
- # Download CUDA libraries and packages
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-devel-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1-10.1.168-1.x86_64.rpm"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-devel-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc-1.0.0-1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl-2.5.6-1+cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- # Install NVIDIA drivers, libraries, and packages
- rpm -i nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-libs-418.67-4.el7.x86_64.rpm
- yum -y install dkms-nvidia
- yum -y install nvidia-driver
- rpm -i nvidia-driver-NVML-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-driver-devel-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-modprobe-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-settings-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-xconfig-418.67-1.el7.x86_64.rpm
- yum -y install nvidia-persistenced
- yum -y install nvidia-driver-cuda
-
- rpm -i cuda-compat-10-1-418.67-1.x86_64.rpm
- rpm -i cuda-license-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvcc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprune-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-compiler-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gdb-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprof-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-memcheck-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cupti-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvtx-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i libcublas10-10.2.0.168-1.x86_64.rpm
- rpm -i libcublas-devel-10.2.0.168-1.x86_64.rpm
- rpm -i cuda-cufft-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-samples-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-documentation-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvvp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-toolkit-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-drivers-418.67-1.x86_64.rpm
- rpm -i cuda-runtime-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-10-1-10.1.168-1.x86_64.rpm
-
- rpm -i libcutensor1-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-devel-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-doc-1.0.0-1.x86_64.rpm
-
- rpm -i libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm
- rpm -i libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm
-
- rpm -i libnccl-2.5.6-1+cuda10.1.x86_64.rpm
- rpm -i libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm
-
- rpm -i libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install beast dependencies
- yum -y install java-1.8.0-openjdk
- yum -y install java-1.8.0-openjdk-devel
- yum -y install ant
-
- # Download, build, and install beagle library
- git clone https://github.com/beagle-dev/beagle-lib.git
- cd /tmp/beagle-lib
- git checkout v3.1.2
- ./autogen.sh
- ./configure --prefix=/opt/beagle
- make install
- export LD_LIBRARY_PATH="/opt/beagle/lib:${LD_LIBRARY_PATH}"
- make check
-
- cd /tmp
-
- # Download, build, and install beas2
- git clone https://github.com/CompEvol/beast2.git
- cd /tmp/beast2
- git checkout v2.6.1
- export JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF8
- ant linux
- mv /tmp/beast2/release/Linux/beast /opt/beast2
- cd /opt/beast2/bin
- sed -i 's/-Xms256m -Xmx8g/-Xms256m -Xmx15g/' beast
-
- # Set PATH to beast2
- export PATH="/opt/beast2/bin:${PATH}"
-
- cd /tmp
-
- # Download, build, and install tracer
- git clone https://github.com/beast-dev/tracer.git
- cd /tmp/tracer
- git checkout v1.7.1
- ant linux
- mv /tmp/tracer/release/Linux/Tracer_v1.7.1 /opt/tracer
-
- # Set PATH to tracer
- export PATH="/opt/tracer/bin:${PATH}"
-
- cd /tmp
-
- # Download, build, and install figtree
- git clone https://github.com/rambaut/figtree.git
- cd /tmp/figtree
- git checkout v1.4.4
- sed -i 's/linux_unix_Release/linux/g' build.xml
- ant linux
- mv /tmp/figtree/release/Linux/FigTree_v1.4.4 /opt/figtree
- cd /opt/figtree/bin
- sed -i "s/lib/\/opt\/figtree\/lib/g" figtree
- chmod +x figtree
-
- # Set PATH to figtree
- export PATH="/opt/figtree/bin:${PATH}"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/caffe/caffe-gpu.def b/archive/comet/caffe/caffe-gpu.def
deleted file mode 100644
index 029c355de3423bb3479be2779af78148a6a622d9..0000000000000000000000000000000000000000
--- a/archive/comet/caffe/caffe-gpu.def
+++ /dev/null
@@ -1,379 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME caffe
- APPLICATION_VERSION 1.0
- APPLICATION_URL https://developer.nvidia.com/cuda-zone
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://caffe.berkeleyvision.org/
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190110
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
- export PYTHONPATH="/opt/caffe/python:${PYTHONPATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install general dependencies for caffe
- apt-get -y install libprotobuf-dev
- apt-get -y install libleveldb-dev
- apt-get -y install libsnappy-dev
- apt-get -y install libopencv-dev
- apt-get -y install libhdf5-dev
- apt-get -y install protobuf-compiler
- apt-get -y install --no-install-recommends libboost-all-dev
- apt-get -y install libatlas-base-dev
- apt-get -y install libgflags-dev
- apt-get -y install libgoogle-glog-dev
- apt-get -y install liblmdb-dev
-
- # Fix for libhdf5: https://github.com/NVIDIA/DIGITS/issues/156
- # https://github.com/BVLC/caffe/issues/2347
- cd /usr/lib/x86_64-linux-gnu
- ln -s libhdf5_serial.so.10.1.0 libhdf5.so
- ln -s libhdf5_serial_hl.so.10.0.2 libhdf5_hl.so
-
- # Install dependencies for pycaffe
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install cython
- apt-get -y install python-numpy
- apt-get -y install python-scipy
- apt-get -y install python-skimage
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install python-h5py
- apt-get -y install libleveldb1v5
- apt-get -y install python-networkx
- apt-get -y install python-nose
- apt-get -y install python-pandas
- apt-get -y install python-dateutil
- apt-get -y install python-protobuf
- apt-get -y install python-gflags
- apt-get -y install python-yaml
- apt-get -y install python-pil
- apt-get -y install python-six
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- cd /opt
-
- # Download and checkout version of caffe to be compiled
- git clone https://github.com/BVLC/caffe.git
- cd /opt/caffe
- git checkout 1.0
-
- # Create caffe Makefile.config file
- echo 'USE_CUDNN := 1' >> Makefile.config
- echo 'CUDA_DIR := /usr/local/cuda' >> Makefile.config
- echo 'CUDA_ARCH := -gencode arch=compute_35,code=sm_37 \' >> Makefile.config
- echo ' -gencode arch=compute_60,code=sm_60' >> Makefile.config
- echo 'BLAS := atlas' >> Makefile.config
- echo 'PYTHON_INCLUDE := /usr/include/python2.7 \' >> Makefile.config
- echo ' /usr/lib/python2.7/dist-packages/numpy/core/include' >> Makefile.config
- echo 'PYTHON_LIB := /usr/lib/x86_64-linux-gnu' >> Makefile.config
- echo 'INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/include/hdf5/serial/' >> Makefile.config
- echo 'LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib' >> Makefile.config
- echo 'USE_NCCL := 1' >> Makefile.config
- echo 'BUILD_DIR := build' >> Makefile.config
- echo 'DISTRIBUTE_DIR := distribute' >> Makefile.config
- echo 'TEST_GPUID := 0' >> Makefile.config
- echo 'Q ?= @' >> Makefile.config
-
- # Build caffe
- make clean
- make all
- make test
-
- cd /opt/caffe/python
-
- # Install any remaining dependencies for pycaffe
- for req in $(cat requirements.txt); do pip install $req; done
-
- cd /opt/caffe
-
- # Build pycaffe
- make pycaffe
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/centos/centos-6-cuda.def b/archive/comet/centos/centos-6-cuda.def
deleted file mode 100644
index 04c53849b3eb55d2cdee28529641bac2914baff2..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos-6-cuda.def
+++ /dev/null
@@ -1,181 +0,0 @@
-Bootstrap: yum
-OSVersion: 6
-MirrorURL: http://mirror.centos.org/centos-6/6/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos + cuda
- APPLICATION_VERSION 6.10 + 7.0
- APPLICATION_URL https://developer.nvidia.com/cuda-zone
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190919
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-7.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-7.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # https://forums.fedoraforum.org/showthread.php?281978-yum-failed-unexpected-file-type-or-format
- rpm -vv --rebuilddb
- yum -y update
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/rhel6/x86_64"
- #declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/rhel7/x86_64/"
-
- # Install NVIDIA package dependencies
- yum -y install dkms
- yum -y install grub
- yum -y install dracut
- yum -y install libvdpau
- yum -y install freeglut-devel
- yum -y install libXmu-devel
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kmod-396.26-2.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/xorg-x11-drv-nvidia-396.26-1.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/xorg-x11-drv-nvidia-libs-396.26-1.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/xorg-x11-drv-nvidia-gl-396.26-1.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/xorg-x11-drv-nvidia-devel-396.26-1.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/xorg-x11-drv-nvidia-diagnostic-396.26-1.el6.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-396.26-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-diagnostic-396.26-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-src-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-7-0-7.0-28.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-7-0-7.0-28.x86_64.rpm"
-
- # Install NVIDIA drivers, libraries, and packages
- rpm -i nvidia-kmod-396.26-2.el6.x86_64.rpm
- rpm -i xorg-x11-drv-nvidia-396.26-1.el6.x86_64.rpm
- rpm -i xorg-x11-drv-nvidia-libs-396.26-1.el6.x86_64.rpm
- rpm -i xorg-x11-drv-nvidia-gl-396.26-1.el6.x86_64.rpm
- rpm -i xorg-x11-drv-nvidia-devel-396.26-1.el6.x86_64.rpm
- rpm -i xorg-x11-drv-nvidia-diagnostic-396.26-1.el6.x86_64.rpm
- rpm -i cuda-drivers-396.26-1.x86_64.rpm
- rpm -i cuda-license-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-misc-headers-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-drivers-diagnostic-396.26-1.x86_64.rpm
- rpm -i cuda-core-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cudart-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-driver-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cudart-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-gdb-src-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-command-line-tools-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-nvrtc-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-nvrtc-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cusolver-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cusolver-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cublas-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cublas-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cufft-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cufft-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-curand-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-curand-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cusparse-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-cusparse-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-npp-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-npp-dev-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-samples-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-documentation-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-visual-tools-7-0-7.0-28.x86_64.rpm
- rpm -i cuda-runtime-7-0-7.0-28.x86_64.rpm
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-7.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-7.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " "
- echo " __________________ __ _______________ "
- echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
- echo " --/ / / / / / /|_/ / __/ / / "
- echo " / /___/ /_/ / / / / /___ / / "
- echo " \____/\____/_/ /_/_____/ /_/ "
- echo " "
-
-%test
diff --git a/archive/comet/centos/centos-6.def b/archive/comet/centos/centos-6.def
deleted file mode 100644
index 6b8c3f131bd9983618d2d33df704c6da8316690a..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos-6.def
+++ /dev/null
@@ -1,98 +0,0 @@
-Bootstrap: yum
-OSVersion: 6
-MirrorURL: http://mirror.centos.org/centos-6/6/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos
- APPLICATION_VERSION 6.10
- APPLICATION_URL https://www.centos.org
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 4096
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190916
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # https://forums.fedoraforum.org/showthread.php?281978-yum-failed-unexpected-file-type-or-format
- rpm -vv --rebuilddb
- yum -y update
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " "
- echo " __________________ __ _______________ "
- echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
- echo " --/ / / / / / /|_/ / __/ / / "
- echo " / /___/ /_/ / / / / /___ / / "
- echo " \____/\____/_/ /_/_____/ /_/ "
- echo " "
-
-%test
diff --git a/archive/comet/centos/centos-cuda-openmpi.def b/archive/comet/centos/centos-cuda-openmpi.def
deleted file mode 100644
index b576d489fccd39910b5a1c878ecd878be0f80450..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos-cuda-openmpi.def
+++ /dev/null
@@ -1,429 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos + cuda + openmpi
- APPLICATION_VERSION 7.7.1908 + 10.1.168 + 3.1.4
- APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200228
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/rhel7/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/rhel7/x86_64"
-
- # Install NVIDIA package dependencies
- yum -y install xorg-x11-server-Xorg
- yum -y install xorg-x11-server-common
- yum -y install xorg-x11-apps
- yum -y install xorg-x11-utils
- yum -y install xorg-x11-xauth
- yum -y install xorg-x11-xkb-utils
- yum -y install cmake
- yum -y install make
- yum -y install dkms
- yum -y install kernel-headers
- yum -y install glibc-devel
- yum -y install glibc-headers
- yum -y install glibc-utils
- yum -y install libwayland-client
- yum -y install libwayland-server
- yum -y install pkgconfig
- yum -y install libvdpau
- yum -y install libva-vdpau-driver
- yum -y install atk
- yum -y install atk-devel
- yum -y install cairo
- yum -y install cairo-devel
- yum -y install cairo-gobject
- yum -y install cairo-gobject-devel
- yum -y install cairo-tools
- yum -y install fontconfig
- yum -y install fontconfig-devel
- yum -y install gdk-pixbuf2
- yum -y install gdk-pixbuf2-devel
- yum -y install gtk3
- yum -y install gtk3-devel
- yum -y install gtk2
- yum -y install gtk2-devel
- yum -y install jansson
- yum -y install freeglut
- yum -y install freeglut-devel
- yum -y install libX11
- yum -y install libX11-devel
- yum -y install libX11-common
- yum -y install libXmu
- yum -y install libXmu-devel
- yum -y install libXi
- yum -y install libXi-devel
- yum -y install mesa-libGLU
- yum -y install mesa-libGLU-devel
- yum -y install java-latest-openjdk
- yum -y install java-latest-openjdk-devel
-
- yum -y install grubby
- yum -y install libtirpc
- yum -y install ocl-icd
- yum -y install opencl-filesystem
- yum -y install vulkan-filesystem
-
- # Download NVIDIA driver, libraries, and packages
- wget --wait=10 "https://developer.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm"
- rpm -i cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm
- yum clean all
-
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/dkms-nvidia-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-devel-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-persistenced-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NVML-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-xconfig-418.67-1.el7.x86_64.rpm"
-
- # Download CUDA libraries and packages
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-devel-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1-10.1.168-1.x86_64.rpm"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-devel-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc-1.0.0-1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl-2.5.6-1+cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- # Install NVIDIA drivers, libraries, and packages
- rpm -i nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-libs-418.67-4.el7.x86_64.rpm
- yum -y install dkms-nvidia
- yum -y install nvidia-driver
- rpm -i nvidia-driver-NVML-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-driver-devel-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-modprobe-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-settings-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-xconfig-418.67-1.el7.x86_64.rpm
- yum -y install nvidia-persistenced
- yum -y install nvidia-driver-cuda
-
- rpm -i cuda-compat-10-1-418.67-1.x86_64.rpm
- rpm -i cuda-license-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvcc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprune-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-compiler-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gdb-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprof-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-memcheck-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cupti-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvtx-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i libcublas10-10.2.0.168-1.x86_64.rpm
- rpm -i libcublas-devel-10.2.0.168-1.x86_64.rpm
- rpm -i cuda-cufft-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-samples-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-documentation-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvvp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-toolkit-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-drivers-418.67-1.x86_64.rpm
- rpm -i cuda-runtime-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-10-1-10.1.168-1.x86_64.rpm
-
- rpm -i libcutensor1-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-devel-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-doc-1.0.0-1.x86_64.rpm
-
- rpm -i libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm
- rpm -i libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm
-
- rpm -i libnccl-2.5.6-1+cuda10.1.x86_64.rpm
- rpm -i libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm
-
- rpm -i libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- rpm -i libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- rpm -i libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- rpm -i libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- rpm -i python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- yum -y install dkms
- yum -y install infiniband-diags
- yum -y install infiniband-diags-devel
- yum -y install libibverbs
- yum -y install libibverbs-devel
- yum -y install ibacm
- yum -y install librdmacm
- yum -y install librdmacm-devel
- yum -y install libmlx4
- yum -y install libmlx5
- yum -y install msflint
- yum -y install libibcm
- yum -y install libibmad
- yum -y install libibmad-devel
- yum -y install libibumad
- yum -y install libibumad-devel
- yum -y install opensm
- yum -y install srptools
-
- # Install additional tools
- yum -y install ibutils
- yum -y install libibverbs-utils
- yum -y install rdmacm-utils
- yum -y install librdmacm-utils
- yum -y install perftest
- yum -y install numactl
-
- # Install libnl
- yum -y install libnl3
- yum -y install libnl3-devel
-
- # Install OpenMPI dependencies
- yum -y install zlib
- yum -y install zlib-devel
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/centos/centos-cuda.def b/archive/comet/centos/centos-cuda.def
deleted file mode 100644
index 5bdc8781ce7bc871a3bc522207fa842ee3c39e3d..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos-cuda.def
+++ /dev/null
@@ -1,341 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos + cuda
- APPLICATION_VERSION 7.7.1908 + 10.1.168
- APPLICATION_URL https://developer.nvidia.com/cuda-zone
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200213
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/rhel7/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/rhel7/x86_64"
-
- # Install NVIDIA package dependencies
- yum -y install xorg-x11-server-Xorg
- yum -y install xorg-x11-server-common
- yum -y install xorg-x11-apps
- yum -y install xorg-x11-utils
- yum -y install xorg-x11-xauth
- yum -y install xorg-x11-xkb-utils
- yum -y install cmake
- yum -y install make
- yum -y install dkms
- yum -y install kernel-headers
- yum -y install glibc-devel
- yum -y install glibc-headers
- yum -y install glibc-utils
- yum -y install libwayland-client
- yum -y install libwayland-server
- yum -y install pkgconfig
- yum -y install libvdpau
- yum -y install libva-vdpau-driver
- yum -y install atk
- yum -y install atk-devel
- yum -y install cairo
- yum -y install cairo-devel
- yum -y install cairo-gobject
- yum -y install cairo-gobject-devel
- yum -y install cairo-tools
- yum -y install fontconfig
- yum -y install fontconfig-devel
- yum -y install gdk-pixbuf2
- yum -y install gdk-pixbuf2-devel
- yum -y install gtk3
- yum -y install gtk3-devel
- yum -y install gtk2
- yum -y install gtk2-devel
- yum -y install jansson
- yum -y install freeglut
- yum -y install freeglut-devel
- yum -y install libX11
- yum -y install libX11-devel
- yum -y install libX11-common
- yum -y install libXmu
- yum -y install libXmu-devel
- yum -y install libXi
- yum -y install libXi-devel
- yum -y install mesa-libGLU
- yum -y install mesa-libGLU-devel
- yum -y install java-latest-openjdk
- yum -y install java-latest-openjdk-devel
-
- yum -y install grubby
- yum -y install libtirpc
- yum -y install ocl-icd
- yum -y install opencl-filesystem
- yum -y install vulkan-filesystem
-
- # Download NVIDIA driver, libraries, and packages
- wget --wait=10 "https://developer.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm"
- rpm -i cuda-repo-rhel7-10-1-local-10.1.168-418.67-1.0-1.x86_64.rpm
- yum clean all
-
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-libs-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/dkms-nvidia-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-devel-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-persistenced-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-cuda-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NVML-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings-418.67-1.el7.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-xconfig-418.67-1.el7.x86_64.rpm"
-
- # Download CUDA libraries and packages
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-devel-10.2.0.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-418.67-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1-10.1.168-1.x86_64.rpm"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-devel-1.0.0-1.x86_64.rpm"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc-1.0.0-1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl-2.5.6-1+cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm"
- wget --wait=10 "${ML_REPO_URL}/python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm"
-
- # Install NVIDIA drivers, libraries, and packages
- rpm -i nvidia-driver-cuda-libs-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-libs-418.67-4.el7.x86_64.rpm
- yum -y install dkms-nvidia
- yum -y install nvidia-driver
- rpm -i nvidia-driver-NVML-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-NvFBCOpenGL-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-libXNVCtrl-devel-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-driver-devel-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-driver-diagnostic-418.67-4.el7.x86_64.rpm
- rpm -i nvidia-modprobe-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-settings-418.67-1.el7.x86_64.rpm
- rpm -i nvidia-xconfig-418.67-1.el7.x86_64.rpm
- yum -y install nvidia-persistenced
- yum -y install nvidia-driver-cuda
-
- rpm -i cuda-compat-10-1-418.67-1.x86_64.rpm
- rpm -i cuda-license-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-misc-headers-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvcc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cuobjdump-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprune-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-compiler-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-driver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cudart-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvdisasm-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gdb-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvprof-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-memcheck-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cupti-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-gpu-library-advisor-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvtx-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-sanitizer-api-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-command-line-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvrtc-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvml-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvgraph-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvjpeg-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusolver-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i libcublas10-10.2.0.168-1.x86_64.rpm
- rpm -i libcublas-devel-10.2.0.168-1.x86_64.rpm
- rpm -i cuda-cufft-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cufft-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-curand-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-cusparse-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-npp-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-samples-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-documentation-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-compute-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nsight-systems-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-nvvp-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-visual-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-tools-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-dev-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-toolkit-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-libraries-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-drivers-418.67-1.x86_64.rpm
- rpm -i cuda-runtime-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-demo-suite-10-1-10.1.168-1.x86_64.rpm
- rpm -i cuda-10-1-10.1.168-1.x86_64.rpm
-
- rpm -i libcutensor1-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-devel-1.0.0-1.x86_64.rpm
- rpm -i libcutensor-doc-1.0.0-1.x86_64.rpm
-
- rpm -i libcudnn7-7.6.5.32-1.cuda10.1.x86_64.rpm
- rpm -i libcudnn7-devel-7.6.5.32-1.cuda10.1.x86_64.rpm
-
- rpm -i libnccl-2.5.6-1+cuda10.1.x86_64.rpm
- rpm -i libnccl-devel-2.5.6-1+cuda10.1.x86_64.rpm
-
- rpm -i libnvinfer6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvinfer-plugin-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvonnxparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers6-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i libnvparsers-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python3-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-6.0.1-1.cuda10.1.x86_64.rpm
- rpm -i python-libnvinfer-devel-6.0.1-1.cuda10.1.x86_64.rpm
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/centos/centos-openmpi.def b/archive/comet/centos/centos-openmpi.def
deleted file mode 100644
index 6e47c9924ce92b6afe01b96e8bec101f5eff040f..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos-openmpi.def
+++ /dev/null
@@ -1,164 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos + openmpi
- APPLICATION_VERSION 7.7.1908 + 3.1.4
- APPLICATION_URL https://www.open-mpi.org/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 4096
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200228
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- yum -y install dkms
- yum -y install infiniband-diags
- yum -y install infiniband-diags-devel
- yum -y install libibverbs
- yum -y install libibverbs-devel
- yum -y install ibacm
- yum -y install librdmacm
- yum -y install librdmacm-devel
- yum -y install libmlx4
- yum -y install libmlx5
- yum -y install msflint
- yum -y install libibcm
- yum -y install libibmad
- yum -y install libibmad-devel
- yum -y install libibumad
- yum -y install libibumad-devel
- yum -y install opensm
- yum -y install srptools
-
- # Install additional tools
- yum -y install ibutils
- yum -y install libibverbs-utils
- yum -y install rdmacm-utils
- yum -y install librdmacm-utils
- yum -y install perftest
- yum -y install numactl
-
- # Install libnl
- yum -y install libnl3
- yum -y install libnl3-devel
-
- # Install OpenMPI dependencies
- yum -y install zlib
- yum -y install zlib-devel
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/centos/centos.def b/archive/comet/centos/centos.def
deleted file mode 100644
index 4405e4368e9664b27a4ecf756f5b456db5ecdafd..0000000000000000000000000000000000000000
--- a/archive/comet/centos/centos.def
+++ /dev/null
@@ -1,75 +0,0 @@
-Bootstrap: yum
-OSVersion: 7
-MirrorURL: http://mirror.centos.org/centos-7/7/os/x86_64/
-Include: yum
-
-%labels
-
- APPLICATION_NAME centos
- APPLICATION_VERSION 7.7.1908
- APPLICATION_URL https://www.centos.org
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 4096
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200129
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Add repositories
- yum -y install epel-release
-
- # Install system metapackages
- yum -y groupinstall "Development Tools"
- yum -y groupinstall "Additional Development"
- yum -y groupinstall "Compatibility Libraries"
-
- # Update all packages to their latest versions
- yum -y update
-
- # Install common packages
- yum -y install bc
- yum -y install cmake
- yum -y install curl
- yum -y install mlocate
- yum -y install rsync
- yum -y install time
- yum -y install wget
- yum -y install which
-
- # Install expect to automate responses for interactive build questions
- yum -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/deepbench/deepbench.def b/archive/comet/deepbench/deepbench.def
deleted file mode 100644
index cfb85a8d1e9156e362b26f7431b596a0f9412436..0000000000000000000000000000000000000000
--- a/archive/comet/deepbench/deepbench.def
+++ /dev/null
@@ -1,317 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME deepbench
- APPLICATION_VERSION unknown
- APPLICATION_URL https://github.com/baidu-research/DeepBench
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 201808524
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_367.48-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn6_6.0.21-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
- dpkg -i libcuda1-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-367_367.48-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_367.48-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_367.48-1_amd64.deb
-
- dpkg -i cuda-license-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-misc-headers-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-core-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-driver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-command-line-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvml-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-samples-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-documentation-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-visual-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-toolkit-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
-
- dpkg -i libcudnn6_6.0.21-1+cuda8.0_amd64.deb
- dpkg -i libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb
-
- dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Download, build, and install CUDA-aware OpenMPI
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- cd /opt
-
- # Donwload, build, and install NCCL tests
- git clone https://github.com/NVIDIA/nccl-tests.git
- cd nccl-tests
- make MPI=1 \
- MPI_HOME='/opt/openmpi-1.8.4' \
- CUDA_HOME='/usr/local/cuda-8.0' \
- NCCL_HOME='/usr/lib/x86_64-linux-gnu'
-
- # Download, build, and install DeepBench
- cd /opt
- git clone https://github.com/baidu-research/DeepBench
- cd DeepBench/code
- git clone https://github.com/baidu-research/baidu-allreduce
- cd baidu-allreduce
- make MPI_ROOT='/opt/openmpi-1.8.4' CUDA_ROOT='/usr/local/cuda-8.0'
- cd ../
- make BAIDU_ALLREDUCE_PATH='/opt/DeepBench/code/baidu-allreduce' \
- CUDA_PATH='/usr/local/cuda-8.0' \
- CUDNN_PATH='/usr/lib/x86_64-linux-gnu' \
- NCCL_PATH='/usr/lib/x86_64-linux-gnu' \
- MPI_PATH='/opt/openmpi-1.8.4' \
- MPI_INCLUDE_PATH='/opt/openmpi-1.8.4/include' \
- ARCH='sm_30,sm_32,sm_35,sm_50,sm_52,sm_60,sm_61,sm_62'
-
- # Set path to baidu-allreduce and Deepbench binaries
- export PATH="/opt/DeepBench/code/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/DeepBench/code/baidu-allreduce:${LD_LIBRARY_PATH}"
-
- # Set container environment variables
- cd /.singularity.d/env
- echo 'export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH}"' >> 90-environment.sh
- echo 'export PATH="/opt/openmpi-1.8.4/bin:${PATH}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"' >> 90-environment.sh
- echo 'export PATH="/opt/DeepBench/code/bin:${PATH}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/opt/DeepBench/code/baidu-allreduce:${LD_LIBRARY_PATH}"' >> 90-environment.sh
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/gromacs/gromacs-cpu.def b/archive/comet/gromacs/gromacs-cpu.def
deleted file mode 100644
index 354efa4924cbc8a8215ea76828c9bad177fe64f7..0000000000000000000000000000000000000000
--- a/archive/comet/gromacs/gromacs-cpu.def
+++ /dev/null
@@ -1,146 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME gromacs
- APPLICATION_VERSION 2019
- APPLICATION_URL http://www.gromacs.org/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 4096
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190501
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Source GROMACS environment variables
- export GROMACS_VERSION='2019'
- export GROMACS_BUILD='tmpi'
- export GROMACS_ROOT_DIR="/opt/software/molecular-dynamics/gromacs"
- . "${GROMACS_ROOT_DIR}/${GROMACS_VERSION}/${GROMACS_BUILD}/bin/GMXRC"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Download, build, and install GROMACS
- declare -xr GROMACS_VERSION='2019'
- declare -xr GROMACS_BUILD='tmpi'
- declare -xr GROMACS_ROOT_DIR="/opt/software/molecular-dynamics/gromacs"
- declare -xr GROMACS_ROOT_URL='http://ftp.gromacs.org/pub'
-
- mkdir -p "${GROMACS_ROOT_DIR}/${GROMACS_VERSION}/${GROMACS_BUILD}
- cd "${GROMACS_ROOT_DIR}/${GROMACS_VERSION}/${GROMACS_BUILD}
-
- wget "${GROMACS_ROOT_URL}/gromacs/gromacs-${GROMACS_VERSION}.tar.gz"
- tar -xzvf "gromacs-${GROMACS_VERSION}.tar.gz"
-
- cd "gromacs-${GROMACS_VERSION}"
- mkdir -p build
- cd build
-
- cmake .. \
- -DCMAKE_C_COMPILER=gcc \
- -DCMAKE_CXX_COMPILER=g++ \
- -DCMAKE_BUILD_TYPE=Release \
- -DCMAKE_INSTALL_PREFIX="${GROMACS_ROOT_DIR}/${GROMACS_VERSION}/${GROMACS_BUILD}" \
- -DGMX_PREFER_STATIC_LIBS=ON \
- -DBUILD_SHARED_LIBS=OFF \
- -DGMX_EXTERNAL_BLAS=OFF \
- -DGMX_EXTERNAL_BOOST=OFF \
- -DGMX_EXTERNAL_LAPACK=OFF \
- -DGMX_FFT_LIBRARY=fftw3 \
- -DGMX_BUILD_OWN_FFTW=ON \
- -DGMX_DOUBLE=OFF \
- -DGMX_SIMD=AVX2_256 \
- -DGMX_MPI=OFF \
- -DGMX_OPENMP=OFF \
- -DGMX_GPU=OFF \
- -DREGRESSIONTEST_DOWNLOAD=ON
-
- make
- make check
- make install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- exec "${@}"
-
-%test
diff --git a/archive/comet/jupyter/jupyter-cpu.def b/archive/comet/jupyter/jupyter-cpu.def
deleted file mode 100644
index 1dc79a31a556c16a9a11fa7e0138985dffc2735f..0000000000000000000000000000000000000000
--- a/archive/comet/jupyter/jupyter-cpu.def
+++ /dev/null
@@ -1,108 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME jupyter
- APPLICATION_VERSION 4.4.0
- APPLICATION_URL https://jupyter.org/index.html
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190516
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
- export PATH="/opt/anaconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install Anaconda2
- wget https://repo.anaconda.com/archive/Anaconda2-2019.03-Linux-x86_64.sh
- chmod +x Anaconda2-2019.03-Linux-x86_64.sh
- ./Anaconda2-2019.03-Linux-x86_64.sh -b -p /opt/anaconda2
-
- # Install Anaconda3
- wget https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh
- chmod +x Anaconda3-2019.03-Linux-x86_64.sh
- ./Anaconda3-2019.03-Linux-x86_64.sh -b -p /opt/anaconda3
-
- # Install additional python(2) packages with Anaconda2
- export PATH="/opt/anaconda2/bin:${PATH}"
- conda install -y jupyterhub
-
- # Install additional python3 packages with Anaconda3
- export PATH="/opt/anaconda3/bin:${PATH}"
- conda install -y jupyterhub
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/keras/keras-tensorflow-cpu.def b/archive/comet/keras/keras-tensorflow-cpu.def
deleted file mode 100644
index ac3a467470a0f1cb3696443a6b87b8b5f22df294..0000000000000000000000000000000000000000
--- a/archive/comet/keras/keras-tensorflow-cpu.def
+++ /dev/null
@@ -1,268 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + tensorflow
- APPLICATION_VERSION 2.2.0 + 1.8
- APPLICATION_URL https://keras.io/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190814
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
- dpkg -i bazel_0.13.1-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- # Download TensorFlow source
- cd /opt
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout r1.8
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=generic\r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.8.0-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- #apt-get -y install ipython
- #apt-get -y install ipython-notebook
- python -m pip install jupyter
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-skimage
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3-numpy
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=generic\r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.8.0-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- #apt-get -y install ipython3
- #apt-get -y install ipython3-notebook
- python3 -m pip install jupyter
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-skimage
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install Keras dependencies for python(2) and python3
- apt-get -y install python-yaml
- apt-get -y install python3-yaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
- tar -xzvf 2.2.0.tar.gz
- cd /opt/keras-2.2.0
- python setup.py install
- python3 setup.py install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/keras/keras-tensorflow-gpu.def b/archive/comet/keras/keras-tensorflow-gpu.def
deleted file mode 100644
index 3610eff12d498a97abceb4edab64ed69cd48272b..0000000000000000000000000000000000000000
--- a/archive/comet/keras/keras-tensorflow-gpu.def
+++ /dev/null
@@ -1,562 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + tensorflow
- APPLICATION_VERSION 2.2.4 + 1.12
- APPLICATION_URL https://keras.io/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190814
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
-
- # Fixing some TensorFlow and libnccl*.deb path issues ...
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-9.2/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.3.4 /usr/local/cuda-9.2/lib64/libnccl.so.2.3.4
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2.3.4 /usr/local/cuda-9.2/lib64/libnccl.so.2
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2 /usr/local/cuda-9.2/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-9.2/include/nccl.h
- ln -s /usr/local/cuda-9.2/lib64 /usr/local/cuda-9.2/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-9.2/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install CUDA-aware OpenMPI
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.17.2/bazel_0.17.2-linux-x86_64.deb
- dpkg -i bazel_0.17.2-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-six
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- pip install keras_applications==1.0.5 --no-deps
- pip install keras_preprocessing==1.0.3 --no-deps
-
- cd /opt
-
- # Download TensorFlow source
- git clone https://github.com/tensorflow/tensorflow
- cd /opt/tensorflow
- git checkout r1.12
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Ignite support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with ROCm support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the CUDA SDK version you want to use. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python.exp
- echo 'send "9.2.88\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where CUDA 9.2 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7\]: "' >> install-tensorflow-python.exp
- echo 'send "7.2.1.38\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where cuDNN 7 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the NCCL version you want to use. If NCCL 2.2 is not installed, then you can use version 1.3 that can be fected automatically but it may have worse performance with multiple GPUs. \[Default is 2.2\]:"' >> install-tensorflow-python.exp
- echo 'send "2.3.4\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,7.0\]"' >> install-tensorflow-python.exp
- echo 'send "3.7,6.0\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- #echo 'expect "Please specify the MPI toolkit folder. \[Default is /opt/openmpi-1.8.4\]: "' >> install-tensorflow-python.exp
- #echo 'send "/opt/openmpi-1.8.4\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=haswell \r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # See https://github.com/tensorflow/tensorflow/issues/17801
- #ln -s /usr/local/cuda-8.0/nvvm/libdevice/libdevice.compute_50.10.bc /usr/local/cuda-8.0/nvvm/libdevice/libdevice.10.bc
-
- # See https://github.com/tensorflow/tensorflow/issues/19203
- # https://github.com/ghostplant/tensorflow-cuda8-optimized/blob/master/Dockerfile.tf18-py35-cuda8-cudnn6021
- #sed -i 's/^#if TF_HAS_.*$/#if !defined(__NVCC__)/g' tensorflow/core/platform/macros.h
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- #bazel build --local_resources 2048,.5,1.0 -c opt --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" --config=cuda --config=gdr --config=verbs //tensorflow/tools/pip_package:build_pip_package
- bazel build --local_resources 2048,.5,1.0 -c opt --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.12.0-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- #apt-get -y install ipython
- #apt-get -y install ipython-notebook
- python -m pip install jupyter
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-skimage
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install Keras-related python packages
- apt-get -y install python-pydot
-
- # Install custom requests from users
- pip install h5py-cache
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-six
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
- apt-get -y install python3-numpy
-
- pip3 install keras_applications==1.0.5 --no-deps
- pip3 install keras_preprocessing==1.0.3 --no-deps
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Ignite support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with ROCm support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the CUDA SDK version you want to use. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python3.exp
- echo 'send "9.2.88\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where CUDA 9.2 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7\]: "' >> install-tensorflow-python3.exp
- echo 'send "7.2.1.38\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where cuDNN 7 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the NCCL version you want to use. If NCCL 2.2 is not installed, then you can use version 1.3 that can be fected automatically but it may have worse performance with multiple GPUs. \[Default is 2.2\]:"' >> install-tensorflow-python3.exp
- echo 'send "2.3.4\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python3.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,7.0\]"' >> install-tensorflow-python3.exp
- echo 'send "3.7,6.0\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- #echo 'expect "Please specify the MPI toolkit folder. \[Default is /opt/openmpi-1.8.4\]: "' >> install-tensorflow-python3.exp
- #echo 'send "/opt/openmpi-1.8.4\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=haswell -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mmovbe -maes -mno-sha -mpclmul -mpopcnt -mabm -mno-lwp -mfma -mno-fma4 -mno-xop -mbmi -mbmi2 -mno-tbm -mavx -mavx2 -msse4.2 -msse4.1 -mlzcnt -mno-rtm -mno-hle -mrdrnd -mf16c -mfsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=haswell \r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- # It is recommended to run bazel clean when switching between two configurations in the same source tree.
- bazel clean
-
- bazel build --local_resources 2048,.5,1.0 -c opt --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.12.0-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- #apt-get -y install ipython3
- #apt-get -y install ipython3-notebook
- python3 -m pip install jupyter
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-skimage
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install Keras-related python3 packages
- apt-get -y install python3-pydot
-
- # Install custom requests from users
- pip3 install h5py-cache
-
- ### Now installing stand-alone version of Keras alongside tensorflow.keras ###
-
- # Install Keras dependencies for python(2) and python3
- apt-get -y install python-yaml
- apt-get -y install python3-yaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.4.tar.gz
- tar -xzvf 2.2.4.tar.gz
- cd /opt/keras-2.2.4
- python setup.py install
- python3 setup.py install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/keras/keras-theano-cpu.def b/archive/comet/keras/keras-theano-cpu.def
deleted file mode 100644
index c5ba5d0bbb365c2111c57e20242f409938bcf48b..0000000000000000000000000000000000000000
--- a/archive/comet/keras/keras-theano-cpu.def
+++ /dev/null
@@ -1,136 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + theano
- APPLICATION_VERSION 2.2.0 + 1.0.3
- APPLICATION_URL https://keras.io/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20181203
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set other environment variables
- export PATH="/opt/miniconda2/bin:${PATH}"
- export MKL_THREADING_LAYER='GNU'
- export KERAS_BACKEND='theano'
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install python(2) dependencies for Theano
- export PATH="/opt/miniconda2/bin:${PATH}"
- conda install -y numpy
- conda install -y scipy
- conda install -y mkl
- conda install -y nose
- conda install -y sphinx
- conda install -y pydot-ng
-
- # Install Theano for python(2)
- conda install -y theano
-
- # Install common python packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y ipython-notebook
- conda install -y sympy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- # Install Keras dependencies for python(2)
- conda install -y yaml
- conda install -y pyyaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
- tar -xzvf 2.2.0.tar.gz
- cd /opt/keras-2.2.0
- python setup.py install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/keras/keras-theano-gpu.def b/archive/comet/keras/keras-theano-gpu.def
deleted file mode 100644
index b06bf04564dff6932be94273e3dd078923149be9..0000000000000000000000000000000000000000
--- a/archive/comet/keras/keras-theano-gpu.def
+++ /dev/null
@@ -1,314 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + theano
- APPLICATION_VERSION 2.2.0 + 1.0.3
- APPLICATION_URL https://keras.io/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20181203
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
- # Set other environment variables
- export PATH="/opt/miniconda2/bin:${PATH}"
- export MKL_THREADING_LAYER='GNU'
- export KERAS_BACKEND='theano'
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install python(2) dependencies for Theano
- export PATH="/opt/miniconda2/bin:${PATH}"
- conda install -y numpy
- conda install -y scipy
- conda install -y mkl
- conda install -y nose
- conda install -y sphinx
- conda install -y pydot-ng
-
- # Install Theano for python(2)
- conda install -y theano
-
- # Install common python packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y ipython-notebook
- conda install -y sympy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- # Install Keras dependencies for python(2)
- conda install -y yaml
- conda install -y pyyaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
- tar -xzvf 2.2.0.tar.gz
- cd /opt/keras-2.2.0
- python setup.py install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/meep/meep.def b/archive/comet/meep/meep.def
deleted file mode 100644
index 78bbfa2c58592c80a39be7d9e6db20465ef04fce..0000000000000000000000000000000000000000
--- a/archive/comet/meep/meep.def
+++ /dev/null
@@ -1,330 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME meep
- APPLICATION_VERSION 1.13.1
- APPLICATION_URL https://www.open-mpi.org/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 2048
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200312
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set paths to MEEP and its dependencies
- export PATH="/opt/harminv-1.4.1/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/harminv-1.4.1/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/libctl-4.5.0/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/libctl-4.5.0/lib:${LD_LIBRARY_PATH}"
- export LD_LIBRARY_PATH="/opt/zlib-1.2.11/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/hdf5-1.10.1/hdf5/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/hdf5-1.10.1/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/h5utils-1.13.1/bin:${PATH}"
- export PATH="/opt/fftw-3.3.7/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/fftw-3.3.7/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/mpb-1.10.0/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/mpb-1.10.0/lib:${LD_LIBRARY_PATH}"
- export PATH="/opt/meep-1.13.1/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/meep-1.13.1/lib:${LD_LIBRARY_PATH}"
- export PYTHONPATH='/opt/meep-1.13.1/lib/python3.6/site-packages'
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Install MEEP dependencies
- apt-get -y install libopenblas-base
- apt-get -y install libopenblas-dev
- apt-get -y install libgmp-dev
- apt-get -y install libgsl-dev
- apt-get -y install libpng-dev
- apt-get -y install swig
- apt-get -y install guile-2.0-dev
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-pkgconfig
- apt-get -y install python3-numpy
- apt-get -y install python3-scipy
- apt-get -y install python3-matplotlib
- apt-get -y install cython3
- apt-get -y install ffmpeg
-
- cd /opt
-
- # Download, build, and install Harminv
- wget https://github.com/NanoComp/harminv/releases/download/v1.4.1/harminv-1.4.1.tar.gz
- tar -xf harminv-1.4.1.tar.gz
- cd harminv-1.4.1
- ./configure --prefix='/opt/harminv-1.4.1' --enable-shared
- make
- make install
-
- export PATH="/opt/harminv-1.4.1/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/harminv-1.4.1/lib:${LD_LIBRARY_PATH}"
-
- cd /opt
-
- # Download, build, and install libctl
- wget https://github.com/NanoComp/libctl/releases/download/v4.5.0/libctl-4.5.0.tar.gz
- tar -xf libctl-4.5.0.tar.gz
- cd libctl-4.5.0
- ./configure --prefix='/opt/libctl-4.5.0' --enable-shared
- make
- make install
-
- export PATH="/opt/libctl-4.5.0/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/libctl-4.5.0/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build and install zlib
- wget http://zlib.net/zlib-1.2.11.tar.gz
- tar -xf zlib-1.2.11.tar.gz
- cd zlib-1.2.11
- ./configure --prefix='/opt/zlib-1.2.11'
- make
- make install
-
- export LD_LIBRARY_PATH="/opt/zlib-1.2.11/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install HDF5
- wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz
- tar -xf hdf5-1.10.1.tar.gz
- cd hdf5-1.10.1
- ./configure CC=mpicc CXX=mpic++ --prefix='/opt/hdf5-1.10.1' --enable-parallel --enable-fortran --enable-shared --with-zlib='/opt/zlib-1.2.11'
- make
- make install
-
- export PATH="/opt/hdf5-1.10.1/hdf5/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/hdf5-1.10.1/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install h5utils
- wget https://github.com/NanoComp/h5utils/releases/download/1.13.1/h5utils-1.13.1.tar.gz
- tar -xf h5utils-1.13.1.tar.gz
- cd h5utils-1.13.1
- ./configure CC='mpicc' CPPFLAGS='-I/opt/hdf5-1.10.1/include' LDFLAGS='-L/opt/hdf5-1.10.1/lib' --prefix='/opt/h5utils-1.13.1'
- make
- make install
-
- export PATH="/opt/h5utils-1.13.1/bin:${PATH}"
-
- cd /tmp
-
- # Download, build, and install FFTW3
- wget http://www.fftw.org/fftw-3.3.7.tar.gz
- tar -xf fftw-3.3.7.tar.gz
- cd fftw-3.3.7
- ./configure CC='mpicc' CFLAGS='-fPIC' --prefix='/opt/fftw-3.3.7' --enable-avx2 --enable-threads --enable-openmp --enable-mpi
- make
- make install
-
- export PATH="/opt/fftw-3.3.7/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/fftw-3.3.7/lib:${LD_LIBRARY_PATH}"
-
- cd /opt
-
- # Download, build, and install mpb
- wget https://github.com/NanoComp/mpb/releases/download/v1.10.0/mpb-1.10.0.tar.gz
- tar -xf mpb-1.10.0.tar.gz
- cd mpb-1.10.0
- ./configure CC='mpicc' CXX='mpic++' CPPFLAGS='-I/opt/hdf5-1.10.1/hdf5/include -I/opt/libctl-4.5.0/include -I/opt/fftw-3.3.7/include' LDFLAGS='-L/opt/hdf5-1.10.1/hdf5/lib -L/opt/libctl-4.5.0/lib -L/opt/fftw-3.3.7/lib' --prefix='/opt/mpb-1.10.0' --with-libctl='/opt/libctl-4.5.0' --enable-shared --with-openmp
- make
- make install
- make distclean
- ./configure CC='mpicc' CXX='mpic++' CPPFLAGS='-I/opt/hdf5-1.10.1/hdf5/include -I/opt/libctl-4.5.0/include -I/opt/fftw-3.3.7/include' LDFLAGS='-L/opt/hdf5-1.10.1/hdf5/lib -L/opt/libctl-4.5.0/lib -L/opt/fftw-3.3.7/lib' --prefix='/opt/mpb-1.10.0' --with-libctl='/opt/libctl-4.5.0' --enable-shared --with-mpi
- make
- make install
-
- export PATH="/opt/mpb-1.10.0/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/mpb-1.10.0/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-
- # Download, build, and install mpi4py
- wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-3.0.3.tar.gz
- tar -xf mpi4py-3.0.3.tar.gz
- cd mpi4py-3.0.3
- python3 setup.py build
- python3 setup.py install
-
- cd /tmp
-
- # Download, build, and install h5py
- wget https://github.com/h5py/h5py/releases/download/2.10.0/h5py-2.10.0.tar.gz
- tar -xf h5py-2.10.0.tar.gz
- cd h5py-2.10.0
- export CC='mpicc'
- python3 setup.py configure --hdf5='/opt/hdf5-1.10.1' --hdf5-version='1.10.1' --mpi
- python3 setup.py build
- python3 setup.py install
-
- cd /opt
-
- # Dowload, build, and install MEEP
- wget https://github.com/NanoComp/meep/releases/download/v1.13.1/meep-1.13.1.tar.gz
- tar -xf meep-1.13.1.tar.gz
- cd meep-1.13.1
- ./configure CC='mpicc' CXX='mpic++' PYTHON='python3' CPPFLAGS='-I/opt/harminv-1.4.1/include -I/opt/hdf5-1.10.1/include -I/opt/libctl-4.5.0/include -I/opt/fftw-3.3.7/include -I/opt/mpb-1.10.0/include' LDFLAGS='-L/opt/harminv-1.4.1/lib -L/opt/hdf5-1.10.1/lib -L/opt/libctl-4.5.0/lib -L/opt/fftw-3.3.7/lib -L/opt/mpb-1.10.0/lib' --prefix='/opt/meep-1.13.1' --with-libctl='/opt/libctl-4.5.0' --enable-shared --with-mpi
- make
- make install
-
- export PATH="/opt/meep-1.13.1/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/meep-1.13.1/lib:${LD_LIBRARY_PATH}"
- export PYTHONPATH='/opt/meep-1.13.1/lib/python3.6/site-packages'
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/mxnet/mxnet-cpu.def b/archive/comet/mxnet/mxnet-cpu.def
deleted file mode 100644
index 4ac849a5fed56988bc99aeca7a5b9aa716c6622d..0000000000000000000000000000000000000000
--- a/archive/comet/mxnet/mxnet-cpu.def
+++ /dev/null
@@ -1,171 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME mxnet-cpu
- APPLICATION_VERSION 1.3.1
- APPLICATION_URL http://mxnet.io
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190115
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install MXNet dependencies
- apt-get -y install libopenblas-dev
- apt-get -y install liblapack-dev
- apt-get -y install libopencv-dev
-
- cd /opt
-
- # Download, build and install MXNet core shared library
- wget https://github.com/apache/incubator-mxnet/releases/download/1.3.1/apache-mxnet-src-1.3.1.rc0-incubating.tar.gz
- tar -xzvf apache-mxnet-src-1.3.1.rc0-incubating.tar.gz
- cd /opt/apache-mxnet-src-1.3.1.rc0-incubating
- make USE_OPENCV=1 USE_BLAS=openblas USE_DIST_KVSTORE=1
-
- # Install MXNet python(2) bindings
- apt-get -y install python-dev
- apt-get -y install python-setuptools
- apt-get -y install python-pip
- apt-get -y install libgfortran3
-
- cd /opt/apache-mxnet-src-1.3.1.rc0-incubating/python
- python setup.py install
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install MXNet python3 bindings
- apt-get -y install python3-dev
- apt-get -y install python3-setuptools
- apt-get -y install python3-pip
-
- python3 setup.py clean --all
- python3 setup.py install
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install graphviz (needed for graph visualization using mxnet.viz).
- apt-get -y install graphviz
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/mxnet/mxnet-gpu.def b/archive/comet/mxnet/mxnet-gpu.def
deleted file mode 100644
index ea2d529d63689836e68565418e75efe670230de9..0000000000000000000000000000000000000000
--- a/archive/comet/mxnet/mxnet-gpu.def
+++ /dev/null
@@ -1,348 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME mxnet-gpu
- APPLICATION_VERSION 1.3.1
- APPLICATION_URL http://mxnet.io
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190115
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install MXNet dependencies
- apt-get -y install libopenblas-dev
- apt-get -y install liblapack-dev
- apt-get -y install libopencv-dev
-
- cd /opt
-
- # Download, build and install MXNet core shared library
- wget https://github.com/apache/incubator-mxnet/releases/download/1.3.1/apache-mxnet-src-1.3.1.rc0-incubating.tar.gz
- tar -xzvf apache-mxnet-src-1.3.1.rc0-incubating.tar.gz
- cd /opt/apache-mxnet-src-1.3.1.rc0-incubating
- make USE_OPENCV=1 USE_BLAS=openblas USE_CUDA=1 USE_CUDA_PATH=/usr/local/cuda USE_CUDNN=1 USE_DIST_KVSTORE=1
-
- # Install MXNet python(2) bindings
- apt-get -y install python-dev
- apt-get -y install python-setuptools
- apt-get -y install python-pip
- apt-get -y install libgfortran3
-
- cd /opt/apache-mxnet-src-1.3.1.rc0-incubating/python
- python setup.py install
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install MXNet python3 bindings
- apt-get -y install python3-dev
- apt-get -y install python3-setuptools
- apt-get -y install python3-pip
-
- python3 setup.py clean --all
- python3 setup.py install
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install graphviz (needed for graph visualization using mxnet.viz).
- apt-get -y install graphviz
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/neon/neon-cpu.def b/archive/comet/neon/neon-cpu.def
deleted file mode 100644
index 17c8c4e9f8eae79eff0fe3903df101569aacf7c7..0000000000000000000000000000000000000000
--- a/archive/comet/neon/neon-cpu.def
+++ /dev/null
@@ -1,208 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME neon
- APPLICATION_VERSION 2.6.0
- APPLICATION_URL https://ai.intel.com/neon/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180524
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install aeon and neon dependencies
- apt-get -y install clang
- apt-get -y install libcurl4-openssl-dev
- apt-get -y install libopencv-dev
- apt-get -y install libsox-dev
- apt-get -y install libboost-filesystem-dev
- apt-get -y install libboost-system-dev
- apt-get -y install libssl-dev
- apt-get -y install ffmpeg
-
- # Install aeon and neon python dependencies
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-virtualenv
- apt-get -y install python-numpy
- apt-get -y install python-h5py
- apt-get -y install python-yaml
- apt-get -y install python-opencv
- apt-get -y install python-future
- apt-get -y install python-configargparse
-
- pip install -y --upgrade setuptools
-
- cd /opt
-
- # Download, build, and install aeon for python
- git clone https://github.com/NervanaSystems/aeon.git
- mkdir -p /opt/aeon/build
- cd /opt/aeon/build
- cmake .. \
- -DCMAKE_BUILD_TYPE='Release' \
- -DPYTHON_EXECUTABLE='/usr/bin/python' \
- -DPYTHON_LIBRARIES='/usr/lib/python2.7' \
- -DPYTHON_INCLUDE_DIRS='/usr/include/python2.7' \
- -DENABLE_AEON_SERVICE='OFF' \
- -DENABLE_AEON_CLIENT='ON' \
- -DENABLE_OPENFABRICS_CONNECTOR='OFF'
- pip install .
-
- cd /opt
-
- # Download, build, and install neon for python
- git clone https://github.com/NervanaSystems/neon.git
- cd /opt/neon
- git checkout latest
- make neon_install
-
- # Install aeon and neon python3 dependencies
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-virtualenv
- apt-get -y install python3-numpy
- apt-get -y install python3-h5py
- apt-get -y install python3-yaml
- apt-get -y install python3-opencv
- apt-get -y install python3-future
- apt-get -y install python3-configargparse
-
- pip3 install -y --upgrade setuptools
-
- # Download, build, and install aeon for python3
- cd /opt/aeon/build
- cmake .. \
- -DCMAKE_BUILD_TYPE='Release' \
- -DPYTHON_EXECUTABLE='/usr/bin/python' \
- -DPYTHON_LIBRARIES='/usr/lib/python3.5' \
- -DPYTHON_INCLUDE_DIRS='/usr/include/python3.5' \
- -DENABLE_AEON_SERVICE='OFF' \
- -DENABLE_AEON_CLIENT='ON' \
- -DENABLE_OPENFABRICS_CONNECTOR='OFF'
- pip3 install .
-
- # Download, build, and install neon for python3
- cd /opt/neon
- sed -i 's/@python setup.py install/@python3 setup.py install/' Makefile
- make neon_install
-
- # Install common python packages for data science and machine
- # learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
-
- # Install common python3 packages for data science and machine
- # learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Set container environment variables
- cd /.singularity.d/env
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
-
- cd /tmp
- python /opt/neon/examples/mnist_mlp.py
diff --git a/archive/comet/pytorch/pytorch-cpu.def b/archive/comet/pytorch/pytorch-cpu.def
deleted file mode 100644
index 7c92cfad8c67d8796a37c2f77610653dfa593501..0000000000000000000000000000000000000000
--- a/archive/comet/pytorch/pytorch-cpu.def
+++ /dev/null
@@ -1,262 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME pytorch
- APPLICATION_VERSION 1.4.0
- APPLICATION_URL http://pytorch.org
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200225
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Setup conda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
- export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
-
- # Install common python packages
- conda install -y jupyterlab
- conda install -y numpy
- conda install -y matplotlib
- conda install -y pandas
- conda install -y plotly
- conda install -y scipy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y seaborn
- conda install -y statsmodels
- conda install -y opencv
-
- # Install GPU-accelerated python packages
- conda install -y numba
-
- # Install additional python packages
- conda install -y astropy
- conda install -y biopython
- conda install -y h5py
- conda install -y nltk
- conda install -y sympy
-
- # Install PyTorch dependencies
- conda install -y numpy
- conda install -y ninja
- conda install -y pyyaml
- conda install -y mkl
- conda install -y mkl-include
- conda install -y setuptools
- conda install -y cmake
- conda install -y cffi
-
- cd /opt
-
- # Download, build, and install PyTorch
- git clone --recursive https://github.com/pytorch/pytorch
- cd pytorch
- git checkout v1.4.0
- git submodule sync
- git submodule update --init --recursive
-
- export CC='mpicc'
- export CXX='mpicxx'
- export CFLAGS='-mtune=generic'
-
- export BLAS='MKL'
- export USE_FBGEMM=1
- export USE_MKLDNN=1
- export USE_NNPACK=1
- export USE_NUMPY=1
- export USE_QNNPACK=1
-
- export USE_DISTRIBUTED=1
- export USE_IBVERBS=1
- export USE_GLOO=1
- export USE_MPI=1
- export USE_C10D_MPI=1
- export USE_NCCL=0
- export USE_SYSTEM_NCCL=0
- export NCCL_INCLUDE_DIR='/usr/include'
-
- export USE_OPENMP=1
- export ATEN_THREADING='OMP'
- export MKL_THREADING='OMP'
-
- export TORCH_CUDA_ARCH_LIST='NONE'
- export USE_CUDA=0
- export USE_CUDNN=0
-
- export USE_FFMPEG=0
- export USE_OPENCV=1
-
- python setup.py install
-
- # Download and install vision package for PyTorch
- git clone https://github.com/pytorch/vision.git
- cd vision
- git checkout v0.5.0
- python setup.py install
-
- cd ../
-
- # Download and install text package for PyTorch
- git clone https://github.com/pytorch/text.git
- cd text
- git checkout 0.5.0
- python setup.py install
-
- cd ../
-
- # Download and install audio package for PyTorch
- git clone https://github.com/pytorch/audio.git
- cd audio
- git checkout v0.4.0
- python setup.py install
-
- cd ../
-
- # Download examples for PyTorch
- git clone https://github.com/pytorch/examples.git
-
- cd /opt
-
- # Install fastai for PyTorch
- git clone https://github.com/fastai/fastai
- cd fastai
- git checkout 1.0.60
- tools/run-after-git-clone
- pip install -e ".[dev]"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
-
- # Update database for mlocate
- updatedb
-
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/pytorch/pytorch-gpu.def b/archive/comet/pytorch/pytorch-gpu.def
deleted file mode 100644
index 766435f4cb08df8d922f10c97ee606c2f1ece7bf..0000000000000000000000000000000000000000
--- a/archive/comet/pytorch/pytorch-gpu.def
+++ /dev/null
@@ -1,518 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME pytorch
- APPLICATION_VERSION 1.4.0
- APPLICATION_URL http://pytorch.org
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200303
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1804/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1804/x86_64"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-common-418_418.67-0ubuntu1_all.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-compute-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-decode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-encode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-gl-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl-dev_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-dkms-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_418.67-0ubuntu1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-diagnostic_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-dev_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1_10.1.168-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-dev_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc_1.0.0-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.5.6-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.5.6-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i libnvidia-common-418_418.67-0ubuntu1_all.deb
- dpkg -i libnvidia-compute-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-decode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-encode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-gl-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl-dev_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-dkms-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-driver-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_418.67-0ubuntu1_amd64.deb
-
- dpkg -i cuda-drivers_418.67-1_amd64.deb
- dpkg -i cuda-drivers-diagnostic_418.67-1_amd64.deb
- dpkg -i cuda-compat-10-1_418.67-1_amd64.deb
- dpkg -i cuda-license-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-misc-headers-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvcc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cuobjdump-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprune-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-compiler-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-driver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvdisasm-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gdb-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprof-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-memcheck-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cupti-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvtx-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-command-line-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvml-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i libcublas10_10.2.0.168-1_amd64.deb
- dpkg -i libcublas-dev_10.2.0.168-1_amd64.deb
- dpkg -i cuda-cufft-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cufft-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-samples-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-documentation-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-compute-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-systems-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvvp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-visual-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-toolkit-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-runtime-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-demo-suite-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-10-1_10.1.168-1_amd64.deb
-
- dpkg -i libcutensor1_1.0.0-1_amd64.deb
- dpkg -i libcutensor-dev_1.0.0-1_amd64.deb
- dpkg -i libcutensor-doc_1.0.0-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb
- dpkg -i libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb
-
- dpkg -i libnccl2_2.5.6-1+cuda10.1_amd64.deb
- dpkg -i libnccl-dev_2.5.6-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Setup conda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
- export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
-
- # Install common python packages
- conda install -y jupyterlab
- conda install -y numpy
- conda install -y matplotlib
- conda install -y pandas
- conda install -y plotly
- conda install -y scipy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y seaborn
- conda install -y statsmodels
- conda install -y opencv
-
- # Install GPU-accelerated python packages
- conda install -y numba
-
- # Install additional python packages
- conda install -y astropy
- conda install -y biopython
- conda install -y h5py
- conda install -y nltk
- conda install -y sympy
-
- # Install PyTorch dependencies
- conda install -y numpy
- conda install -y ninja
- conda install -y pyyaml
- conda install -y mkl
- conda install -y mkl-include
- conda install -y setuptools
- conda install -y cmake
- conda install -y cffi
-
- # Add LAPACK support for the GPU
- conda install -y magma-cuda101 -c pytorch
-
- cd /opt
-
- # Download, build, and install PyTorch
- git clone --recursive https://github.com/pytorch/pytorch
- cd pytorch
- git checkout v1.4.0
- git submodule sync
- git submodule update --init --recursive
-
- export CC='mpicc'
- export CXX='mpicxx'
- export CFLAGS='-mtune=generic'
-
- export BLAS='MKL'
- export USE_FBGEMM=1
- export USE_MKLDNN=1
- export USE_NNPACK=1
- export USE_NUMPY=1
- export USE_QNNPACK=1
-
- export USE_DISTRIBUTED=1
- export USE_IBVERBS=1
- export USE_GLOO=1
- export USE_MPI=1
- export USE_C10D_MPI=1
- export USE_NCCL=1
- export USE_SYSTEM_NCCL=1
- export NCCL_INCLUDE_DIR='/usr/include'
-
- export USE_OPENMP=1
- export ATEN_THREADING='OMP'
- export MKL_THREADING='OMP'
-
- export TORCH_CUDA_ARCH_LIST='3.0;3.5;3.7;5.2;6.0;6.1;7.0;7.5'
- export USE_CUDA=1
- export USE_CUDNN=1
-
- export USE_FFMPEG=0
- export USE_OPENCV=1
-
- python setup.py install
-
- # Download and install vision package for PyTorch
- git clone https://github.com/pytorch/vision.git
- cd vision
- git checkout v0.5.0
- python setup.py install
-
- cd ../
-
- # Download and install text package for PyTorch
- git clone https://github.com/pytorch/text.git
- cd text
- git checkout 0.5.0
- python setup.py install
-
- cd ../
-
- # Download and install audio package for PyTorch
- git clone https://github.com/pytorch/audio.git
- cd audio
- git checkout v0.4.0
- python setup.py install
-
- cd ../
-
- # Download examples for PyTorch
- git clone https://github.com/pytorch/examples.git
-
- cd /opt
-
- # Install fastai for PyTorch
- git clone https://github.com/fastai/fastai
- cd fastai
- git checkout 1.0.60
- tools/run-after-git-clone
- pip install -e ".[dev]"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
-
- # Update database for mlocate
- updatedb
-
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/smcpp/smcpp.def b/archive/comet/smcpp/smcpp.def
deleted file mode 100644
index faead3d2130174e1d88c8183f5da17fcbf9ed449..0000000000000000000000000000000000000000
--- a/archive/comet/smcpp/smcpp.def
+++ /dev/null
@@ -1,103 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME smcpp
- APPLICATION_VERSION unkown
- APPLICATION_URL https://github.com/popgenmethods/smcpp
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190515
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set miniconda3 environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Set miniconda3 environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
- # Install smcpp
- conda install -c terhorst -c bioconda smcpp
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/tensorflow/tensorflow-cpu.def b/archive/comet/tensorflow/tensorflow-cpu.def
deleted file mode 100644
index 47ccb9be75b9bddb8998f0aa6e92eef6544cdbd5..0000000000000000000000000000000000000000
--- a/archive/comet/tensorflow/tensorflow-cpu.def
+++ /dev/null
@@ -1,252 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME tensorflow
- APPLICATION_VERSION 1.15.2
- APPLICATION_URL https://www.tensorflow.org/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 20480
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200311
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- cd /opt
-
- # Setup conda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
- # Install dependencies for Bazel
- apt-get -y install g++
- apt-get -y install unzip
- apt-get -y install zip
- apt-get -y install openjdk-11-jdk
-
- # Download, build, and install Bazel
- mkdir -p bazel
- cd bazel
- wget https://github.com/bazelbuild/bazel/releases/download/0.25.3/bazel-0.25.3-dist.zip
- unzip -o bazel-0.25.3-dist.zip
- export EXTRA_BAZEL_ARGS="--host_javabase=@local_jdk//:jdk"
- ./compile.sh
-
- # Set path to Bazel
- export PATH="/opt/bazel/output:${PATH}"
-
- # Install common python packages
- conda install -y jupyterlab
- conda install -y numpy
- conda install -y matplotlib
- conda install -y pandas
- conda install -y plotly
- conda install -y scipy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y seaborn
- conda install -y statsmodels
- conda install -y opencv
-
- # Install additional python packages
- conda install -y astropy
- conda install -y biopython
- conda install -y h5py
- conda install -y nltk
- conda install -y sympy
-
- cd /opt
-
- # Install dependencies for TensorFlow
- conda install -y pip
- conda install -y six
- conda install -y numpy
- conda install -y wheel
- conda install -y setuptools
- conda install -y mock
- conda install -y future
-
- pip install keras_applications --no-deps
- pip install keras_preprocessing --no-deps
-
- # Download, build, and install TensorFlow
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout v1.15.2
-
- export PYTHON_BIN_PATH='/opt/miniconda3/bin/python'
- export PYTHON_LIB_PATH='/opt/miniconda3/lib/python3.7/site-packages'
- export TF_ENABLE_XLA=1
- export TF_NEED_OPENCL_SYCL=0
- export TF_NEED_ROCM=0
- export TF_NEED_CUDA=0
- export TF_DOWNLOAD_CLANG=0
- export TF_NEED_MPI=1
- export MPI_HOME='/opt/openmpi-3.1.4'
- export CC_OPT_FLAGS='-mtune=generic'
- export TF_SET_ANDROID_WORKSPACE=0
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous
- # builds may cause some conflicts. See 'dangling symbolic links' at
- # https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --local_resources 2048,.5,1.0 -c opt --config=mkl --config=verbs --config=numa //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
- pip install tensorflow_pkg/tensorflow-1.15.2-cp37-cp37m-linux_x86_64.whl
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/tensorflow/tensorflow-gpu.def b/archive/comet/tensorflow/tensorflow-gpu.def
deleted file mode 100644
index aede34c3a85cafcda86ab624835474d463b6b8fb..0000000000000000000000000000000000000000
--- a/archive/comet/tensorflow/tensorflow-gpu.def
+++ /dev/null
@@ -1,513 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME tensorflow
- APPLICATION_VERSION 1.15.2
- APPLICATION_URL https://www.tensorflow.org
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200318
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export CUDA_HOME='/usr/local/cuda-10.1'
- export PATH="${CUDA_HOME}/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1804/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1804/x86_64"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-common-418_418.67-0ubuntu1_all.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-compute-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-decode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-encode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-gl-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl-dev_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-dkms-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_418.67-0ubuntu1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-diagnostic_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-dev_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1_10.1.168-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-dev_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc_1.0.0-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.5.6-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.5.6-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i libnvidia-common-418_418.67-0ubuntu1_all.deb
- dpkg -i libnvidia-compute-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-decode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-encode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-gl-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl-dev_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-dkms-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-driver-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_418.67-0ubuntu1_amd64.deb
-
- dpkg -i cuda-drivers_418.67-1_amd64.deb
- dpkg -i cuda-drivers-diagnostic_418.67-1_amd64.deb
- dpkg -i cuda-compat-10-1_418.67-1_amd64.deb
- dpkg -i cuda-license-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-misc-headers-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvcc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cuobjdump-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprune-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-compiler-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-driver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvdisasm-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gdb-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprof-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-memcheck-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cupti-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvtx-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-command-line-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvml-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i libcublas10_10.2.0.168-1_amd64.deb
- dpkg -i libcublas-dev_10.2.0.168-1_amd64.deb
- dpkg -i cuda-cufft-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cufft-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-samples-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-documentation-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-compute-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-systems-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvvp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-visual-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-toolkit-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-runtime-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-demo-suite-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-10-1_10.1.168-1_amd64.deb
-
- dpkg -i libcutensor1_1.0.0-1_amd64.deb
- dpkg -i libcutensor-dev_1.0.0-1_amd64.deb
- dpkg -i libcutensor-doc_1.0.0-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb
- dpkg -i libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb
-
- dpkg -i libnccl2_2.5.6-1+cuda10.1_amd64.deb
- dpkg -i libnccl-dev_2.5.6-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export CUDA_HOME='/usr/local/cuda-10.1'
- export PATH="${CUDA_HOME}/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx' --enable-cuda --with-cuda-include="${CUDA_HOME}/include" --with-cuda-libpath="${CUDA_HOME}/lib64"
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- cd /opt
-
- # Setup conda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
- # Install dependencies for Bazel
- apt-get -y install g++
- apt-get -y install unzip
- apt-get -y install zip
- apt-get -y install openjdk-11-jdk
-
- # Download, build, and install Bazel
- mkdir -p bazel
- cd bazel
- wget https://github.com/bazelbuild/bazel/releases/download/0.25.3/bazel-0.25.3-dist.zip
- unzip -o bazel-0.25.3-dist.zip
- export EXTRA_BAZEL_ARGS="--host_javabase=@local_jdk//:jdk"
- ./compile.sh
-
- # Set path to Bazel
- export PATH="/opt/bazel/output:${PATH}"
-
- # Install common python packages
- conda install -y jupyterlab
- conda install -y numpy
- conda install -y matplotlib
- conda install -y pandas
- conda install -y plotly
- conda install -y scipy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y seaborn
- conda install -y statsmodels
- conda install -y opencv
-
- # Install GPU-accelerated python packages
- conda install -y numba
-
- # Install additional python packages
- conda install -y astropy
- conda install -y biopython
- conda install -y h5py
- conda install -y nltk
- conda install -y sympy
-
- cd /opt
-
- # Install dependencies for TensorFlow
- conda install -y pip
- conda install -y six
- conda install -y numpy
- conda install -y wheel
- conda install -y setuptools
- conda install -y mock
- conda install -y future
-
- pip install keras_applications --no-deps
- pip install keras_preprocessing --no-deps
-
- # Download, build, and install TensorFlow
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout v1.15.2
-
- export PYTHON_BIN_PATH='/opt/miniconda3/bin/python'
- export PYTHON_LIB_PATH='/opt/miniconda3/lib/python3.7/site-packages'
- export TF_ENABLE_XLA=1
- export TF_NEED_OPENCL_SYCL=0
- export TF_NEED_ROCM=0
- export TF_NEED_CUDA=1
- export TF_NEED_TENSORRT=0
- export TF_CUDA_COMPUTE_CAPABILITIES='3.5,3.7,5.2,6.0,6.1,7.0,7.5'
- export TF_CUDA_CLANG=0
- export GCC_HOST_COMPILER_PATH='/usr/bin/gcc'
- export TF_NEED_MPI=1
- export MPI_HOME='/opt/openmpi-3.1.4'
- export CC_OPT_FLAGS='-mtune=generic'
- export TF_SET_ANDROID_WORKSPACE=0
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous
- # builds may cause some conflicts. See 'dangling symbolic links' at
- # https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --local_resources 2048,.5,1.0 -c opt --config=mkl --config=cuda --config=gdr --config=verbs --config=numa //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
- pip install tensorflow_pkg/tensorflow-1.15.2-cp37-cp37m-linux_x86_64.whl
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/theano/theano-cpu.def b/archive/comet/theano/theano-cpu.def
deleted file mode 100644
index 10587a4d99b2615cc74d2c552eeb69c64c198370..0000000000000000000000000000000000000000
--- a/archive/comet/theano/theano-cpu.def
+++ /dev/null
@@ -1,123 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME theano
- APPLICATION_VERSION 1.0.3
- APPLICATION_URL http://www.deeplearning.net/software/theano/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20181203
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set other environment variables
- export PATH="/opt/miniconda2/bin:${PATH}"
- export MKL_THREADING_LAYER="GNU"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install python(2) dependencies for Theano
- export PATH="/opt/miniconda2/bin:${PATH}"
- conda install -y numpy
- conda install -y scipy
- conda install -y mkl
- conda install -y nose
- conda install -y sphinx
- conda install -y pydot-ng
-
- # Install Theano for python(2)
- conda install -y theano
-
- # Install common python packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y ipython-notebook
- conda install -y sympy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/theano/theano-gpu.def b/archive/comet/theano/theano-gpu.def
deleted file mode 100644
index 63e36d67a567a19cc82e40c956006599f9c3b5ce..0000000000000000000000000000000000000000
--- a/archive/comet/theano/theano-gpu.def
+++ /dev/null
@@ -1,301 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME theano
- APPLICATION_VERSION 1.0.3
- APPLICATION_URL http://www.deeplearning.net/software/theano/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20181203
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
- # Set other environment variables
- export PATH="/opt/miniconda2/bin:${PATH}"
- export MKL_THREADING_LAYER="GNU"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.3.4-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.3.4-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.2.1.38-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.2.1.38-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install python(2) dependencies for Theano
- export PATH="/opt/miniconda2/bin:${PATH}"
- conda install -y numpy
- conda install -y scipy
- conda install -y mkl
- conda install -y nose
- conda install -y sphinx
- conda install -y pydot-ng
-
- # Install Theano for python(2)
- conda install -y theano
-
- # Install common python packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y ipython-notebook
- conda install -y sympy
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/torch/torch-gpu.def b/archive/comet/torch/torch-gpu.def
deleted file mode 100644
index d091d1a12bb125cbdbf8e046d89e54a54886d70e..0000000000000000000000000000000000000000
--- a/archive/comet/torch/torch-gpu.def
+++ /dev/null
@@ -1,250 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME torch7-nv
- APPLICATION_VERSION 0.10.7
- APPLICATION_URL http://torch.ch/
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180524
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-367-dev_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-367_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_367.48-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_367.48-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn6_6.0.21-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.1.2-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.1.2-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/torch7-nv_0.10.7-1ubuntu16.04+cuda8.0_amd64.deb"
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-367-dev_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_367.48-0ubuntu1_amd64.deb
- dpkg -i libcuda1-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-367_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-367_367.48-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_367.48-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_367.48-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_367.48-1_amd64.deb
-
- dpkg -i cuda-license-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-misc-headers-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-core-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-driver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-command-line-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvml-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-samples-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-documentation-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-visual-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-toolkit-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
-
- dpkg -i libcudnn6_6.0.21-1+cuda8.0_amd64.deb
- dpkg -i libcudnn6-dev_6.0.21-1+cuda8.0_amd64.deb
-
- dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
-
- dpkg -i torch7-nv_0.10.7-1ubuntu16.04+cuda8.0_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set container environment variables
- cd /.singularity.d/env
- echo 'export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"' >> 90-environment.sh
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
-
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- nvcc --version
-
diff --git a/archive/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def b/archive/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def
deleted file mode 100644
index 1c0a29a4866518b116c60c0f0a7f83eb428af6fc..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def
+++ /dev/null
@@ -1,385 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda + opencl + openmpi
- APPLICATION_VERSION 16.04 + 9.2.88 + 16.1.2 + 1.8.4
- APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190912
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.4.8-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.4.8-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.4.8-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.4.8-1+cuda9.2_amd64.deb
-
- # Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-9.2/lib64/libcudnn_static.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-9.2/lib64/libcudnn_static_v7.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7 /usr/local/cuda-9.2/lib64/libcudnn.so
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-9.2/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2 /usr/local/cuda-9.2/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-9.2/include/nccl.h
- ln -s /usr/local/cuda-9.2/lib64 /usr/local/cuda-9.2/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-9.2/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Location of Intel repository
- declare -r INTEL_ROOT_URL='http://registrationcenter-download.intel.com'
-
- # Install generic OpenCL packages
- apt-get -y install ocl-icd-libopencl1
- apt-get -y install opencl-headers
- apt-get -y install clinfo
- apt-get -y install ocl-icd-opencl-dev
-
- # Install packages for turing rpm into deb
- apt-get -y install rpm
- apt-get -y install alien
- apt-get -y install libnuma1
-
- # Download OpenCL runtime rpm, convert to deb, then install
- wget "${INTEL_ROOT_URL}/akdlm/irc_nas/12556/opencl_runtime_16.1.2_x64_rh_6.4.0.37.tgz"
- tar -xzf opencl_runtime_16.1.2_x64_rh_6.4.0.37.tgz
-
- cd opencl_runtime_16.1.2_x64_rh_6.4.0.37/rpm
-
- fakeroot alien --to-deb opencl-1.2-base-6.4.0.37-1.x86_64.rpm
- fakeroot alien --to-deb opencl-1.2-intel-cpu-6.4.0.37-1.x86_64.rpm
-
- dpkg -i opencl-1.2-base_6.4.0.37-2_amd64.deb
- dpkg -i opencl-1.2-intel-cpu_6.4.0.37-2_amd64.deb
-
- # Add path to clinfo
- echo '/opt/intel/opencl-1.2-6.4.0.37/lib64/clinfo' > /etc/ld.so.conf.d/intelOpenCL.conf
-
- # Create a vendors dir and add intel.icd
- mkdir -p /etc/OpenCL/vendors
- ln /opt/intel/opencl-1.2-6.4.0.37/etc/intel64.icd /etc/OpenCL/vendors/intel64.icd
- ldconfig
-
- # Test OpenCL installation
- clinfo
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install CUDA-aware OpenMPI
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
- make all install
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " "
- echo " __________________ __ _______________ "
- echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
- echo " --/ / / / / / /|_/ / __/ / / "
- echo " / /___/ /_/ / / / / /___ / / "
- echo " \____/\____/_/ /_/_____/ /_/ "
- echo " "
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu-cuda-opencl.def b/archive/comet/ubuntu/ubuntu-cuda-opencl.def
deleted file mode 100644
index 0aa60c0032986db510de09117d19c8e2a59f847e..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-cuda-opencl.def
+++ /dev/null
@@ -1,341 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda + opencl
- APPLICATION_VERSION 16.04 + 9.2.88 + 16.1.2
- APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime
-
- SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.6.1
- SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190912
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.4.8-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.4.8-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.4.8-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.4.8-1+cuda9.2_amd64.deb
-
- # Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-9.2/lib64/libcudnn_static.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-9.2/lib64/libcudnn_static_v7.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7 /usr/local/cuda-9.2/lib64/libcudnn.so
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-9.2/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2 /usr/local/cuda-9.2/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-9.2/include/nccl.h
- ln -s /usr/local/cuda-9.2/lib64 /usr/local/cuda-9.2/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-9.2/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Location of Intel repository
- declare -r INTEL_ROOT_URL='http://registrationcenter-download.intel.com'
-
- # Install generic OpenCL packages
- apt-get -y install ocl-icd-libopencl1
- apt-get -y install opencl-headers
- apt-get -y install clinfo
- apt-get -y install ocl-icd-opencl-dev
-
- # Install packages for turing rpm into deb
- apt-get -y install rpm
- apt-get -y install alien
- apt-get -y install libnuma1
-
- # Download OpenCL runtime rpm, convert to deb, then install
- wget "${INTEL_ROOT_URL}/akdlm/irc_nas/12556/opencl_runtime_16.1.2_x64_rh_6.4.0.37.tgz"
- tar -xzf opencl_runtime_16.1.2_x64_rh_6.4.0.37.tgz
-
- cd opencl_runtime_16.1.2_x64_rh_6.4.0.37/rpm
-
- fakeroot alien --to-deb opencl-1.2-base-6.4.0.37-1.x86_64.rpm
- fakeroot alien --to-deb opencl-1.2-intel-cpu-6.4.0.37-1.x86_64.rpm
-
- dpkg -i opencl-1.2-base_6.4.0.37-2_amd64.deb
- dpkg -i opencl-1.2-intel-cpu_6.4.0.37-2_amd64.deb
-
- # Add path to clinfo
- echo '/opt/intel/opencl-1.2-6.4.0.37/lib64/clinfo' > /etc/ld.so.conf.d/intelOpenCL.conf
-
- # Create a vendors dir and add intel.icd
- mkdir -p /etc/OpenCL/vendors
- ln /opt/intel/opencl-1.2-6.4.0.37/etc/intel64.icd /etc/OpenCL/vendors/intel64.icd
- ldconfig
-
- # Test OpenCL installation
- clinfo
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " "
- echo " __________________ __ _______________ "
- echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
- echo " --/ / / / / / /|_/ / __/ / / "
- echo " / /___/ /_/ / / / / /___ / / "
- echo " \____/\____/_/ /_/_____/ /_/ "
- echo " "
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu-cuda-openmpi.def b/archive/comet/ubuntu/ubuntu-cuda-openmpi.def
deleted file mode 100644
index 357d52463376c965e18217c57f3ed56830373bca..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-cuda-openmpi.def
+++ /dev/null
@@ -1,432 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda + openmpi
- APPLICATION_VERSION 18.04 + 10.1.168 + 3.1.4
- APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200303
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export CUDA_HOME='/usr/local/cuda-10.1'
- export PATH="${CUDA_HOME}/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1804/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1804/x86_64"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-common-418_418.67-0ubuntu1_all.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-compute-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-decode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-encode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-gl-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl-dev_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-dkms-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_418.67-0ubuntu1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-diagnostic_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-dev_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1_10.1.168-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-dev_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc_1.0.0-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.5.6-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.5.6-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i libnvidia-common-418_418.67-0ubuntu1_all.deb
- dpkg -i libnvidia-compute-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-decode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-encode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-gl-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl-dev_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-dkms-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-driver-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_418.67-0ubuntu1_amd64.deb
-
- dpkg -i cuda-drivers_418.67-1_amd64.deb
- dpkg -i cuda-drivers-diagnostic_418.67-1_amd64.deb
- dpkg -i cuda-compat-10-1_418.67-1_amd64.deb
- dpkg -i cuda-license-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-misc-headers-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvcc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cuobjdump-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprune-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-compiler-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-driver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvdisasm-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gdb-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprof-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-memcheck-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cupti-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvtx-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-command-line-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvml-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i libcublas10_10.2.0.168-1_amd64.deb
- dpkg -i libcublas-dev_10.2.0.168-1_amd64.deb
- dpkg -i cuda-cufft-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cufft-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-samples-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-documentation-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-compute-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-systems-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvvp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-visual-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-toolkit-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-runtime-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-demo-suite-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-10-1_10.1.168-1_amd64.deb
-
- dpkg -i libcutensor1_1.0.0-1_amd64.deb
- dpkg -i libcutensor-dev_1.0.0-1_amd64.deb
- dpkg -i libcutensor-doc_1.0.0-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb
- dpkg -i libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb
-
- dpkg -i libnccl2_2.5.6-1+cuda10.1_amd64.deb
- dpkg -i libnccl-dev_2.5.6-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export CUDA_HOME='/usr/local/cuda-10.1'
- export PATH="${CUDA_HOME}/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx' --enable-cuda --with-cuda-include="${CUDA_HOME}/include" --with-cuda-libpath="${CUDA_HOME}/lib64"
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu-cuda.def b/archive/comet/ubuntu/ubuntu-cuda.def
deleted file mode 100644
index ab2d454d50ea3acafec07f17140febd6f248f3df..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-cuda.def
+++ /dev/null
@@ -1,352 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda
- APPLICATION_VERSION 18.04 + 10.1.168
- APPLICATION_URL https://developer.nvidia.com/cuda-zone
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200303
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1804/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1804/x86_64"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-common-418_418.67-0ubuntu1_all.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-compute-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-decode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-encode-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-gl-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl-dev_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-dkms-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-utils-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-driver-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_418.67-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_418.67-0ubuntu1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers-diagnostic_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compat-10-1_418.67-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas10_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcublas-dev_10.2.0.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-compute-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-systems-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-10-1_10.1.168-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-10-1_10.1.168-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor1_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-dev_1.0.0-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcutensor-doc_1.0.0-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.5.6-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.5.6-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnvparsers6_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb"
-
- #https://developer.nvidia.com/compute/machine-learning/tensorrt/secure/7.0/7.0.0.11/local_repo/nv-tensorrt-repo-ubuntu1804-cuda10.0-trt7.0.0.11-ga-20191216_1-1_amd64.deb
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i libnvidia-common-418_418.67-0ubuntu1_all.deb
- dpkg -i libnvidia-compute-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-cfg1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-decode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-encode-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-fbc1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-gl-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-ifr1-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_418.67-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl-dev_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-source-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-kernel-common-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-dkms-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-compute-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-utils-418_418.67-0ubuntu1_amd64.deb
- dpkg -i xserver-xorg-video-nvidia-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-driver-418_418.67-0ubuntu1_amd64.deb
- dpkg -i libnvidia-diagnostic-418_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_418.67-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_418.67-0ubuntu1_amd64.deb
-
- dpkg -i cuda-drivers_418.67-1_amd64.deb
- dpkg -i cuda-drivers-diagnostic_418.67-1_amd64.deb
- dpkg -i cuda-compat-10-1_418.67-1_amd64.deb
- dpkg -i cuda-license-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-misc-headers-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvcc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cuobjdump-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprune-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-compiler-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-driver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cudart-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvdisasm-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gdb-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvprof-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-memcheck-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cupti-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvtx-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-sanitizer-api-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-command-line-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvml-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvjpeg-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusolver-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i libcublas10_10.2.0.168-1_amd64.deb
- dpkg -i libcublas-dev_10.2.0.168-1_amd64.deb
- dpkg -i cuda-cufft-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cufft-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-curand-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-cusparse-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-npp-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-samples-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-documentation-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-compute-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nsight-systems-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-nvvp-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-visual-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-tools-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-dev-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-toolkit-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-libraries-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-runtime-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-demo-suite-10-1_10.1.168-1_amd64.deb
- dpkg -i cuda-10-1_10.1.168-1_amd64.deb
-
- dpkg -i libcutensor1_1.0.0-1_amd64.deb
- dpkg -i libcutensor-dev_1.0.0-1_amd64.deb
- dpkg -i libcutensor-doc_1.0.0-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.5.32-1+cuda10.1_amd64.deb
- dpkg -i libcudnn7-dev_7.6.5.32-1+cuda10.1_amd64.deb
-
- dpkg -i libnccl2_2.5.6-1+cuda10.1_amd64.deb
- dpkg -i libnccl-dev_2.5.6-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvinfer-plugin6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvinfer-plugin-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvonnxparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvonnxparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i libnvparsers6_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i libnvparsers-dev_6.0.1-1+cuda10.1_amd64.deb
-
- dpkg -i python3-libnvinfer_6.0.1-1+cuda10.1_amd64.deb
- dpkg -i python3-libnvinfer-dev_6.0.1-1+cuda10.1_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-10.1/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-10.1/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu-mvapich2.def b/archive/comet/ubuntu/ubuntu-mvapich2.def
deleted file mode 100644
index 5b770ebe3bc3a18806e13f51cce3af6c99d635b1..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-mvapich2.def
+++ /dev/null
@@ -1,174 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME ubuntu + mvapich2
- APPLICATION_VERSION 18.04 + 2.3.2
- APPLICATION_URL http://mvapich.cse.ohio-state.edu/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 2048
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200228
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to MVAPICH2 binaries and libraries
- export PATH="/opt/mvapich2/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install mvapich2 (build) dependencies
- apt-get -y install bison
-
- # Download, build, and install mvapich2
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.2.tar.gz
- tar -xzvf mvapich2-2.3.2.tar.gz
- cd mvapich2-2.3.2
- ./configure --prefix=/opt/mvapich2
- make
- make install
-
- cd /tmp
-
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu-openmpi.def b/archive/comet/ubuntu/ubuntu-openmpi.def
deleted file mode 100644
index c0fe77d7b406fdfbbe2fa6edd059b8ecfe0ea1cf..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu-openmpi.def
+++ /dev/null
@@ -1,177 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME ubuntu + openmpi
- APPLICATION_VERSION 18.04 + 3.1.4
- APPLICATION_URL https://www.open-mpi.org/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 2048
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200227
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install OpenMPI
- wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
- tar -xzvf openmpi-3.1.4.tar.gz
- cd openmpi-3.1.4
- ./configure --prefix=/opt/openmpi-3.1.4
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
-
- cd /tmp
-w
- # Download, build, and install OSU Microbenchmarks
- wget http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.6.2.tar.gz
- tar -xzvf osu-micro-benchmarks-5.6.2.tar.gz
- cd osu-micro-benchmarks-5.6.2
- ./configure --prefix='/opt/omb-5.6.2' CC='mpicc' CXX='mpicxx'
- make
- make install
-
- # Reorganize OSU Microbenchmarks directory structure
- cd /opt/omb-5.6.2
- mv libexec/osu-micro-benchmarks/mpi/collective ./
- mv libexec/osu-micro-benchmarks/mpi/one-sided ./
- mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
- mv libexec/osu-micro-benchmarks/mpi/startup ./
- rm -rf libexec
-
- # Set paths to OSU Microbenchmarks binaries
- export PATH="/opt/omb-5.6.2/collective:${PATH}"
- export PATH="/opt/omb-5.6.2/one-sided:${PATH}"
- export PATH="/opt/omb-5.6.2/pt2pt:${PATH}"
- export PATH="/opt/omb-5.6.2/startup:${PATH}"
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm *.deb
- rm -rf openmpi-3.1.4*
- rm -rf osu-micro-benchmarks-5.6.2*
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/comet/ubuntu/ubuntu.def b/archive/comet/ubuntu/ubuntu.def
deleted file mode 100644
index 3efc3925cef8a6968ba35ecb8d805f389337a6b4..0000000000000000000000000000000000000000
--- a/archive/comet/ubuntu/ubuntu.def
+++ /dev/null
@@ -1,96 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: bionic
-
-%labels
-
- APPLICATION_NAME ubuntu
- APPLICATION_VERSION 18.04
- APPLICATION_URL https://www.ubuntu.com/
-
- SINGULARITY_VERSION 2.6.1
- SINGULARITY_IMAGE_SIZE 2048
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20200225
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Clean up /tmp directory
- cd /tmp
- rm Miniconda3-latest-Linux-x86_64.sh
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/naked-singularity.sh b/archive/naked-singularity.sh
deleted file mode 100755
index 0a275020af27b0282f5a91e493cce74189373533..0000000000000000000000000000000000000000
--- a/archive/naked-singularity.sh
+++ /dev/null
@@ -1,513 +0,0 @@
-# ======================================================================
-#
-# NAME
-#
-# naked-singularity.sh
-#
-# DESCRIPTION
-#
-# A bash script to help users create Singularity containers from the
-# definition (or recipe) files available in the naked-singularity
-# repository.
-#
-# USAGE
-#
-# 1. Install Singularity on your local desktop, laptop, or virtual
-# machine.
-#
-# ./naked-singularity.sh install
-#
-# 2. Build a simple Ubuntu Singularity container for Comet at SDSC.
-#
-# ./naked-singularity.sh build -s comet -a ubuntu -d ubuntu.def
-#
-# 3. Uninstall Singularity from your local desktop, laptop, or
-# virtual machine.
-#
-# ./naked-singularity.sh uninstall
-#
-# LAST UPDATED
-#
-# Tuesday, April 30th, 2019
-#
-# ----------------------------------------------------------------------
-
-naked_out() {
-
- echo "naked-singularity: ${@}" >&1
-
-}
-
-
-naked_err() {
-
- echo "naked-singularity: ERROR :: ${@}" >&2
-
-}
-
-
-naked_warn() {
-
- echo "naked-singularity: WARNING :: ${@}" >&2
-
-}
-
-
-naked_build() {
-
- local path_to_definition_file="${naked_dir}/definition-files"
- local path_to_image="${naked_dir}/images"
-
- local system=''
- local application=''
- local definition_file=''
- local image=''
- local -i image_size='-1'
- local writable='false'
- local force_overwrite='false'
-
- naked_out "Read in all command-line options for 'build' command ..."
-
- while (( "${#}" > 0 )); do
- naked_out "Read in command-line option '${1}' with input value '${2}' ... "
- case "${1}" in
- -s | --system )
- system="${2}"
- shift 2
- ;;
- -a | --application )
- application="${2}"
- shift 2
- ;;
- -d | --definition-file )
- definition_file="${2}"
- shift 2
- ;;
- -i | --image )
- image="${2}"
- shift 2
- ;;
- -z | --image-size )
- image_size="${2}"
- shift 2
- ;;
- -w | --writable )
- writable='true'
- shift 1
- ;;
- -f | --force-overwrite )
- force_overwrite='true'
- shift 1
- ;;
- *)
- naked_err "Command-line option ${1} not recognized or not supported."
- return 1
- esac
- done
-
- naked_out "All command-line options for 'build' command have been read ... "
-
- naked_out 'Check if DEFINITION FILE is exists ...'
-
- if [[ -z "${system}" ]]; then
- naked_err 'No SYSTEM name was provided.'
- naked_err 'Use the -s (or --system) command-line option to specify the name of the target SYSTEM.'
- naked_err 'Listing all SYSTEMs to choose from ...'
- echo "ls ${path_to_definition_file}"
- echo "$(ls "${path_to_definition_file}")"
- return 1
- fi
-
- path_to_definition_file+="/${system}"
-
- if [[ ! -d "${path_to_definition_file}" ]]; then
- naked_err "${path_to_definition_file} does not exist."
- naked_err 'Use the -s (or --system) command-line option to specify the name of the target SYSTEM.'
- naked_err 'Listing all SYSTEMs to choose from ...'
- echo "ls ${path_to_definition_file%/${system}}"
- echo "$(ls "${path_to_definition_file%/${system}}")"
- return 1
- fi
-
- if [[ -z "${application}" ]]; then
- naked_err 'No APPLICATION name was provided.'
- naked_err 'Use the -a (or --application) command-line option to specify the name of the APPLICATION to be run on the target SYSTEM.'
- naked_err 'Listing all APPLICATIONs to choose from ...'
- echo "ls ${path_to_definition_file}"
- echo "$(ls "${path_to_definition_file}")"
- return 1
- fi
-
- path_to_definition_file+="/${application}"
-
- if [[ ! -d "${path_to_definition_file}" ]]; then
- naked_err "${path_to_definition_file} does not exist."
- naked_err 'Use the -a (or --application) command-line option to specify the name of the APPLICATION to be run on the target SYSTEM.'
- naked_err 'Listing all APPLICATIONs to choose from ...'
- echo "ls ${path_to_definition_file%/${application}}"
- echo "$(ls "${path_to_definition_file%/${application}}")"
- return 1
- fi
-
- if [[ -z "${definition_file}" ]]; then
- naked_err 'No DEFINITION FILE was provided.'
- naked_err 'Use the -d (or --definition-file) command-line option to specify the name of the DEFINITION FILE.'
- naked_err 'Listing all DEFINITION FILEs to choose from ...'
- echo "ls ${path_to_definition_file}"
- echo "$(ls "${path_to_definition_file}")"
- return 1
- fi
-
- path_to_definition_file+="/${definition_file}"
-
- if [[ ! -f "${path_to_definition_file}" ]]; then
- naked_err "${path_to_definition_file} does not exist."
- naked_err 'Use the -d (or --definition-file) command-line option to specify the name of the DEFINITION FILE.'
- naked_err 'Listing all DEFINITION FILEs to choose from ...'
- echo "ls ${path_to_definition_file%/${definition_file}}"
- echo "$(ls "${path_to_definition_file%/${definition_file}}")"
- return 1
- fi
-
- naked_out "DEFINITION FILE exists ... ${path_to_definition_file}"
-
- naked_out 'Check if IMAGE exists ...'
-
- if [[ -z "${image}" ]]; then
- naked_warn 'WARNING :: No IMAGE name was provided.'
- naked_warn 'Use the -i (or --image) command-line option to specify the name of the IMAGE.'
- image="$(echo "${definition_file}" | sed 's/.def//')"
- if [[ "${writable}" = 'true' ]]; then
- image+='.img'
- else
- image+='.simg'
- fi
- naked_out "Setting IMAGE name ... ${image}"
- fi
-
- path_to_image+="/${system}"
- path_to_image+="/${application}"
- path_to_image+="/${image}"
-
- if [[ ! -f "${path_to_image}" ]]; then
- naked_out "${path_to_image} does not exist yet ..."
- naked_out "Prepare to build a new Singularity IMAGE from ${path_to_definition_file} ..."
- naked_out 'Make parent directories to accomodate new IMAGE if they do not exist already ...'
- echo "mkdir -p $(dirname ${path_to_image})"
- mkdir -p "$(dirname "${path_to_image}")"
- if [[ "${writable}" = 'true' ]]; then
- naked_out "Build new $(basename "${path_to_image}") as a writable ext3 Singularity IMAGE ..."
- if (( "${image_size}" <= 0 )); then
- naked_warn 'WARNING :: IMAGE_SIZE is less than or equal to zero.'
- naked_warn 'IMAGE_SIZE is the size of the IMAGE in integer-valued units of MiB.'
- naked_warn 'Attempting to set IMAGE SIZE from DEFINITION FILE ...'
- grep 'SINGULARITY_IMAGE_SIZE' "${path_to_definition_file}"
- if [[ "${?}" -ne 0 ]]; then
- naked_err 'SINGULARITY_IMAGE_SIZE not found in DEFINITION FILE ... '
- return 1
- else
- naked_out 'Setting IMAGE_SIZE equal to SINGULARITY_IMAGE_SIZE ... '
- image_size="$(grep 'SINGULARITY_IMAGE_SIZE' "${path_to_definition_file}" | \
- sed s'/ SINGULARITY_IMAGE_SIZE //')"
- fi
- fi
- naked_out 'Creating writable ext3 Singularity IMAGE now ...'
- echo "singularity image.create --size ${image_size} ${path_to_image}"
- singularity image.create --size "${image_size}" "${path_to_image}"
- naked_out 'IMAGE created ...'
- naked_out 'Starting build now ...'
- echo "sudo singularity build --writable ${path_to_image} ${path_to_definition_file}"
- sudo singularity build --writable "${path_to_image}" "${path_to_definition_file}"
- else
- naked_out "Build $(basename "${path_to_image}") as a read-only squashfs Singularity IMAGE ..."
- naked_out 'Starting build now ...'
- echo "sudo singularity build ${path_to_image} ${path_to_definition_file}"
- sudo singularity build "${path_to_image}" "${path_to_definition_file}"
- fi
- else
- naked_err "${path_to_image} already exists ..."
- naked_err 'Cannot overwrite existing IMAGE ...'
- return 1
- fi
-
- naked_out 'Build complete.'
-
- return 0
-
-}
-
-
-naked_inspect() {
-
- echo 'run singularity inspect command ... '
-
-}
-
-
-naked_install() {
-
- local operating_system='ubuntu'
- local prefix='/usr/local'
- local version='2.6.1'
-
- naked_out "Read in all command-line options of the 'install' command ..."
-
- while (( "${#}" > 0 )); do
- naked_out "Read in command-line option '${1}' with input value '${2}' ... "
- case "${1}" in
- -o | --os )
- operating_system="${2,,}"
- shift 2
- ;;
- -p | --prefix )
- prefix="${2}"
- shift 2
- ;;
- -v | --version )
- version="${2}"
- shift 2
- ;;
- *)
- naked_err "Command-line option ${1} not recognized or not supported."
- return 1
- esac
- done
-
- naked_out "All command-line options for 'install' command have been read ... "
-
- naked_out 'Checking if Singularity is already installed on this system ...'
- echo 'singularity --version'
- singularity --version
- if [[ "${?}" -eq 0 ]]; then
- naked_err 'Singularity is already installed on this system!'
- naked_err 'Please uninstall the existing version of Singularity prior to installing a new version.'
- return 1
- fi
-
- naked_out 'Singularity is not yet installed on this system ...'
-
- if [[ "${operating_system}" = 'centos' ]]; then
-
- naked_out 'Running update ...'
- echo 'sudo yum -y update'
- sudo yum -y update
-
- naked_out 'Installing Singularity dependencies ...'
- echo "sudo yum groupinstall -y 'Development Tools'"
- sudo yum groupinstall -y 'Development Tools'
- echo 'sudo yum install -y libarchive-devel'
- sudo yum install -y libarchive-devel
- echo 'sudo yum install -y epel-release'
- sudo yum install -y epel-release
- echo 'sudo yum install -y debootstrap'
- sudo yum install -y debootstrap
- echo 'sudo yum install -y debian-keyring'
- sudo yum install -y debian-keyring
-
- elif [[ "${operating_system}" = 'ubuntu' ]]; then
-
- naked_out 'Running update ...'
- echo 'sudo apt-get -y update'
- sudo apt-get -y update
-
- naked_out 'Installing Singularity dependencies ...'
- echo 'sudo apt-get -y install python'
- sudo apt-get -y install python
- echo 'sudo apt-get -y install dh-autoreconf'
- sudo apt-get -y install dh-autoreconf
- echo 'sudo apt-get -y install build-essential'
- sudo apt-get -y install build-essential
- echo 'sudo apt-get -y install libarchive-dev'
- sudo apt-get -y install libarchive-dev
- echo 'sudo apt-get -y install debootstrap'
- sudo apt-get -y install debootstrap
- echo 'sudo apt-get -y install squashfs-tools'
- sudo apt-get -y install squashfs-tools
-
- else
-
- naked_err 'Operating system not recognized or not supported.'
- return 1
-
- fi
-
- naked_out 'Downloading Singularity source code...'
- echo "wget https://github.com/singularityware/singularity/releases/download/${version}/singularity-${version}.tar.gz"
- wget "https://github.com/singularityware/singularity/releases/download/${version}/singularity-${version}.tar.gz"
-
- naked_out 'Extracting Singularity source code...'
- echo "tar -xzvf singularity-${version}.tar.gz"
- tar -xzvf singularity-${version}.tar.gz
-
- naked_out 'Configuring Singularity ...'
- echo "cd singularity-${version}"
- cd "singularity-${version}"
- echo "./configure --prefix=${prefix}"
- ./configure --prefix="${prefix}"
-
- naked_out 'Compiling Singularity ...'
- echo 'make'
- make
-
- naked_out 'Installing Singularity ...'
- echo 'sudo make install'
- sudo make install
-
- naked_out 'Checking if Singularity was installed successully ...'
- singularity --version
- if [[ "${?}" -ne 0 ]]; then
- naked_err 'Singularity was NOT installed successfully ...'
- return 1
- fi
-
- naked_out 'Singularity was installed successfully!'
-
- naked_out 'Cleaning up ...'
- cd ../
- rm -rf "singularity-${version}.tar.gz"
- rm -rf "singularity-${version}"
-
- return 0
-
-}
-
-
-naked_shell() {
-
- echo 'run singularity shell command ... '
-
-}
-
-
-naked_uninstall() {
-
- local prefix='/usr/local'
-
- naked_out "Read in all command-line options of the 'uninstall' command ..."
-
- while (( "${#}" > 0 )); do
- naked_out "Read in command-line option '${1}' with input value '${2}' ... "
- case "${1}" in
- -p | --prefix )
- prefix="${2}"
- shift 2
- ;;
- *)
- naked_err "Command-line option ${1} not recognized or not supported."
- return 1
- esac
- done
-
- naked_out "All command-line options for 'uninstall' command have been read ... "
-
- naked_out 'Checking if Singularity is installed ...'
- echo 'singularity --version'
- singularity --version
- if [[ "${?}" -ne 0 ]]; then
- naked_err 'Singularity is not installed on this system.'
- return 1
- fi
-
- naked_out 'Uninstalling Singularity ...'
- sudo rm -rf "${prefix}/libexec/singularity"
- sudo rm -rf "${prefix}/etc/singularity"
- sudo rm -rf "${prefix}/include/singularity"
- sudo rm -rf "${prefix}/lib/singularity"
- sudo rm -rf "${prefix}/var/lib/singularity"
- sudo rm "${prefix}/bin/singularity"
- sudo rm "${prefix}/bin/run-singularity"
- sudo rm "${prefix}/etc/bash_completion.d/singularity"
- sudo rm "${prefix}/man/man1/singularity.1"
-
- naked_out 'Checking if Singularity was uninstalled successfully ...'
- which singularity
- if [[ "${?}" -eq 0 ]]; then
- naked_err 'Singularity was NOT uninstalled!'
- return 1
- fi
-
- naked_out 'Singularity was uninstalled successfully!'
-
- return 0
-
-}
-
-
-naked_upload() {
-
- echo 'Upload image to users HOME directory on target system ...'
-
-}
-
-
-naked_verify() {
-
- echo 'Verify checksums of definition file and image match ... '
-
-}
-
-
-main() {
-
- local naked_command=''
- local naked_dir="${PWD}"
-
- if (( "${#}" > 0 )); then # at least one command-line arguments was
- # provided. The first argument is expected to be main command issued
- # by the user. Read in that command and then determine if it is a
- # valid command.
-
- naked_command="${1}"
- shift 1
-
- if [[ "${naked_command}" = 'build' ]]; then
-
- naked_build "${@}"
- if [[ "${?}" -ne 0 ]]; then
- exit 1
- fi
-
- elif [[ "${naked_command}" = 'install' ]]; then
-
- naked_install "${@}"
- if [[ "${?}" -ne 0 ]]; then
- exit 1
- fi
-
- elif [[ "${naked_command}" = 'uninstall' ]]; then
-
- naked_uninstall "${@}"
- if [[ "${?}" -ne 0 ]]; then
- exit 1
- fi
-
- elif [[ "${naked_command}" = 'help' || \
- "${naked_command}" = '-h' || \
- "${naked_command}" = '--help' ]]; then # return help.
-
- echo "USAGE: naked-singularity.sh <command> [options] {values}"
- echo ""
- echo "Finish writing help later ... ."
-
- else
-
- naked_err 'Command not recognized or not supported.'
- exit 1
-
- fi
-
- else
-
- naked_err 'No command-line arguments were provided.'
- exit 1
-
- fi
-
- exit 0
-
-}
-
-
-main "${@}"
-
-# ======================================================================
diff --git a/archive/tscc/keras/keras-tensorflow-cpu.def b/archive/tscc/keras/keras-tensorflow-cpu.def
deleted file mode 100644
index 613a2cc9904dc294802bd62cfe53088b25f2ad7b..0000000000000000000000000000000000000000
--- a/archive/tscc/keras/keras-tensorflow-cpu.def
+++ /dev/null
@@ -1,267 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + tensorflow
- APPLICATION_VERSION 2.2.0 + 1.8
- APPLICATION_URL https://www.tensorflow.org
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180910
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
- dpkg -i bazel_0.13.1-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- # Download TensorFlow source
- cd /opt
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout r1.8
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.8.0-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
- apt-get -y install python3-numpy
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.8.0-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install Keras dependencies for python(2) and python3
- apt-get -y install python-yaml
- apt-get -y install python3-yaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
- tar -xzvf 2.2.0.tar.gz
- cd /opt/keras-2.2.0
- python setup.py install
- python3 setup.py install
-
- # Set container environment variables
- cd /.singularity.d/env
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/tscc/keras/keras-tensorflow-gpu.def b/archive/tscc/keras/keras-tensorflow-gpu.def
deleted file mode 100644
index bd01777b9936ec5f81b69c0d455d7e3772b52c95..0000000000000000000000000000000000000000
--- a/archive/tscc/keras/keras-tensorflow-gpu.def
+++ /dev/null
@@ -1,461 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME keras + tensorflow
- APPLICATION_VERSION 2.2.0 + 1.7.1
- APPLICATION_URL https://keras.io/
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180910
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-384-dev_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_384.66-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.2.12-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.2.12-1+cuda8.0_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-384-dev_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_384.66-0ubuntu1_amd64.deb
- dpkg -i libcuda1-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-384_384.66-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_384.66-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_384.66-1_amd64.deb
-
- dpkg -i cuda-license-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-misc-headers-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-core-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-driver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-command-line-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvml-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-samples-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-documentation-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-visual-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-toolkit-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
-
- dpkg -i libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb
- dpkg -i libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb
-
- dpkg -i libnccl2_2.2.12-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_2.2.12-1+cuda8.0_amd64.deb
-
- # Fixing some TensorFlow and libnccl*.deb path issues ...
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-8.0/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.2.12 /usr/local/cuda-8.0/lib64/libnccl.so.2.2.12
- ln -s /usr/local/cuda-8.0/lib64/libnccl.so.2.2.12 /usr/local/cuda-8.0/lib64/libnccl.so.2
- ln -s /usr/local/cuda-8.0/lib64/libnccl.so.2 /usr/local/cuda-8.0/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-8.0/include/nccl.h
- ln -s /usr/local/cuda-8.0/lib64 /usr/local/cuda-8.0/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-8.0/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
- dpkg -i bazel_0.13.1-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- cd /opt
-
- # Download TensorFlow source
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout r1.7
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python.exp
- echo 'send "8.0\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7.0\]: "' >> install-tensorflow-python.exp
- echo 'send "7.1.4.18\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where cuDNN 7.1.4.18 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> install-tensorflow-python.exp
- echo 'send "3.0,3.5,3.7,5.2,6.1\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # See https://github.com/tensorflow/tensorflow/issues/17801
- ln -s /usr/local/cuda-8.0/nvvm/libdevice/libdevice.compute_50.10.bc /usr/local/cuda-8.0/nvvm/libdevice/libdevice.10.bc
-
- # See https://github.com/tensorflow/tensorflow/issues/19203
- # https://github.com/ghostplant/tensorflow-cuda8-optimized/blob/master/Dockerfile.tf18-py35-cuda8-cudnn6021
- sed -i 's/^#if TF_HAS_.*$/#if !defined(__NVCC__)/g' tensorflow/core/platform/macros.h
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.7.1-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
- apt-get -y install python3-numpy
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python3.exp
- echo 'send "8.0\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7.0\]: "' >> install-tensorflow-python3.exp
- echo 'send "7.1.4.18\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where cuDNN 7.1.4.18 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python3.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> install-tensorflow-python3.exp
- echo 'send "3.0,3.5,3.7,5.2,6.1\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.7.1-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Install Keras dependencies for python(2) and python3
- apt-get -y install python-yaml
- apt-get -y install python3-yaml
-
- cd /opt
-
- # Download, build, and install Keras
- wget https://github.com/keras-team/keras/archive/2.2.0.tar.gz
- tar -xzvf 2.2.0.tar.gz
- cd /opt/keras-2.2.0
- python setup.py install
- python3 setup.py install
-
- # Set container environment variables
- cd /.singularity.d/env
- echo 'export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"' >> 90-environment.sh
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/tscc/pytorch/pytorch-gpu.def b/archive/tscc/pytorch/pytorch-gpu.def
deleted file mode 100644
index 53095e36686c840544899a8c358c040f8ecf0729..0000000000000000000000000000000000000000
--- a/archive/tscc/pytorch/pytorch-gpu.def
+++ /dev/null
@@ -1,461 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME pytorch
- APPLICATION_VERSION 1.1.0
- APPLICATION_URL http://pytorch.org/
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190927
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.4.8-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.4.8-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.4.8-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.4.8-1+cuda9.2_amd64.deb
-
- # Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-9.2/lib64/libcudnn_static.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-9.2/lib64/libcudnn_static_v7.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7 /usr/local/cuda-9.2/lib64/libcudnn.so
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-9.2/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2 /usr/local/cuda-9.2/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-9.2/include/nccl.h
- ln -s /usr/local/cuda-9.2/lib64 /usr/local/cuda-9.2/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-9.2/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install CUDA-aware OpenMPI
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Install PyTorch dependencies for python(2)
- export PATH="/opt/miniconda2/bin:${PATH}"
- export CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
- conda install -y numpy
- conda install -y ninja
- conda install -y pyyaml
- conda install -y mkl
- conda install -y mkl-include
- conda install -y setuptools
- conda install -y cmake
- conda install -y cffi
- conda install -y typing
- conda install -y mkldnn -c mingfeima
-
- # Add LAPACK support for the GPU
- conda install -y magma-cuda92 -c pytorch
-
- # Install common python packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y jupyter
- conda install -y sympy
- conda install -y nose
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- cd /opt
-
- # Download, build, and install PyTorch for python(2)
- export CC='mpicc'
- export CXX='mpicxx'
- export CFLAGS='-march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge'
- export USE_OPENMP=1
- export USE_NNPACK=1
- export USE_QNNPACK=1
- export USE_MKLDNN=1
- export USE_DISTRIBUTED=1
- export USE_GLOO=1
- export USE_GLOO_IBVERBS=1
- export USE_IBVERBS=1
- export USE_MPI=1
- export USE_C10D_MPI=1
- export USE_CUDA=1
- export USE_CUDNN=1
- export USE_NCCL=1
- export USE_OPENCV=1
- export USE_FBGEMM=0
- export TORCH_CUDA_ARCH_LIST='3.0;3.5;3.7;5.2;6.1'
- git clone --recursive https://github.com/pytorch/pytorch
- cd /opt/pytorch
- git checkout v1.1.0
- git submodule sync
- git submodule update --init
- python setup.py install
-
- # Download and install PyTorch Vision package for python(2)
- git clone https://github.com/pytorch/vision.git
- cd /opt/pytorch/vision
- git checkout v0.3.0
- python setup.py install
-
- # Install PyTorch dependencies for python3
- export PATH="/opt/miniconda3/bin:${PATH}"
- xport CMAKE_PREFIX_PATH=${CONDA_PREFIX:-"$(dirname $(which conda))/../"}
- conda install -y numpy
- conda install -y ninja
- conda install -y pyyaml
- conda install -y mkl
- conda install -y mkl-include
- conda install -y setuptools
- conda install -y cmake
- conda install -y cffi
- conda install -y typing
- conda install -y mkldnn -c mingfeima
-
- # Add LAPACK support for the GPU
- conda install -y magma-cuda92 -c pytorch
-
- # Install common python3 packages for data science and machine
- # learning applications
- conda install -y pandas
- conda install -y matplotlib
- conda install -y ipython
- conda install -y jupyter
- conda install -y sympy
- conda install -y nose
- conda install -y scikit-learn
- conda install -y scikit-image
- conda install -y nltk
- conda install -y statsmodels
- conda install -y opencv
-
- # Download, build, and install PyTorch for python3
- cd /opt/pytorch
- python setup.py clean --all
- python setup.py install
-
- # Download and install PyTorch Vision package for python3
- cd /opt/pytorch/vision
- python setup.py clean --all
- python setup.py install
-
- # Download the PyTorch examples repository
- cd /opt/pytorch
- git clone https://github.com/pytorch/examples.git
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " ______ ____ _____ _____ "
- echo " /_ __// __// ___// ___/ "
- echo " / / _\ \ / /__ / /__ "
- echo " /_/ /___/ \___/ \___/ "
- echo " "
-
-%test
diff --git a/archive/tscc/tensorflow/tensorflow-cpu.def b/archive/tscc/tensorflow/tensorflow-cpu.def
deleted file mode 100644
index bdce21c7541d7b23b031201fe054d95c62a883bf..0000000000000000000000000000000000000000
--- a/archive/tscc/tensorflow/tensorflow-cpu.def
+++ /dev/null
@@ -1,254 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME tensorflow
- APPLICATION_VERSION 1.8
- APPLICATION_URL https://www.tensorflow.org
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 16384
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180726
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
- dpkg -i bazel_0.13.1-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- # Download TensorFlow source
- cd /opt
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout r1.8
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.8.0-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
- apt-get -y install python3-numpy
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to download a fresh release of clang? (Experimental) \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- bazel build --config=opt //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.8.0-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Set container environment variables
- cd /.singularity.d/env
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/tscc/tensorflow/tensorflow-gpu.def b/archive/tscc/tensorflow/tensorflow-gpu.def
deleted file mode 100644
index 831ce97aac098b18a854972433c778d61ad1b033..0000000000000000000000000000000000000000
--- a/archive/tscc/tensorflow/tensorflow-gpu.def
+++ /dev/null
@@ -1,448 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME tensorflow
- APPLICATION_VERSION 1.7.1
- APPLICATION_URL https://www.tensorflow.org
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 32768
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20180726
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-384-dev_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-384_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_384.66-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_384.66-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.2.12-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.2.12-1+cuda8.0_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-384-dev_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_384.66-0ubuntu1_amd64.deb
- dpkg -i libcuda1-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-384_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-384_384.66-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_384.66-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_384.66-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_384.66-1_amd64.deb
-
- dpkg -i cuda-license-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-misc-headers-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-core-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-driver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-command-line-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvml-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-samples-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-documentation-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-visual-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-toolkit-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
-
- dpkg -i libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb
- dpkg -i libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb
-
- dpkg -i libnccl2_2.2.12-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_2.2.12-1+cuda8.0_amd64.deb
-
- # Fixing some TensorFlow and libnccl*.deb path issues ...
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-8.0/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.2.12 /usr/local/cuda-8.0/lib64/libnccl.so.2.2.12
- ln -s /usr/local/cuda-8.0/lib64/libnccl.so.2.2.12 /usr/local/cuda-8.0/lib64/libnccl.so.2
- ln -s /usr/local/cuda-8.0/lib64/libnccl.so.2 /usr/local/cuda-8.0/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-8.0/include/nccl.h
- ln -s /usr/local/cuda-8.0/lib64 /usr/local/cuda-8.0/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-8.0/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install Bazel from Debian Package
- apt-get -y install openjdk-8-jdk
- apt-get -y install zlib1g-dev
- wget https://github.com/bazelbuild/bazel/releases/download/0.13.1/bazel_0.13.1-linux-x86_64.deb
- dpkg -i bazel_0.13.1-linux-x86_64.deb
-
- # Install TensorFlow python(2) dependencies
- apt-get -y install python
- apt-get -y install python-dev
- apt-get -y install python-pip
- apt-get -y install python-wheel
- apt-get -y install python-enum34
- apt-get -y install python-mock
- apt-get -y install python-numpy
-
- cd /opt
-
- # Download TensorFlow source
- git clone https://github.com/tensorflow/tensorflow
- cd tensorflow
- git checkout r1.7
-
- # Build and install TensorFlow for python(2)
- echo '#!/usr/bin/expect -f' > install-tensorflow-python.exp
- echo 'spawn ./configure' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/python\r"' >> install-tensorflow-python.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python2.7/dist-packages\]\r"' >> install-tensorflow-python.exp
- echo 'send "/usr/local/lib/python2.7/dist-packages\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "Y\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python.exp
- echo 'send "8.0\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7.0\]: "' >> install-tensorflow-python.exp
- echo 'send "7.1.4.18\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify the location where cuDNN 7.1.4.18 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> install-tensorflow-python.exp
- echo 'send "3.0,3.5,3.7,5.2,6.1\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python.exp
- echo 'send "N\r"' >> install-tensorflow-python.exp
- echo 'expect "> "' >> install-tensorflow-python.exp
-
- chmod +x install-tensorflow-python.exp
- ./install-tensorflow-python.exp
-
- # See https://github.com/tensorflow/tensorflow/issues/17801
- ln -s /usr/local/cuda-8.0/nvvm/libdevice/libdevice.compute_50.10.bc /usr/local/cuda-8.0/nvvm/libdevice/libdevice.10.bc
-
- # See https://github.com/tensorflow/tensorflow/issues/19203
- # https://github.com/ghostplant/tensorflow-cuda8-optimized/blob/master/Dockerfile.tf18-py35-cuda8-cudnn6021
- sed -i 's/^#if TF_HAS_.*$/#if !defined(__NVCC__)/g' tensorflow/core/platform/macros.h
-
- # Clear /home/root/.cache prior to bazel build. Otherwise, previous builds may cause some conflicts. See 'dangling symbolic links' at https://github.com/tensorflow/tensorflow/issues/13928
- rm -rf /home/root/.cache
-
- bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip install tensorflow_pkg/tensorflow-1.7.1-cp27-cp27mu-linux_x86_64.whl
-
- # Install common python packages for data science and machine learning applications
- apt-get -y install python-scipy
- apt-get -y install python-pandas
- apt-get -y install python-matplotlib
- apt-get -y install ipython
- apt-get -y install ipython-notebook
- apt-get -y install python-sympy
- apt-get -y install python-nose
- apt-get -y install python-sklearn
- apt-get -y install python-mlpy
- apt-get -y install python-nltk
- apt-get -y install python-statsmodels
- apt-get -y install libopencv-dev
- apt-get -y install python-opencv
-
- # Install common python packages for the biological and biomedical sciences
- apt-get -y install python-biopython
- apt-get -y install python-biopython-sql
-
- # Install other common python packages
- apt-get -y install python-h5py
-
- # Install TensorFlow python3 dependencies
- apt-get -y install python3
- apt-get -y install python3-dev
- apt-get -y install python3-pip
- apt-get -y install python3-wheel
- apt-get -y install python3-mock
- apt-get -y install python3-numpy
-
- # Build and install TensorFlow for python3
- echo '#!/usr/bin/expect -f' > install-tensorflow-python3.exp
- echo 'spawn ./configure' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location of python. \[Default is /usr/bin/python\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/python3\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please input the desired Python library path to use. Default is \[/usr/local/lib/python3.5/dist-packages\]\r"' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/lib/python3.5/dist-packages\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with jemalloc as malloc support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Google Cloud Platform support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Hadoop File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Amazon S3 File System support? \[Y/n\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with Apache Kafka Platform support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with XLA JIT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with GDR support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with VERBS support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with OpenCL SYCL support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with CUDA support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "Y\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the CUDA SDK version you want to use, e.g. 7.0. \[Leave empty to default to CUDA 9.0\]: "' >> install-tensorflow-python3.exp
- echo 'send "8.0\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where CUDA 8.0 toolkit is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/local/cuda\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the cuDNN version you want to use. \[Leave empty to default to cuDNN 7.0\]: "' >> install-tensorflow-python3.exp
- echo 'send "7.1.4.18\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify the location where cuDNN 7.1.4.18 library is installed. Refer to README.md for more details. \[Default is /usr/local/cuda\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/lib/x86_64-linux-gnu\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with TensorRT support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify a list of comma-separated Cuda compute capabilities you want to build with.\r"' >> install-tensorflow-python3.exp
- echo 'expect "You can find the compute capability of your device at: https://developer.nvidia.com/cuda-gpus.\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please note that each additional compute capability significantly increases your build time and binary size. \[Default is: 3.5,5.2\]"' >> install-tensorflow-python3.exp
- echo 'send "3.0,3.5,3.7,5.2,6.1\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you want to use clang as CUDA compiler? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify which gcc should be used by nvcc as the host compiler. \[Default is /usr/bin/gcc\]: "' >> install-tensorflow-python3.exp
- echo 'send "/usr/bin/gcc\r"' >> install-tensorflow-python3.exp
- echo 'expect "Do you wish to build TensorFlow with MPI support? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "Please specify optimization flags to use during compilation when bazel option \"--config=opt\" is specified \[Default is -march=native\]: "' >> install-tensorflow-python3.exp
- echo 'send " -march=sandybridge -mmmx -mno-3dnow -msse -msse2 -msse3 -mssse3 -mno-sse4a -mcx16 -msahf -mno-movbe -maes -mno-sha -mpclmul -mpopcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-bmi2 -mno-tbm -mavx -mno-avx2 -msse4.2 -msse4.1 -mno-lzcnt -mno-rtm -mno-hle -mno-rdrnd -mno-f16c -mno-fsgsbase -mno-rdseed -mno-prfchw -mno-adx -mfxsr -mxsave -mxsaveopt -mno-avx512f -mno-avx512er -mno-avx512cd -mno-avx512pf -mno-prefetchwt1 -mtune=sandybridge\r"' >> install-tensorflow-python3.exp
- echo 'expect "Would you like to interactively configure ./WORKSPACE for Android builds? \[y/N\]: "' >> install-tensorflow-python3.exp
- echo 'send "N\r"' >> install-tensorflow-python3.exp
- echo 'expect "> "' >> install-tensorflow-python3.exp
-
- chmod +x install-tensorflow-python3.exp
- ./install-tensorflow-python3.exp
-
- bazel build --config=opt --config=cuda //tensorflow/tools/pip_package:build_pip_package
- bazel-bin/tensorflow/tools/pip_package/build_pip_package tensorflow_pkg
-
- pip3 install tensorflow_pkg/tensorflow-1.7.1-cp35-cp35m-linux_x86_64.whl
-
- # Install common python3 packages for data science and machine learning applications
- apt-get -y install python3-scipy
- apt-get -y install python3-pandas
- apt-get -y install python3-matplotlib
- apt-get -y install ipython3
- apt-get -y install ipython3-notebook
- apt-get -y install python3-sympy
- apt-get -y install python3-nose
- apt-get -y install python3-sklearn
- apt-get -y install python3-nltk
-
- # Install common python3 packages for the biological and biomedical sciences
- apt-get -y install python3-biopython
- apt-get -y install python3-biopython-sql
-
- # Install other common python3 packages
- apt-get -y install python3-h5py
-
- # Set container environment variables
- cd /.singularity.d/env
- echo 'export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"' >> 90-environment.sh
- echo 'export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"' >> 90-environment.sh
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
diff --git a/archive/tscc/ubuntu/ubuntu-cuda-openmpi.def b/archive/tscc/ubuntu/ubuntu-cuda-openmpi.def
deleted file mode 100644
index 322e2bf54a50ad770cf7dda7117d6c1f109a8233..0000000000000000000000000000000000000000
--- a/archive/tscc/ubuntu/ubuntu-cuda-openmpi.def
+++ /dev/null
@@ -1,350 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda + openmpi
- APPLICATION_VERSION 16.04 + 9.2.88 + 1.8.4
- APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190924
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install gfortran
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /cvmfs /oasis /projects /scratch
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvcc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cuobjdump-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprune-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-compiler-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvdisasm-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gdb-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvprof-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-memcheck-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cupti-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvtx-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nsight-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvvp-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-tools-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-dev-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-libraries-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-9-2_9.2.88-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-9-2_9.2.88-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.4.8-1+cuda9.2_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.4.8-1+cuda9.2_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-misc-headers-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvcc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cuobjdump-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprune-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-compiler-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-core-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-driver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cudart-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvdisasm-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gdb-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvprof-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-memcheck-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cupti-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-gpu-library-advisor-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvtx-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-command-line-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvml-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusolver-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cublas-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cufft-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-curand-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-cusparse-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-npp-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-samples-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-documentation-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nsight-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-nvvp-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-visual-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-tools-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-dev-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-toolkit-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-libraries-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-runtime-9-2_9.2.88-1_amd64.deb
- dpkg -i cuda-demo-suite-9-2_9.2.88-1_amd64.deb
-
- dpkg -i libcudnn7_7.6.2.24-1+cuda9.2_amd64.deb
- dpkg -i libcudnn7-dev_7.6.2.24-1+cuda9.2_amd64.deb
-
- dpkg -i libnccl2_2.4.8-1+cuda9.2_amd64.deb
- dpkg -i libnccl-dev_2.4.8-1+cuda9.2_amd64.deb
-
- # Fixing some path-related issues associated with deb-based install of libcudnn and libnccl ...
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static.a /usr/local/cuda-9.2/lib64/libcudnn_static.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn_static_v7.a /usr/local/cuda-9.2/lib64/libcudnn_static_v7.a
- mv /usr/lib/x86_64-linux-gnu/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7.6.2 /usr/local/cuda-9.2/lib64/libcudnn.so.7
- ln -s /usr/local/cuda-9.2/lib64/libcudnn.so.7 /usr/local/cuda-9.2/lib64/libcudnn.so
- mv /usr/lib/x86_64-linux-gnu/libnccl_static.a /usr/local/cuda-9.2/lib64/libnccl_static.a
- mv /usr/lib/x86_64-linux-gnu/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2.4.8 /usr/local/cuda-9.2/lib64/libnccl.so.2
- ln -s /usr/local/cuda-9.2/lib64/libnccl.so.2 /usr/local/cuda-9.2/lib64/libnccl.so
- mv /usr/include/nccl.h /usr/local/cuda-9.2/include/nccl.h
- ln -s /usr/local/cuda-9.2/lib64 /usr/local/cuda-9.2/lib
- mv /usr/share/doc/libnccl2/NCCL-SLA.txt.gz /usr/local/cuda-9.2/NCCL-SLA.txt
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Install basic drivers for user space access to Ethernet, RDMA,
- # and Infiniband. See https://community.mellanox.com/docs/DOC-2431
- apt-get -y install dkms
- apt-get -y install infiniband-diags
- apt-get -y install libibverbs-dev
- apt-get -y install ibacm
- apt-get -y install librdmacm-dev
- apt-get -y install libmlx4-dev
- apt-get -y install libmlx5-dev
- apt-get -y install mstflint
- apt-get -y install libibcm-dev
- apt-get -y install libibmad-dev
- apt-get -y install libibumad-dev
- apt-get -y install opensm
- apt-get -y install srptools
-
- # Install additional tools
- apt-get -y install ibutils
- apt-get -y install ibverbs-utils
- apt-get -y install rdmacm-utils
- apt-get -y install perftest
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install libnl
- apt-get -y install libnl-3-200
- apt-get -y install libnl-route-3-200
- apt-get -y install libnl-route-3-dev
- apt-get -y install libnl-utils
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- # Download, build, and install CUDA-aware OpenMPI
- wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz
- tar -xzvf openmpi-1.8.4.tar.gz
- cd openmpi-1.8.4
- ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
- make all install
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
- export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " ______ ____ _____ _____ "
- echo " /_ __// __// ___// ___/ "
- echo " / / _\ \ / /__ / /__ "
- echo " /_/ /___/ \___/ \___/ "
- echo " "
-
-%test
diff --git a/archive/tscc/ubuntu/ubuntu-cuda.def b/archive/tscc/ubuntu/ubuntu-cuda.def
deleted file mode 100644
index 5f6ee39ff1d6b2e33320cca48fee4bffbaf8065a..0000000000000000000000000000000000000000
--- a/archive/tscc/ubuntu/ubuntu-cuda.def
+++ /dev/null
@@ -1,256 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME ubuntu + cuda
- APPLICATION_VERSION 16.04 + 8.0.44
- APPLICATION_URL https://developer.nvidia.com/cuda-zone
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 8192
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190920
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /oasis /projects
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Location of NVIDIA repositories
- declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
- declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
- declare -r ML_REPO_URL="${NVIDIA_ROOT_URL}/machine-learning/repos/ubuntu1604/x86_64/"
-
- # Install NVIDIA package dependencies
- apt-get -y install x11-common
- apt-get -y install xserver-xorg-core
- apt-get -y install xserver-xorg-legacy
- apt-get -y install cmake
- apt-get -y install make
- apt-get -y install dkms
- apt-get -y install linux-libc-dev
- apt-get -y install libc6-dev
- apt-get -y install lib32gcc1
- apt-get -y install libc6-i386
- apt-get -y install libgl1
- apt-get -y install libwayland-client0
- apt-get -y install libwayland-server0
- apt-get -y install pkg-config
- apt-get -y install screen-resolution-extra
- apt-get -y install libvdpau1
- apt-get -y install libatk1.0-0
- apt-get -y install libcairo-gobject2
- apt-get -y install libcairo2
- apt-get -y install libfontconfig1
- apt-get -y install libgdk-pixbuf2.0-0
- apt-get -y install libgtk-3-0
- apt-get -y install libgtk2.0-0
- apt-get -y install libjansson4
- apt-get -y install freeglut3-dev
- apt-get -y install libx11-dev
- apt-get -y install libxmu-dev
- apt-get -y install libxi-dev
- apt-get -y install libglu1-mesa
- apt-get -y install libglu1-mesa-dev
- apt-get -y install default-jre
-
- # Download NVIDIA drivers, libraries, and packages
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-396-dev_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-modprobe_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libcuda1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/libxnvctrl0_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/nvidia-settings_396.26-0ubuntu1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-drivers_396.26-1_amd64.deb"
-
- wget --wait=10 "${CUDA_REPO_URL}/cuda-license-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-misc-headers-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-core-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-driver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cudart-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-command-line-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvml-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cublas-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cufft-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-curand-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-npp-dev-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-samples-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-documentation-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-visual-tools-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-toolkit-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-runtime-8-0_8.0.44-1_amd64.deb"
- wget --wait=10 "${CUDA_REPO_URL}/cuda-demo-suite-8-0_8.0.44-1_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb"
-
- wget --wait=10 "${ML_REPO_URL}/libnccl2_2.2.12-1+cuda8.0_amd64.deb"
- wget --wait=10 "${ML_REPO_URL}/libnccl-dev_2.2.12-1+cuda8.0_amd64.deb"
-
- # Fix for "update-alternatives: error: error creating symbolic link '/usr/lib/nvidia/alternate-install-present.dpkg-tmp': No such file or directory"
- mkdir -p /usr/lib/nvidia
-
- # Install NVIDIA drivers, libraries, and packages
- dpkg -i nvidia-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-396-dev_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-modprobe_396.26-0ubuntu1_amd64.deb
- dpkg -i libcuda1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-libopencl1-396_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-opencl-icd-396_396.26-0ubuntu1_amd64.deb
- dpkg -i libxnvctrl0_396.26-0ubuntu1_amd64.deb
- dpkg -i nvidia-settings_396.26-0ubuntu1_amd64.deb
- dpkg -i cuda-drivers_396.26-1_amd64.deb
-
- dpkg -i cuda-license-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-misc-headers-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-core-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-driver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cudart-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-command-line-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvrtc-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvml-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-nvgraph-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusolver-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cublas-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cufft-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-curand-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-cusparse-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-npp-dev-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-samples-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-documentation-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-visual-tools-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-toolkit-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-runtime-8-0_8.0.44-1_amd64.deb
- dpkg -i cuda-demo-suite-8-0_8.0.44-1_amd64.deb
-
- dpkg -i libcudnn7_7.1.4.18-1+cuda8.0_amd64.deb
- dpkg -i libcudnn7-dev_7.1.4.18-1+cuda8.0_amd64.deb
-
- dpkg -i libnccl2_2.2.12-1+cuda8.0_amd64.deb
- dpkg -i libnccl-dev_2.2.12-1+cuda8.0_amd64.deb
-
- # Set paths to CUDA binaries and libraries
- export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
- export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
- export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " ______ ____ _____ _____ "
- echo " /_ __// __// ___// ___/ "
- echo " / / _\ \ / /__ / /__ "
- echo " /_/ /___/ \___/ \___/ "
- echo " "
-
-%test
diff --git a/archive/tscc/ubuntu/ubuntu.def b/archive/tscc/ubuntu/ubuntu.def
deleted file mode 100644
index 19563df4753c4cbec08e632b05b8348b31fc7058..0000000000000000000000000000000000000000
--- a/archive/tscc/ubuntu/ubuntu.def
+++ /dev/null
@@ -1,109 +0,0 @@
-Bootstrap: debootstrap
-MirrorURL: http://us.archive.ubuntu.com/ubuntu
-OSVersion: xenial
-
-%labels
-
- APPLICATION_NAME ubuntu
- APPLICATION_VERSION 16.04
- APPLICATION_URL https://www.ubuntu.com/
-
- SYSTEM_NAME tscc
- SYSTEM_SINGULARITY_VERSION 2.5.2
- SYSTEM_URL https://www.sdsc.edu/support/user_guides/tscc.html
-
- SINGULARITY_IMAGE_SIZE 2048
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20190920
-
-%setup
-
-%environment
-
- # Set system locale
- export LC_ALL=C
-
- # Set default miniconda environment
- export PATH="/opt/miniconda3/bin:${PATH}"
-
-%post -c /bin/bash
-
- # Set system locale
- export LC_ALL=C
-
- # Install system metapackages
- apt-get -y install ubuntu-standard
- apt-get -y install ubuntu-server
-
- # Add repositories
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-updates restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-backports restricted"
-
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security main"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security universe"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
- add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
-
- # Upgrade all packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install common packages from 'main'
- apt-get -y install autoconf
- apt-get -y install automake
- apt-get -y install build-essential
- apt-get -y install cmake
- apt-get -y install libtool
- apt-get -y install pkg-config
- apt-get -y install wget
- apt-get -y install gfortran
- apt-get -y install zip
-
- # Install expect to automate responses for interactive build questions
- apt-get -y install expect
-
- # Make filesystem mount points
- mkdir /oasis /projects
-
- # Use /tmp to store temporary files within the container during the
- # bootstraping process
- cd /tmp
-
- # Install miniconda2
- wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
- chmod +x Miniconda2-latest-Linux-x86_64.sh
- ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/miniconda2
-
- # Install miniconda3
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
- chmod +x Miniconda3-latest-Linux-x86_64.sh
- ./Miniconda3-latest-Linux-x86_64.sh -b -p /opt/miniconda3
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
- echo " ______ ____ _____ _____ "
- echo " /_ __// __// ___// ___/ "
- echo " / / _\ \ / /__ / /__ "
- echo " /_/ /___/ \___/ \___/ "
- echo " "
-
-%test
diff --git a/naked-singularity.sh b/install-singularity.sh
similarity index 98%
rename from naked-singularity.sh
rename to install-singularity.sh
index 8c1ebb42f068a7c7aaf05ece0a1e94a18abcbf9a..cc26e9e696ec51bcbcc78ce3d669a0e87b99faf8 100755
--- a/naked-singularity.sh
+++ b/install-singularity.sh
@@ -2,7 +2,7 @@
# ======================================================================
# NAME
#
-# naked-singularity.sh
+# install-singularity.sh
#
# DESCRIPTION
#
@@ -14,7 +14,7 @@
#
# Install Singularity from source.
#
-# ./naked-singularity.sh install
+# ./install-singularity.sh install
#
# LAST UPDATED
#
@@ -378,7 +378,7 @@ naked::uninstall() {
naked::help() {
- log::output 'USAGE: naked-singularity.sh <command> [options] {value}'
+ log::output 'USAGE: install-singularity.sh <command> [options] {value}'
log::output ''
return 0