From 8bfa10a5bf30611f1dae1d3eca9ed45248871788 Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Wed, 27 Mar 2019 16:44:54 -0700
Subject: [PATCH] naked-singularity-v0.6.4 :: added new R.def file for Comet;
includes MySQL client libraries to support RMySQL package
---
README | 4 +-
definition-files/comet/R/R.def | 202 +++++++++++++++++++++++++++++++++
2 files changed, 204 insertions(+), 2 deletions(-)
create mode 100644 definition-files/comet/R/R.def
diff --git a/README b/README
index d53fb0f..2f308c3 100644
--- a/README
+++ b/README
@@ -46,8 +46,8 @@ AUTHOR
VERSION
- 0.6.3
+ 0.6.4
LAST UPDATED
- Friday, January 18th, 2019
+ Wednesday, March 27th, 2019
diff --git a/definition-files/comet/R/R.def b/definition-files/comet/R/R.def
new file mode 100644
index 0000000..a53d60c
--- /dev/null
+++ b/definition-files/comet/R/R.def
@@ -0,0 +1,202 @@
+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
--
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