From e41633e0f2f4e9c64d5fa0dcdad20ac483e6d9ed Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Fri, 2 Mar 2018 11:07:37 -0800
Subject: [PATCH] naked-singularity-v0.1.4 :: rewrote and added additional
comments to ubuntu.def and ubuntu-cuda.def; also modified PATH and
LD_LIBRARY_PATH within ubuntu-cuda.def via Singularity environment variables
to include CUDA binaries and libraries by default
---
.../us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def | 39 +++++++------------
.../us/ucsd/sdsc/comet/ubuntu/ubuntu.def | 20 +++++-----
2 files changed, 26 insertions(+), 33 deletions(-)
diff --git a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
index 5456bef..e6670e1 100644
--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- LAST_UPDATED 20180226
+ LAST_UPDATED 20180302
%setup
@@ -20,11 +20,14 @@ OSVersion: xenial
%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"
@@ -45,6 +48,7 @@ OSVersion: xenial
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
+ # Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade
# Install common packages from 'main'
@@ -62,19 +66,11 @@ OSVersion: xenial
# Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
- # Build and install additional software packages in /opt
- cd /opt
-
- # Install Miniconda -- a free minimal installer for conda
- #
- # Miniconda is a small, bootstrap version of Anaconda that includes
- # only conda, Python, the packages they depend on and a small number
- # of other useful packages, including pip, zlib and a few others.
- # Use the 'conda install' command to install more than 720
- # additional conda packages from the Anaconda repository.
- #
- # https://conda.io/docs/index.html
+ # Use /tmp to store temporary files within the container during the
+ # bootstraping process
+ cd /tmp
+ # Install miniconda2
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x Miniconda2-latest-Linux-x86_64.sh
@@ -104,9 +100,7 @@ OSVersion: xenial
chmod +x install-miniconda2.exp
./install-miniconda2.exp
- rm Miniconda2-latest-Linux-x86_64.sh
- rm install-miniconda2.exp
-
+ # Install miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
@@ -136,9 +130,6 @@ OSVersion: xenial
chmod +x install-miniconda3.exp
./install-miniconda3.exp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm install-miniconda3.exp
-
# Location of NVIDIA repositories
declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute'
declare -r CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
@@ -272,12 +263,15 @@ OSVersion: xenial
dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
- rm *.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
@@ -287,8 +281,5 @@ OSVersion: xenial
%test
- # Test if nvcc was installed properly
- 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/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
index c8ced8e..efbc3dc 100644
--- a/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
+++ b/definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
- LAST_UPDATED 20180226
+ LAST_UPDATED 20180302
%setup
@@ -20,11 +20,14 @@ OSVersion: xenial
%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"
@@ -45,6 +48,7 @@ OSVersion: xenial
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'
@@ -62,8 +66,9 @@ OSVersion: xenial
# Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch
- # Build and install additional software packages in /opt
- cd /opt
+ # 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
@@ -95,9 +100,6 @@ OSVersion: xenial
chmod +x install-miniconda2.exp
./install-miniconda2.exp
- rm Miniconda2-latest-Linux-x86_64.sh
- rm install-miniconda2.exp
-
# Install miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
@@ -128,11 +130,11 @@ OSVersion: xenial
chmod +x install-miniconda3.exp
./install-miniconda3.exp
- rm Miniconda3-latest-Linux-x86_64.sh
- rm install-miniconda3.exp
+ # Set container environment variables
+ cd /.singularity.d/env
# Update database for mlocate
- updatedb
+ updatedb
%files
--
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