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Commit e41633e0 authored by Marty Kandes's avatar Marty Kandes
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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
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definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu-cuda.def
+ 15
− 24
View file @ e41633e0
...@@ -12,7 +12,7 @@ OSVersion: xenial ...@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2 SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
LAST_UPDATED 20180226 LAST_UPDATED 20180302
%setup %setup
...@@ -20,11 +20,14 @@ OSVersion: xenial ...@@ -20,11 +20,14 @@ OSVersion: xenial
%post -c /bin/bash %post -c /bin/bash
# Set system locale
export LC_ALL=C export LC_ALL=C
# Install system metapackages
apt-get -y install ubuntu-standard apt-get -y install ubuntu-standard
apt-get -y install ubuntu-server apt-get -y install ubuntu-server
# Add repositories
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
...@@ -45,6 +48,7 @@ OSVersion: xenial ...@@ -45,6 +48,7 @@ OSVersion: xenial
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
# Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade apt-get -y update && apt-get -y upgrade
# Install common packages from 'main' # Install common packages from 'main'
...@@ -62,19 +66,11 @@ OSVersion: xenial ...@@ -62,19 +66,11 @@ OSVersion: xenial
# Make filesystem mount points # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch mkdir /cvmfs /oasis /projects /scratch
# Build and install additional software packages in /opt # Use /tmp to store temporary files within the container during the
cd /opt # bootstraping process
cd /tmp
# 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
# Install miniconda2
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
chmod +x Miniconda2-latest-Linux-x86_64.sh chmod +x Miniconda2-latest-Linux-x86_64.sh
...@@ -104,9 +100,7 @@ OSVersion: xenial ...@@ -104,9 +100,7 @@ OSVersion: xenial
chmod +x install-miniconda2.exp chmod +x install-miniconda2.exp
./install-miniconda2.exp ./install-miniconda2.exp
rm Miniconda2-latest-Linux-x86_64.sh # Install miniconda3
rm install-miniconda2.exp
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh
...@@ -136,9 +130,6 @@ OSVersion: xenial ...@@ -136,9 +130,6 @@ OSVersion: xenial
chmod +x install-miniconda3.exp chmod +x install-miniconda3.exp
./install-miniconda3.exp ./install-miniconda3.exp
rm Miniconda3-latest-Linux-x86_64.sh
rm install-miniconda3.exp
# Location of NVIDIA repositories # Location of NVIDIA repositories
declare -r NVIDIA_ROOT_URL='http://developer.download.nvidia.com/compute' 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 CUDA_REPO_URL="${NVIDIA_ROOT_URL}/cuda/repos/ubuntu1604/x86_64"
...@@ -272,12 +263,15 @@ OSVersion: xenial ...@@ -272,12 +263,15 @@ OSVersion: xenial
dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb dpkg -i libnccl2_2.1.2-1+cuda8.0_amd64.deb
dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb dpkg -i libnccl-dev_2.1.2-1+cuda8.0_amd64.deb
rm *.deb
# Set paths to CUDA binaries and libraries # Set paths to CUDA binaries and libraries
export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}" export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${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:+:${LD_LIBRARY_PATH}}"' >> 90-environment.sh
# Update database for mlocate # Update database for mlocate
updatedb updatedb
...@@ -287,8 +281,5 @@ OSVersion: xenial ...@@ -287,8 +281,5 @@ OSVersion: xenial
%test %test
# Test if nvcc was installed properly
export PATH="/usr/local/cuda-8.0/bin${PATH:+:${PATH}}"
export LD_LIBRARY_PATH="/usr/local/cuda-8.0/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
nvcc --version nvcc --version
definition-files/us/ucsd/sdsc/comet/ubuntu/ubuntu.def
+ 11
− 9
View file @ e41633e0
...@@ -12,7 +12,7 @@ OSVersion: xenial ...@@ -12,7 +12,7 @@ OSVersion: xenial
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.3.2 SYSTEM_SINGULARITY_VERSION 2.3.2
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
LAST_UPDATED 20180226 LAST_UPDATED 20180302
%setup %setup
...@@ -20,11 +20,14 @@ OSVersion: xenial ...@@ -20,11 +20,14 @@ OSVersion: xenial
%post -c /bin/bash %post -c /bin/bash
# Set system locale
export LC_ALL=C export LC_ALL=C
# Install system metapackages
apt-get -y install ubuntu-standard apt-get -y install ubuntu-standard
apt-get -y install ubuntu-server apt-get -y install ubuntu-server
# Add repositories
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} main"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} universe"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION} multiverse"
...@@ -45,6 +48,7 @@ OSVersion: xenial ...@@ -45,6 +48,7 @@ OSVersion: xenial
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security multiverse"
add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted" add-apt-repository -y "deb ${MIRRORURL} ${OSVERSION}-security restricted"
# Upgrade all packages to their latest versions
apt-get -y update && apt-get -y upgrade apt-get -y update && apt-get -y upgrade
# Install common packages from 'main' # Install common packages from 'main'
...@@ -62,8 +66,9 @@ OSVersion: xenial ...@@ -62,8 +66,9 @@ OSVersion: xenial
# Make filesystem mount points # Make filesystem mount points
mkdir /cvmfs /oasis /projects /scratch mkdir /cvmfs /oasis /projects /scratch
# Build and install additional software packages in /opt # Use /tmp to store temporary files within the container during the
cd /opt # bootstraping process
cd /tmp
# Install miniconda2 # Install miniconda2
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
...@@ -95,9 +100,6 @@ OSVersion: xenial ...@@ -95,9 +100,6 @@ OSVersion: xenial
chmod +x install-miniconda2.exp chmod +x install-miniconda2.exp
./install-miniconda2.exp ./install-miniconda2.exp
rm Miniconda2-latest-Linux-x86_64.sh
rm install-miniconda2.exp
# Install miniconda3 # Install miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh chmod +x Miniconda3-latest-Linux-x86_64.sh
...@@ -128,8 +130,8 @@ OSVersion: xenial ...@@ -128,8 +130,8 @@ OSVersion: xenial
chmod +x install-miniconda3.exp chmod +x install-miniconda3.exp
./install-miniconda3.exp ./install-miniconda3.exp
rm Miniconda3-latest-Linux-x86_64.sh # Set container environment variables
rm install-miniconda3.exp cd /.singularity.d/env
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
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