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Commit bc647edd authored by Marty Kandes's avatar Marty Kandes
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naked-singularity-v0.7.5 :: cleaned up base ubuntu definition files; 

placed miniconda3 in PATH by default
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README
+ 2
− 2
View file @ bc647edd
...@@ -46,8 +46,8 @@ AUTHOR ...@@ -46,8 +46,8 @@ AUTHOR
VERSION VERSION
0.7.4 0.7.5
LAST UPDATED LAST UPDATED
Thursday, May 16th, 2019 Wednesday, August 14th, 2019
definition-files/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def
+ 9
− 7
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 8192 SINGULARITY_IMAGE_SIZE 8192
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20181203 LAST_UPDATED 20190814
%setup %setup
...@@ -30,9 +30,14 @@ OSVersion: xenial ...@@ -30,9 +30,14 @@ OSVersion: xenial
export PATH="/usr/local/cuda-9.2/bin${PATH:+:${PATH}}" 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="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64" export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
# Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}"
%post -c /bin/bash %post -c /bin/bash
# Set system locale # Set system locale
...@@ -72,8 +77,9 @@ OSVersion: xenial ...@@ -72,8 +77,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
...@@ -347,10 +353,6 @@ OSVersion: xenial ...@@ -347,10 +353,6 @@ OSVersion: xenial
./configure --prefix=/opt/openmpi-1.8.4 --with-cuda ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
make all install make all install
# Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
definition-files/comet/ubuntu/ubuntu-cuda-opencl.def
+ 7
− 3
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 8192 SINGULARITY_IMAGE_SIZE 8192
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20181203 LAST_UPDATED 20190814
%setup %setup
...@@ -31,6 +31,9 @@ OSVersion: xenial ...@@ -31,6 +31,9 @@ OSVersion: xenial
export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64" export 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 %post -c /bin/bash
# Set system locale # Set system locale
...@@ -70,8 +73,9 @@ OSVersion: xenial ...@@ -70,8 +73,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
......
definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def
+ 7
− 7
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 8192 SINGULARITY_IMAGE_SIZE 8192
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20181203 LAST_UPDATED 20190814
%setup %setup
...@@ -33,6 +33,9 @@ OSVersion: xenial ...@@ -33,6 +33,9 @@ OSVersion: xenial
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
# Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}"
%post -c /bin/bash %post -c /bin/bash
# Set system locale # Set system locale
...@@ -72,8 +75,9 @@ OSVersion: xenial ...@@ -72,8 +75,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
...@@ -310,10 +314,6 @@ OSVersion: xenial ...@@ -310,10 +314,6 @@ OSVersion: xenial
./configure --prefix=/opt/openmpi-1.8.4 --with-cuda ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda
make all install make all install
# Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
definition-files/comet/ubuntu/ubuntu-cuda.def
+ 7
− 8
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...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://developer.nvidia.com/cuda-zone APPLICATION_URL https://developer.nvidia.com/cuda-zone
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 8192 SINGULARITY_IMAGE_SIZE 8192
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20181203 LAST_UPDATED 20190814
%setup %setup
...@@ -31,6 +31,9 @@ OSVersion: xenial ...@@ -31,6 +31,9 @@ OSVersion: xenial
export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}"
export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64" export 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 %post -c /bin/bash
# Set system locale # Set system locale
...@@ -70,8 +73,9 @@ OSVersion: xenial ...@@ -70,8 +73,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
...@@ -263,11 +267,6 @@ OSVersion: xenial ...@@ -263,11 +267,6 @@ OSVersion: xenial
dpkg -i libnccl2_2.3.4-1+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 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="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64"
# Update database for mlocate # Update database for mlocate
updatedb updatedb
......
definition-files/comet/ubuntu/ubuntu-mvapich2.def
+ 19
− 12
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL http://mvapich.cse.ohio-state.edu/ APPLICATION_URL http://mvapich.cse.ohio-state.edu/
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.1 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20180619 LAST_UPDATED 20190814
%setup %setup
...@@ -26,6 +26,13 @@ OSVersion: xenial ...@@ -26,6 +26,13 @@ OSVersion: xenial
# Set system locale # Set system locale
export LC_ALL=C export LC_ALL=C
# Set paths to MVAPICH2 binaries and libraries
export PATH="/opt/mvapich2/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}"
# Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}"
%post -c /bin/bash %post -c /bin/bash
# Set system locale # Set system locale
...@@ -65,8 +72,9 @@ OSVersion: xenial ...@@ -65,8 +72,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
...@@ -130,11 +138,6 @@ OSVersion: xenial ...@@ -130,11 +138,6 @@ OSVersion: xenial
make make
make install make install
# Set container environment variables
cd /.singularity.d/env
echo 'export PATH="/opt/mvapich2/bin:${PATH}"' >> 90-environment.sh
echo 'export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}"' >> 90-environment.sh
# Update database for mlocate # Update database for mlocate
updatedb updatedb
...@@ -142,8 +145,12 @@ OSVersion: xenial ...@@ -142,8 +145,12 @@ OSVersion: xenial
%runscript %runscript
%test echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
#export PATH="/opt/mvapich2/bin:${PATH}" %test
#export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}"
#mpirun --version
definition-files/comet/ubuntu/ubuntu-openmpi.def
+ 20
− 13
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://www.open-mpi.org/ APPLICATION_URL https://www.open-mpi.org/
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.1 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20180619 LAST_UPDATED 20190814
%setup %setup
...@@ -26,6 +26,13 @@ OSVersion: xenial ...@@ -26,6 +26,13 @@ OSVersion: xenial
# Set system locale # Set system locale
export LC_ALL=C export LC_ALL=C
# 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:${PATH}"
%post -c /bin/bash %post -c /bin/bash
# Set system locale # Set system locale
...@@ -65,8 +72,9 @@ OSVersion: xenial ...@@ -65,8 +72,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
...@@ -133,11 +141,6 @@ OSVersion: xenial ...@@ -133,11 +141,6 @@ OSVersion: xenial
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-1.8.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
# Set container environment variables
cd /.singularity.d/env
echo 'export PATH="/opt/openmpi-1.8.4/bin:${PATH}"' >> 90-environment.sh
echo 'export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"' >> 90-environment.sh
# Update database for mlocate # Update database for mlocate
updatedb updatedb
...@@ -145,8 +148,12 @@ OSVersion: xenial ...@@ -145,8 +148,12 @@ OSVersion: xenial
%runscript %runscript
%test echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
#export PATH="/opt/openmpi-1.8.4/bin:${PATH}" %test
#export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}"
#mpirun --version
definition-files/comet/ubuntu/ubuntu.def
+ 7
− 3
View file @ bc647edd
...@@ -9,7 +9,7 @@ OSVersion: xenial ...@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://www.ubuntu.com/ APPLICATION_URL https://www.ubuntu.com/
SYSTEM_NAME comet SYSTEM_NAME comet
SYSTEM_SINGULARITY_VERSION 2.5.2 SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
...@@ -17,7 +17,7 @@ OSVersion: xenial ...@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20181003 LAST_UPDATED 20190812
%setup %setup
...@@ -26,6 +26,9 @@ OSVersion: xenial ...@@ -26,6 +26,9 @@ OSVersion: xenial
# Set system locale # Set system locale
export LC_ALL=C export LC_ALL=C
# Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}"
%post -c /bin/bash %post -c /bin/bash
# Set system locale # Set system locale
...@@ -65,8 +68,9 @@ OSVersion: xenial ...@@ -65,8 +68,9 @@ OSVersion: xenial
apt-get -y install build-essential apt-get -y install build-essential
apt-get -y install cmake apt-get -y install cmake
apt-get -y install libtool apt-get -y install libtool
apt-get -y install pkg-config
apt-get -y install gfortran apt-get -y install gfortran
apt-get -y install pkg-config
apt-get -y install wget
apt-get -y install zip apt-get -y install zip
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
......
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