diff --git a/README b/README index bb23a7901faa0818d7d858083bb89db999b9106e..65e125d039751812dd84a7b1181aa6913e4149ad 100644 --- a/README +++ b/README @@ -46,8 +46,8 @@ AUTHOR VERSION - 0.7.4 + 0.7.5 LAST UPDATED - Thursday, May 16th, 2019 + Wednesday, August 14th, 2019 diff --git a/definition-files/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def b/definition-files/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def index 17f1100bc01f9a8c18e3536615c0515304790ab6..1b7c218419f476854938a2151f3b2073f1fc4b8e 100644 --- a/definition-files/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def +++ b/definition-files/comet/ubuntu/ubuntu-cuda-opencl-openmpi.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime 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 SINGULARITY_IMAGE_SIZE 8192 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20181203 + LAST_UPDATED 20190814 %setup @@ -30,9 +30,14 @@ OSVersion: xenial 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 @@ -72,8 +77,9 @@ OSVersion: xenial 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 pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions @@ -347,10 +353,6 @@ OSVersion: xenial ./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 diff --git a/definition-files/comet/ubuntu/ubuntu-cuda-opencl.def b/definition-files/comet/ubuntu/ubuntu-cuda-opencl.def index b0ff3aeef98132ac098da6ef3da2b5694fdea638..eae3fc3dae987d8319e01247d0fab43ba90fce68 100644 --- a/definition-files/comet/ubuntu/ubuntu-cuda-opencl.def +++ b/definition-files/comet/ubuntu/ubuntu-cuda-opencl.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://software.intel.com/en-us/articles/opencl-drivers#latest_CPU_runtime 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 SINGULARITY_IMAGE_SIZE 8192 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20181203 + LAST_UPDATED 20190814 %setup @@ -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="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64" + # Set default miniconda environment + export PATH="/opt/miniconda3/bin:${PATH}" + %post -c /bin/bash # Set system locale @@ -70,8 +73,9 @@ OSVersion: xenial 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 pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions diff --git a/definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def b/definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def index 7c74e4f3ff41d0d7d4eec9962a3abdfe8b5bba2b..859b3ca78fa4f96b098fc86221995378907e6f78 100644 --- a/definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def +++ b/definition-files/comet/ubuntu/ubuntu-cuda-openmpi.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://www.open-mpi.org/faq/?category=runcuda 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 SINGULARITY_IMAGE_SIZE 8192 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20181203 + LAST_UPDATED 20190814 %setup @@ -33,6 +33,9 @@ OSVersion: xenial 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:${PATH}" + %post -c /bin/bash # Set system locale @@ -72,8 +75,9 @@ OSVersion: xenial apt-get -y install build-essential apt-get -y install cmake apt-get -y install libtool - apt-get -y install pkg-config apt-get -y install gfortran + apt-get -y install pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions @@ -310,10 +314,6 @@ OSVersion: xenial ./configure --prefix=/opt/openmpi-1.8.4 --with-cuda make all install - # Set paths to OpenMPI binaries and libraries - export PATH="/opt/openmpi-1.8.4/bin:${PATH}" - export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" - # Update database for mlocate updatedb diff --git a/definition-files/comet/ubuntu/ubuntu-cuda.def b/definition-files/comet/ubuntu/ubuntu-cuda.def index 7305a8dd2e48c31ef14ca59314e926a172af3153..3369f7db7cb6fabbe78e299d6b51659defb9613b 100644 --- a/definition-files/comet/ubuntu/ubuntu-cuda.def +++ b/definition-files/comet/ubuntu/ubuntu-cuda.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://developer.nvidia.com/cuda-zone SYSTEM_NAME comet - SYSTEM_SINGULARITY_VERSION 2.5.2 + SYSTEM_SINGULARITY_VERSION 2.6.1 SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SINGULARITY_IMAGE_SIZE 8192 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20181203 + LAST_UPDATED 20190814 %setup @@ -31,6 +31,9 @@ OSVersion: xenial export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/usr/local/cuda/extras/CUPTI/lib64" + # Set default miniconda environment + export PATH="/opt/miniconda3/bin:${PATH}" + %post -c /bin/bash # Set system locale @@ -70,8 +73,9 @@ OSVersion: xenial apt-get -y install build-essential apt-get -y install cmake apt-get -y install libtool - apt-get -y install pkg-config apt-get -y install gfortran + apt-get -y install pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions @@ -263,11 +267,6 @@ OSVersion: xenial dpkg -i libnccl2_2.3.4-1+cuda9.2_amd64.deb dpkg -i libnccl-dev_2.3.4-1+cuda9.2_amd64.deb - # Set paths to CUDA binaries and libraries - export PATH="/usr/local/cuda-9.2/bin${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" - # Update database for mlocate updatedb diff --git a/definition-files/comet/ubuntu/ubuntu-mvapich2.def b/definition-files/comet/ubuntu/ubuntu-mvapich2.def index d438a0a32cb0daac6251fb2fb8b58c3e3f852e75..e71931da71c2abed191cddf4e39061768d4ec253 100644 --- a/definition-files/comet/ubuntu/ubuntu-mvapich2.def +++ b/definition-files/comet/ubuntu/ubuntu-mvapich2.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL http://mvapich.cse.ohio-state.edu/ 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 SINGULARITY_IMAGE_SIZE 2048 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20180619 + LAST_UPDATED 20190814 %setup @@ -26,6 +26,13 @@ OSVersion: xenial # 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 default miniconda environment + export PATH="/opt/miniconda3/bin:${PATH}" + %post -c /bin/bash # Set system locale @@ -65,8 +72,9 @@ OSVersion: xenial apt-get -y install build-essential apt-get -y install cmake apt-get -y install libtool - apt-get -y install pkg-config apt-get -y install gfortran + apt-get -y install pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions @@ -130,11 +138,6 @@ OSVersion: xenial make make install - # Set container environment variables - cd /.singularity.d/env - echo 'export PATH="/opt/mvapich2/bin:${PATH}"' >> 90-environment.sh - echo 'export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}"' >> 90-environment.sh - # Update database for mlocate updatedb @@ -142,8 +145,12 @@ OSVersion: xenial %runscript -%test + echo " " + echo " __________________ __ _______________ " + echo " -----/ ____/ __ \/ |/ / ____/_ __/ " + echo " --/ / / / / / /|_/ / __/ / / " + echo " / /___/ /_/ / / / / /___ / / " + echo " \____/\____/_/ /_/_____/ /_/ " + echo " " - #export PATH="/opt/mvapich2/bin:${PATH}" - #export LD_LIBRARY_PATH="/opt/mvapich2/lib:${LD_LIBRARY_PATH}" - #mpirun --version +%test diff --git a/definition-files/comet/ubuntu/ubuntu-openmpi.def b/definition-files/comet/ubuntu/ubuntu-openmpi.def index 9aaa5ccc1af38146afc0594ab1a035a9737f6c4a..7f72e6e5926866e459d05515480c3e5e2e730789 100644 --- a/definition-files/comet/ubuntu/ubuntu-openmpi.def +++ b/definition-files/comet/ubuntu/ubuntu-openmpi.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://www.open-mpi.org/ SYSTEM_NAME comet - SYSTEM_SINGULARITY_VERSION 2.5.1 + SYSTEM_SINGULARITY_VERSION 2.6.1 SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html SINGULARITY_IMAGE_SIZE 2048 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20180619 + LAST_UPDATED 20190814 %setup @@ -26,6 +26,13 @@ OSVersion: xenial # Set system locale export LC_ALL=C + # Set paths to OpenMPI binaries and libraries + export PATH="/opt/openmpi-1.8.4/bin:${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 # Set system locale @@ -65,8 +72,9 @@ OSVersion: xenial 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 pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions @@ -127,17 +135,12 @@ OSVersion: xenial tar -xzvf openmpi-1.8.4.tar.gz cd openmpi-1.8.4 ./configure --prefix=/opt/openmpi-1.8.4 - 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}" - # 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 updatedb @@ -145,8 +148,12 @@ OSVersion: xenial %runscript -%test + echo " " + echo " __________________ __ _______________ " + echo " -----/ ____/ __ \/ |/ / ____/_ __/ " + echo " --/ / / / / / /|_/ / __/ / / " + echo " / /___/ /_/ / / / / /___ / / " + echo " \____/\____/_/ /_/_____/ /_/ " + echo " " - #export PATH="/opt/openmpi-1.8.4/bin:${PATH}" - #export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" - #mpirun --version +%test diff --git a/definition-files/comet/ubuntu/ubuntu.def b/definition-files/comet/ubuntu/ubuntu.def index 254df0fc8e38f9cbd4a0f920923b175f3982a18e..ededd8c0651aede3a634a6247e1e86468dfe11e7 100644 --- a/definition-files/comet/ubuntu/ubuntu.def +++ b/definition-files/comet/ubuntu/ubuntu.def @@ -9,7 +9,7 @@ OSVersion: xenial APPLICATION_URL https://www.ubuntu.com/ 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 SINGULARITY_IMAGE_SIZE 2048 @@ -17,7 +17,7 @@ OSVersion: xenial AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20181003 + LAST_UPDATED 20190812 %setup @@ -26,6 +26,9 @@ OSVersion: xenial # Set system locale export LC_ALL=C + # Set default miniconda environment + export PATH="/opt/miniconda3/bin:${PATH}" + %post -c /bin/bash # Set system locale @@ -65,8 +68,9 @@ OSVersion: xenial 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 pkg-config + apt-get -y install wget apt-get -y install zip # Install expect to automate responses for interactive build questions