From 3c69af55b704bffaf3d5e97882d015ab857016cf Mon Sep 17 00:00:00 2001 From: Marty Kandes <mkandes@sdsc.edu> Date: Wed, 8 Jan 2020 12:01:50 -0800 Subject: [PATCH] naked-singularity-v0.8.7 :: started updating container definition files for recent upgrade of Comet to CentOS 7; updated base ubuntu.def to bionic (v18.04); ubuntu-openmpi.def to bionic (v18.04) and openmpi v3.1.4; ubuntu-mvapich2.def to bionic (v18.04) and mvapich2 v2.3.2; removed prior filesystem mount points as Comet's Singularity configuration now allows bind mounts by users --- README | 4 +- .../comet/ubuntu/ubuntu-mvapich2.def | 28 ++++---------- .../comet/ubuntu/ubuntu-openmpi.def | 38 ++++++------------- definition-files/comet/ubuntu/ubuntu.def | 22 ++--------- 4 files changed, 25 insertions(+), 67 deletions(-) diff --git a/README b/README index c0b2ea6..8ceaa07 100644 --- a/README +++ b/README @@ -46,8 +46,8 @@ AUTHOR VERSION - 0.8.6 + 0.8.7 LAST UPDATED - Thursday, October 17th, 2019 + Wednesday, January 8th, 2020 diff --git a/definition-files/comet/ubuntu/ubuntu-mvapich2.def b/definition-files/comet/ubuntu/ubuntu-mvapich2.def index e71931d..21a5efb 100644 --- a/definition-files/comet/ubuntu/ubuntu-mvapich2.def +++ b/definition-files/comet/ubuntu/ubuntu-mvapich2.def @@ -1,23 +1,20 @@ Bootstrap: debootstrap MirrorURL: http://us.archive.ubuntu.com/ubuntu -OSVersion: xenial +OSVersion: bionic %labels APPLICATION_NAME ubuntu + mvapich2 - APPLICATION_VERSION 16.04 + 2.1 + APPLICATION_VERSION 18.04 + 2.3.2 APPLICATION_URL http://mvapich.cse.ohio-state.edu/ - SYSTEM_NAME comet - SYSTEM_SINGULARITY_VERSION 2.6.1 - SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html - + SINGULARITY_VERSION 2.6.1 SINGULARITY_IMAGE_SIZE 2048 AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20190814 + LAST_UPDATED 20200107 %setup @@ -80,9 +77,6 @@ OSVersion: xenial # 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 @@ -131,9 +125,9 @@ OSVersion: xenial apt-get -y install bison # Download, build, and install mvapich2 - wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz - tar -xzvf mvapich2-2.1.tar.gz - cd mvapich2-2.1 + wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.2.tar.gz + tar -xzvf mvapich2-2.3.2.tar.gz + cd mvapich2-2.3.2 ./configure --prefix=/opt/mvapich2 make make install @@ -145,12 +139,4 @@ OSVersion: xenial %runscript - echo " " - echo " __________________ __ _______________ " - echo " -----/ ____/ __ \/ |/ / ____/_ __/ " - echo " --/ / / / / / /|_/ / __/ / / " - echo " / /___/ /_/ / / / / /___ / / " - echo " \____/\____/_/ /_/_____/ /_/ " - echo " " - %test diff --git a/definition-files/comet/ubuntu/ubuntu-openmpi.def b/definition-files/comet/ubuntu/ubuntu-openmpi.def index 7f72e6e..10d17f9 100644 --- a/definition-files/comet/ubuntu/ubuntu-openmpi.def +++ b/definition-files/comet/ubuntu/ubuntu-openmpi.def @@ -1,23 +1,20 @@ Bootstrap: debootstrap MirrorURL: http://us.archive.ubuntu.com/ubuntu -OSVersion: xenial +OSVersion: bionic %labels APPLICATION_NAME ubuntu + openmpi - APPLICATION_VERSION 16.04 + 1.8.4 + APPLICATION_VERSION 18.04 + 3.1.4 APPLICATION_URL https://www.open-mpi.org/ - SYSTEM_NAME comet - SYSTEM_SINGULARITY_VERSION 2.6.1 - SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html - + SINGULARITY_VERSION 2.6.1 SINGULARITY_IMAGE_SIZE 2048 AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20190814 + LAST_UPDATED 20200107 %setup @@ -27,8 +24,8 @@ OSVersion: xenial 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}" + export PATH="/opt/openmpi-3.1.4/bin:${PATH}" + export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}" # Set default miniconda environment export PATH="/opt/miniconda3/bin:${PATH}" @@ -80,9 +77,6 @@ OSVersion: xenial # Install expect to automate responses for interactive build questions apt-get -y install expect - # Make filesystem mount points - mkdir /cvmfs /oasis /projects /scratch - # Use /tmp to store temporary files within the container during the # bootstraping process cd /tmp @@ -131,15 +125,15 @@ OSVersion: xenial apt-get -y install zlib1g-dev # Download, build, and install OpenMPI - wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz - tar -xzvf openmpi-1.8.4.tar.gz - cd openmpi-1.8.4 - ./configure --prefix=/opt/openmpi-1.8.4 + wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz + tar -xzvf openmpi-3.1.4.tar.gz + cd openmpi-3.1.4 + ./configure --prefix=/opt/openmpi-3.1.4 make all install # Set paths to OpenMPI binaries and libraries - export PATH="/opt/openmpi-1.8.4/bin:${PATH}" - export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" + export PATH="/opt/openmpi-3.1.4/bin:${PATH}" + export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}" # Update database for mlocate updatedb @@ -148,12 +142,4 @@ OSVersion: xenial %runscript - echo " " - echo " __________________ __ _______________ " - echo " -----/ ____/ __ \/ |/ / ____/_ __/ " - echo " --/ / / / / / /|_/ / __/ / / " - echo " / /___/ /_/ / / / / /___ / / " - echo " \____/\____/_/ /_/_____/ /_/ " - echo " " - %test diff --git a/definition-files/comet/ubuntu/ubuntu.def b/definition-files/comet/ubuntu/ubuntu.def index ededd8c..9b3963e 100644 --- a/definition-files/comet/ubuntu/ubuntu.def +++ b/definition-files/comet/ubuntu/ubuntu.def @@ -1,23 +1,20 @@ Bootstrap: debootstrap MirrorURL: http://us.archive.ubuntu.com/ubuntu -OSVersion: xenial +OSVersion: bionic %labels APPLICATION_NAME ubuntu - APPLICATION_VERSION 16.04 + APPLICATION_VERSION 18.04 APPLICATION_URL https://www.ubuntu.com/ - SYSTEM_NAME comet - SYSTEM_SINGULARITY_VERSION 2.6.1 - SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html - + SINGULARITY_VERSION 2.6.1 SINGULARITY_IMAGE_SIZE 2048 AUTHOR_NAME Marty Kandes AUTHOR_EMAIL mkandes@sdsc.edu - LAST_UPDATED 20190812 + LAST_UPDATED 20191214 %setup @@ -76,9 +73,6 @@ OSVersion: xenial # 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 @@ -100,12 +94,4 @@ OSVersion: xenial %runscript - echo " " - echo " __________________ __ _______________ " - echo " -----/ ____/ __ \/ |/ / ____/_ __/ " - echo " --/ / / / / / /|_/ / __/ / / " - echo " / /___/ /_/ / / / / /___ / / " - echo " \____/\____/_/ /_/_____/ /_/ " - echo " " - %test -- GitLab