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Commit 3c69af55 authored by Marty Kandes's avatar Marty Kandes
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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
parent 7cd0e013
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README
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...@@ -46,8 +46,8 @@ AUTHOR ...@@ -46,8 +46,8 @@ AUTHOR
VERSION VERSION
0.8.6 0.8.7
LAST UPDATED LAST UPDATED
Thursday, October 17th, 2019 Wednesday, January 8th, 2020
definition-files/comet/ubuntu/ubuntu-mvapich2.def
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Bootstrap: debootstrap Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial OSVersion: bionic
%labels %labels
APPLICATION_NAME ubuntu + mvapich2 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/ APPLICATION_URL http://mvapich.cse.ohio-state.edu/
SYSTEM_NAME comet SINGULARITY_VERSION 2.6.1
SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20190814 LAST_UPDATED 20200107
%setup %setup
...@@ -80,9 +77,6 @@ OSVersion: xenial ...@@ -80,9 +77,6 @@ OSVersion: xenial
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
apt-get -y install expect 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 # Use /tmp to store temporary files within the container during the
# bootstraping process # bootstraping process
cd /tmp cd /tmp
...@@ -131,9 +125,9 @@ OSVersion: xenial ...@@ -131,9 +125,9 @@ OSVersion: xenial
apt-get -y install bison apt-get -y install bison
# Download, build, and install mvapich2 # Download, build, and install mvapich2
wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz wget http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.3.2.tar.gz
tar -xzvf mvapich2-2.1.tar.gz tar -xzvf mvapich2-2.3.2.tar.gz
cd mvapich2-2.1 cd mvapich2-2.3.2
./configure --prefix=/opt/mvapich2 ./configure --prefix=/opt/mvapich2
make make
make install make install
...@@ -145,12 +139,4 @@ OSVersion: xenial ...@@ -145,12 +139,4 @@ OSVersion: xenial
%runscript %runscript
echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
%test %test
definition-files/comet/ubuntu/ubuntu-openmpi.def
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Bootstrap: debootstrap Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial OSVersion: bionic
%labels %labels
APPLICATION_NAME ubuntu + openmpi 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/ APPLICATION_URL https://www.open-mpi.org/
SYSTEM_NAME comet SINGULARITY_VERSION 2.6.1
SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20190814 LAST_UPDATED 20200107
%setup %setup
...@@ -27,8 +24,8 @@ OSVersion: xenial ...@@ -27,8 +24,8 @@ OSVersion: xenial
export LC_ALL=C export LC_ALL=C
# Set paths to OpenMPI binaries and libraries # Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
# Set default miniconda environment # Set default miniconda environment
export PATH="/opt/miniconda3/bin:${PATH}" export PATH="/opt/miniconda3/bin:${PATH}"
...@@ -80,9 +77,6 @@ OSVersion: xenial ...@@ -80,9 +77,6 @@ OSVersion: xenial
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
apt-get -y install expect 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 # Use /tmp to store temporary files within the container during the
# bootstraping process # bootstraping process
cd /tmp cd /tmp
...@@ -131,15 +125,15 @@ OSVersion: xenial ...@@ -131,15 +125,15 @@ OSVersion: xenial
apt-get -y install zlib1g-dev apt-get -y install zlib1g-dev
# Download, build, and install OpenMPI # Download, build, and install OpenMPI
wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.4.tar.gz
tar -xzvf openmpi-1.8.4.tar.gz tar -xzvf openmpi-3.1.4.tar.gz
cd openmpi-1.8.4 cd openmpi-3.1.4
./configure --prefix=/opt/openmpi-1.8.4 ./configure --prefix=/opt/openmpi-3.1.4
make all install make all install
# Set paths to OpenMPI binaries and libraries # Set paths to OpenMPI binaries and libraries
export PATH="/opt/openmpi-1.8.4/bin:${PATH}" export PATH="/opt/openmpi-3.1.4/bin:${PATH}"
export LD_LIBRARY_PATH="/opt/openmpi-1.8.4/lib:${LD_LIBRARY_PATH}" export LD_LIBRARY_PATH="/opt/openmpi-3.1.4/lib:${LD_LIBRARY_PATH}"
# Update database for mlocate # Update database for mlocate
updatedb updatedb
...@@ -148,12 +142,4 @@ OSVersion: xenial ...@@ -148,12 +142,4 @@ OSVersion: xenial
%runscript %runscript
echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
%test %test
definition-files/comet/ubuntu/ubuntu.def
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Bootstrap: debootstrap Bootstrap: debootstrap
MirrorURL: http://us.archive.ubuntu.com/ubuntu MirrorURL: http://us.archive.ubuntu.com/ubuntu
OSVersion: xenial OSVersion: bionic
%labels %labels
APPLICATION_NAME ubuntu APPLICATION_NAME ubuntu
APPLICATION_VERSION 16.04 APPLICATION_VERSION 18.04
APPLICATION_URL https://www.ubuntu.com/ APPLICATION_URL https://www.ubuntu.com/
SYSTEM_NAME comet SINGULARITY_VERSION 2.6.1
SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048 SINGULARITY_IMAGE_SIZE 2048
AUTHOR_NAME Marty Kandes AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20190812 LAST_UPDATED 20191214
%setup %setup
...@@ -76,9 +73,6 @@ OSVersion: xenial ...@@ -76,9 +73,6 @@ OSVersion: xenial
# Install expect to automate responses for interactive build questions # Install expect to automate responses for interactive build questions
apt-get -y install expect 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 # Use /tmp to store temporary files within the container during the
# bootstraping process # bootstraping process
cd /tmp cd /tmp
...@@ -100,12 +94,4 @@ OSVersion: xenial ...@@ -100,12 +94,4 @@ OSVersion: xenial
%runscript %runscript
echo " "
echo " __________________ __ _______________ "
echo " -----/ ____/ __ \/ |/ / ____/_ __/ "
echo " --/ / / / / / /|_/ / __/ / / "
echo " / /___/ /_/ / / / / /___ / / "
echo " \____/\____/_/ /_/_____/ /_/ "
echo " "
%test %test
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