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
-- 
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