From bc647edd864beac52931f09c9d84de4ee13064aa Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Wed, 14 Aug 2019 10:16:25 -0700
Subject: [PATCH] naked-singularity-v0.7.5 :: cleaned up base ubuntu definition
files; placed miniconda3 in PATH by default
---
README | 4 +--
.../ubuntu/ubuntu-cuda-opencl-openmpi.def | 16 +++++----
.../comet/ubuntu/ubuntu-cuda-opencl.def | 10 ++++--
.../comet/ubuntu/ubuntu-cuda-openmpi.def | 14 ++++----
definition-files/comet/ubuntu/ubuntu-cuda.def | 15 ++++-----
.../comet/ubuntu/ubuntu-mvapich2.def | 31 ++++++++++-------
.../comet/ubuntu/ubuntu-openmpi.def | 33 +++++++++++--------
definition-files/comet/ubuntu/ubuntu.def | 10 ++++--
8 files changed, 78 insertions(+), 55 deletions(-)
diff --git a/README b/README
index bb23a79..65e125d 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 17f1100..1b7c218 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 b0ff3ae..eae3fc3 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 7c74e4f..859b3ca 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:${LD_LIBRARY_PATH}"
-
# Update database for mlocate
updatedb
diff --git a/definition-files/comet/ubuntu/ubuntu-cuda.def b/definition-files/comet/ubuntu/ubuntu-cuda.def
index 7305a8d..3369f7d 100644
--- a/definition-files/comet/ubuntu/ubuntu-cuda.def
+++ b/definition-files/comet/ubuntu/ubuntu-cuda.def
@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://developer.nvidia.com/cuda-zone
SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.2
+ SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 8192
@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
- LAST_UPDATED 20181203
+ LAST_UPDATED 20190814
%setup
@@ -31,6 +31,9 @@ OSVersion: xenial
export LD_LIBRARY_PATH="/usr/local/cuda-9.2/lib64${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 d438a0a..e71931d 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:${LD_LIBRARY_PATH}"
- #mpirun --version
+%test
diff --git a/definition-files/comet/ubuntu/ubuntu-openmpi.def b/definition-files/comet/ubuntu/ubuntu-openmpi.def
index 9aaa5cc..7f72e6e 100644
--- a/definition-files/comet/ubuntu/ubuntu-openmpi.def
+++ b/definition-files/comet/ubuntu/ubuntu-openmpi.def
@@ -9,7 +9,7 @@ OSVersion: xenial
APPLICATION_URL https://www.open-mpi.org/
SYSTEM_NAME comet
- SYSTEM_SINGULARITY_VERSION 2.5.1
+ SYSTEM_SINGULARITY_VERSION 2.6.1
SYSTEM_URL http://www.sdsc.edu/support/user_guides/comet.html
SINGULARITY_IMAGE_SIZE 2048
@@ -17,7 +17,7 @@ OSVersion: xenial
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
- LAST_UPDATED 20180619
+ LAST_UPDATED 20190814
%setup
@@ -26,6 +26,13 @@ OSVersion: xenial
# Set system locale
export LC_ALL=C
+ # Set paths to OpenMPI binaries and libraries
+ export PATH="/opt/openmpi-1.8.4/bin:${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 254df0f..ededd8c 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
--
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