From 98ddcb526a339e855f709ade98d3de67f8085e14 Mon Sep 17 00:00:00 2001
From: Marty Kandes <mkandes@sdsc.edu>
Date: Sun, 21 Mar 2021 22:31:50 +0000
Subject: [PATCH] Update OMB 5.7 def file to use OpenMPI 4.0.5
Also removed Singularity.ubuntu-18.04-openmpi-4.1.0 as it is not needed
at this time.
---
...ularity.omb-5.7-ubuntu-18.04-openmpi-4.0.5 | 115 +++++++++++++++
.../Singularity.ubuntu-18.04-openmpi-4.1.0 | 134 ------------------
2 files changed, 115 insertions(+), 134 deletions(-)
create mode 100644 definition-files/omb/Singularity.omb-5.7-ubuntu-18.04-openmpi-4.0.5
delete mode 100644 definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.1.0
diff --git a/definition-files/omb/Singularity.omb-5.7-ubuntu-18.04-openmpi-4.0.5 b/definition-files/omb/Singularity.omb-5.7-ubuntu-18.04-openmpi-4.0.5
new file mode 100644
index 0000000..c4511bb
--- /dev/null
+++ b/definition-files/omb/Singularity.omb-5.7-ubuntu-18.04-openmpi-4.0.5
@@ -0,0 +1,115 @@
+Bootstrap: shub
+From: mkandes/naked-singularity:ubuntu-18.04-openmpi-4.0.5
+
+%labels
+
+ APPLICATION_NAME OSU Micro-Benchmarks
+ APPLICATION_VERSION 5.7
+ APPLICATION_URL http://mvapich.cse.ohio-state.edu/benchmarks
+
+ AUTHOR_NAME Marty Kandes
+ AUTHOR_EMAIL mkandes@sdsc.edu
+
+ LAST_UPDATED 20210321
+
+%setup
+
+%environment
+
+ # Set OMB major and minor version numbers, root and
+ # installation directories
+ export OMB_ROOT_URL='http://mvapich.cse.ohio-state.edu/download/mvapich'
+ export OMB_MAJOR='5'
+ export OMB_MINOR='7'
+ export OMB_VERSION="${OMB_MAJOR}.${OMB_MINOR}"
+ export OMB_ROOT_DIR='/opt/omb'
+ export OMB_INSTALL_DIR="${OMB_ROOT_DIR}/${OMB_VERSION}"
+
+ # Set paths to OSU Microbenchmarks binaries
+ export PATH="${OMB_INSTALL_DIR}/collective:${PATH}"
+ export PATH="${OMB_INSTALL_DIR}/one-sided:${PATH}"
+ export PATH="${OMB_INSTALL_DIR}/pt2pt:${PATH}"
+ export PATH="${OMB_INSTALL_DIR}/startup:${PATH}"
+
+%post -c /bin/bash
+
+ # Set operating system mirror URL
+ export MIRRORURL='http://us.archive.ubuntu.com/ubuntu'
+
+ # Set operating system version
+ export OSVERSION='bionic'
+
+ # Set system locale
+ export LC_ALL='C'
+
+ # Set debian frontend interface
+ export DEBIAN_FRONTEND='noninteractive'
+
+ # Set Mellanox OFED version, operating system, and hardware platform
+ export MLNX_ROOT_URL='http://www.mellanox.com/downloads/ofed'
+ export MLNX_OFED_VERSION='4.7-3.2.9.0'
+ export MLNX_OS_VERSION='ubuntu18.04'
+ export MLNX_PLATFORM='x86_64'
+
+ # Set OpenMPI major, minor, and revision numbers, root and
+ # installation directories
+ export OMPI_ROOT_URL='https://download.open-mpi.org/release/open-mpi'
+ export OMPI_MAJOR='4'
+ export OMPI_MINOR='0'
+ export OMPI_REVISION='5'
+ export OMPI_VERSION="${OMPI_MAJOR}.${OMPI_MINOR}.${OMPI_REVISION}"
+ export OMPI_ROOT_DIR='/opt/openmpi'
+ export OMPI_INSTALL_DIR="${OMPI_ROOT_DIR}/${OMPI_VERSION}"
+
+ # Set paths to OpenMPI binaries and libraries
+ export PATH="${OMPI_INSTALL_DIR}/bin:${PATH}"
+ export LD_LIBRARY_PATH="${OMPI_INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
+
+ # Upgrade all software packages to their latest versions
+ apt-get -y update && apt-get -y upgrade
+
+ cd /tmp
+
+ # Set OMB major and minor version numbers, root and
+ # installation directories
+ export OMB_ROOT_URL='http://mvapich.cse.ohio-state.edu/download/mvapich'
+ export OMB_MAJOR='5'
+ export OMB_MINOR='7'
+ export OMB_VERSION="${OMB_MAJOR}.${OMB_MINOR}"
+ export OMB_ROOT_DIR='/opt/omb'
+ export OMB_INSTALL_DIR="${OMB_ROOT_DIR}/${OMB_VERSION}"
+
+ # Download, build, and install OSU Microbenchmarks
+ wget "${OMB_ROOT_URL}/osu-micro-benchmarks-${OMB_VERSION}.tar.gz"
+ tar -xf "osu-micro-benchmarks-${OMB_VERSION}.tar.gz"
+ cd "osu-micro-benchmarks-${OMB_VERSION}"
+ ./configure --prefix="${OMB_INSTALL_DIR}" CC='mpicc' CXX='mpicxx'
+ make
+ make install
+
+ # Reorganize OSU Microbenchmarks directory structure
+ cd "${OMB_INSTALL_DIR}"
+ mv libexec/osu-micro-benchmarks/mpi/collective ./
+ mv libexec/osu-micro-benchmarks/mpi/one-sided ./
+ mv libexec/osu-micro-benchmarks/mpi/pt2pt ./
+ mv libexec/osu-micro-benchmarks/mpi/startup ./
+ rm -rf libexec
+
+ cd /tmp
+
+ # Remove OMB build directory and source tarball
+ rm -rf "osu-micro-benchmarks-${OMB_VERSION}"
+ rm "osu-micro-benchmarks-${OMB_VERSION}.tar.gz"
+
+ # Cleanup
+ apt-get -y autoremove --purge
+ apt-get -y clean
+
+ # Update database for mlocate
+ updatedb
+
+%files
+
+%runscript
+
+%test
diff --git a/definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.1.0 b/definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.1.0
deleted file mode 100644
index cb0c679..0000000
--- a/definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.1.0
+++ /dev/null
@@ -1,134 +0,0 @@
-Bootstrap: shub
-From: mkandes/naked-singularity:ubuntu-18.04
-
-%labels
-
- APPLICATION_NAME ubuntu + openmpi
- APPLICATION_VERSION 18.04 + 4.1.0
- APPLICATION_URL https://www.open-mpi.org
-
- AUTHOR_NAME Marty Kandes
- AUTHOR_EMAIL mkandes@sdsc.edu
-
- LAST_UPDATED 20210319
-
-%setup
-
-%environment
-
- # Set Mellanox OFED version, operating system, and hardware platform
- export MLNX_ROOT_URL='http://www.mellanox.com/downloads/ofed'
- export MLNX_OFED_VERSION='4.7-3.2.9.0'
- export MLNX_OS_VERSION='ubuntu18.04'
- export MLNX_PLATFORM='x86_64'
-
- # Set OpenMPI major, minor, and revision numbers, root and
- # installation directories
- export OMPI_ROOT_URL='https://download.open-mpi.org/release/open-mpi'
- export OMPI_MAJOR='4'
- export OMPI_MINOR='1'
- export OMPI_REVISION='0'
- export OMPI_VERSION="${OMPI_MAJOR}.${OMPI_MINOR}.${OMPI_REVISION}"
- export OMPI_ROOT_DIR='/opt/openmpi'
- export OMPI_INSTALL_DIR="${OMPI_ROOT_DIR}/${OMPI_VERSION}"
-
- # Set paths to OpenMPI binaries and libraries
- export PATH="${OMPI_INSTALL_DIR}/bin:${PATH}"
- export LD_LIBRARY_PATH="${OMPI_INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
-
-%post -c /bin/bash
-
- # Set operating system mirror URL
- export MIRRORURL='http://us.archive.ubuntu.com/ubuntu'
-
- # Set operating system version
- export OSVERSION='bionic'
-
- # Set system locale
- export LC_ALL='C'
-
- # Set debian frontend interface
- export DEBIAN_FRONTEND='noninteractive'
-
- # Upgrade all software packages to their latest versions
- apt-get -y update && apt-get -y upgrade
-
- # Install all dependencies and/or prerequisites for Mellanox OFED
- apt-get -y install bison
- apt-get -y install chrpath
- apt-get -y install debhelper
- apt-get -y install dpatch
- apt-get -y install flex
- apt-get -y install graphviz
- apt-get -y install libnl-3-dev
- apt-get -y install libnl-route-3-200
- apt-get -y install tcl-dev
- apt-get -y install tk-dev
- apt-get -y install swig
-
- cd /tmp
-
- # Set Mellanox OFED version, operating system, and hardware platform
- export MLNX_ROOT_URL='http://www.mellanox.com/downloads/ofed'
- export MLNX_OFED_VERSION='4.7-3.2.9.0'
- export MLNX_OS_VERSION='ubuntu18.04'
- export MLNX_PLATFORM='x86_64'
-
- # Download and install Mellanox OFED drivers and supporting
- # libraries for userspace access to Ethernet, RDMA, and Infiniband.
- # https://docs.mellanox.com/pages/releaseview.action?pageId=15049785
- wget "${MLNX_ROOT_URL}/MLNX_OFED-${MLNX_OFED_VERSION}/MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-${MLNX_OS_VERSION}-${MLNX_PLATFORM}.tgz"
- tar -xf "MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-${MLNX_OS_VERSION}-${MLNX_PLATFORM}.tgz"
- cd "MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-${MLNX_OS_VERSION}-${MLNX_PLATFORM}"
- ./mlnxofedinstall --user-space-only --without-fw-update --force
-
- cd /tmp
-
- # Remove Mellanox OFED archive directory and tarball
- rm -rf "MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-${MLNX_OS_VERSION}-${MLNX_PLATFORM}"
- rm "MLNX_OFED_LINUX-${MLNX_OFED_VERSION}-${MLNX_OS_VERSION}-${MLNX_PLATFORM}.tgz"
-
- # Install additional tools
- apt-get -y install numactl
- apt-get -y install libnuma-dev
-
- # Install OpenMPI dependencies
- apt-get -y install zlib1g-dev
-
- cd /tmp
-
- # Set OpenMPI major, minor, and revision numbers, root and
- # installation directories
- export OMPI_ROOT_URL='https://download.open-mpi.org/release/open-mpi'
- export OMPI_MAJOR='4'
- export OMPI_MINOR='1'
- export OMPI_REVISION='0'
- export OMPI_VERSION="${OMPI_MAJOR}.${OMPI_MINOR}.${OMPI_REVISION}"
- export OMPI_ROOT_DIR='/opt/openmpi'
- export OMPI_INSTALL_DIR="${OMPI_ROOT_DIR}/${OMPI_VERSION}"
-
- # Download, build, and install OpenMPI
- wget "${OMPI_ROOT_URL}/v${OMPI_MAJOR}.${OMPI_MINOR}/openmpi-${OMPI_VERSION}.tar.gz"
- tar -xf "openmpi-${OMPI_VERSION}.tar.gz"
- cd "openmpi-${OMPI_VERSION}"
- ./configure --prefix="${OMPI_INSTALL_DIR}" --without-verbs
- make all install
-
- cd /tmp
-
- # Remove OpenMPI build directory and source tarball
- rm -rf "openmpi-${OMPI_VERSION}"
- rm "openmpi-${OMPI_VERSION}.tar.gz"
-
- # Cleanup
- apt-get -y autoremove --purge
- apt-get -y clean
-
- # Update database for mlocate
- updatedb
-
-%files
-
-%runscript
-
-%test
--
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