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Commit 2409b188 authored by Marty Kandes's avatar Marty Kandes
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Remove all def files that depend on OpenMPI 4.0.4 

Removed all container definition files that depend on OpenMPI 4.0.4 due
to the bug/issue described in commits 210cd3ed and 8c59ea28. While OpenMPI
4.0.4 is currently the base OpenMPI version deployed on Expanse @ SDSC,
running Singularity containers with OpenMPI 4.0.5 against OpenMPi 4.0.4
on the host has not been a problem. Moreover, we will plan to update the
base OpenMPI version on Expanse to OpenMPI 4.0.5 on next update of Spack
instances (in the next month or two).
parent ddef565d
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definition-files/hpl/Singularity.hpl-2.3-ubuntu-18.04-openmpi-4.0.4-openblas-0.3.14 deleted 100644 → 0
+ 0
− 161
View file @ ddef565d
Bootstrap: shub
From: mkandes/naked-singularity:ubuntu-18.04-openmpi-4.0.4
%labels
APPLICATION_NAME High-Performance Linpack (HPL)
APPLICATION_VERSION 2.3
APPLICATION_URL https://www.netlib.org/benchmark/hpl
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20210318
%setup
%environment
# Set OpenBLAS version number, target architecture, maximum number
# of threads, root and installation directories
export OPENBLAS_REPO_URL='https://github.com/xianyi/OpenBLAS.git'
export OPENBLAS_VERSION='0.3.14'
export OPENBLAS_ROOT_DIR='/opt/openblas'
export OPENBLAS_INSTALL_DIR="${OPENBLAS_ROOT_DIR}/${OPENBLAS_VERSION}"
export OPENBLAS_USE_OPENMP=1
export OPENBLAS_DYNAMIC_ARCH=1
export OPENBLAS_TARGET_ARCH='HASWELL'
export OPENBLAS_MAX_NUM_THREADS=256
# Set path to OpenBLAS libraries
export LD_LIBRARY_PATH="${OPENBLAS_INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
# Set HPL version number, target architecture, root and installation
# directories
export HPL_ROOT_URL='http://www.netlib.org/benchmark/hpl'
export HPL_VERSION='2.3'
export HPL_ARCH='linux64'
export HPL_ROOT_DIR='/opt/hpl'
export HPL_INSTALL_DIR="${HPL_ROOT_DIR}/${HPL_VERSION}"
# Set path to HPL binary
export PATH="${HPL_INSTALL_DIR}/bin:${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='4'
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:${LD_LIBRARY_PATH}"
# Upgrade all software packages to their latest versions
apt-get -y update && apt-get -y upgrade
cd /tmp
# Set OpenBLAS version number, target architecture, maximum number
# of threads, root and installation directories
export OPENBLAS_REPO_URL='https://github.com/xianyi/OpenBLAS.git'
export OPENBLAS_VERSION='0.3.14'
export OPENBLAS_ROOT_DIR='/opt/openblas'
export OPENBLAS_INSTALL_DIR="${OPENBLAS_ROOT_DIR}/${OPENBLAS_VERSION}"
export OPENBLAS_USE_OPENMP=1
export OPENBLAS_DYNAMIC_ARCH=1
export OPENBLAS_TARGET_ARCH='HASWELL'
export OPENBLAS_MAX_NUM_THREADS=256
# Download, build, and install OpenBLAS
git clone "${OPENBLAS_REPO_URL}"
cd OpenBLAS
git checkout "v${OPENBLAS_VERSION}"
if (( "${OPENBLAS_DYNAMIC_ARCH}" == 1 )); then
make FC='gfortran' BINARY=64 USE_OPENMP="${OPENBLAS_USE_OPENMP}" DYNAMIC_ARCH=1 NUM_THREADS="${OPENBLAS_MAX_NUM_THREADS}"
else
make FC='gfortran' BINARY=64 USE_OPENMP="${OPENBLAS_USE_OPENMP}" TARGET="${OPENBLAS_TARGET_ARCH}" NUM_THREADS="${OPENBLAS_MAX_NUM_THREADS}"
fi
make PREFIX="${OPENBLAS_INSTALL_DIR}" install
# Set path to OpenBLAS libraries
export LD_LIBRARY_PATH="${OPENBLAS_INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
cd /tmp
# Remove OpenBLAS build directory
rm -rf OpenBLAS
# Set HPL version number, target architecture, root and installation
# directories
export HPL_ROOT_URL='http://www.netlib.org/benchmark/hpl'
export HPL_VERSION='2.3'
export HPL_ARCH='linux64'
export HPL_ROOT_DIR='/opt/hpl'
export HPL_INSTALL_DIR="${HPL_ROOT_DIR}/${HPL_VERSION}"
# Download, build, and install HPL
wget "${HPL_ROOT_URL}/hpl-${HPL_VERSION}.tar.gz"
tar -xf "hpl-${HPL_VERSION}.tar.gz"
cd "hpl-${HPL_VERSION}/setup"
source make_generic
mv Make.UNKNOWN Make.linux64
sed -i 's/ARCH = UNKNOWN/ARCH = linux64/' Make.linux64
sed -i 's/TOPdir = $(HOME)\/hpl/TOPdir =/' Make.linux64
sed -i "s/TOPdir =/TOPdir = \/opt\/hpl\/${HPL_VERSION}/" Make.linux64
sed -i 's/MPdir = /MPdir = \/opt\/openmpi/4.0.4/' Make.linux64
sed -i 's/MPinc = /MPinc = -I$(MPdir)\/include/' Make.linux64
sed -i 's/MPlib = /MPlib = $(MPdir)\/lib\/libmpi.so/' Make.linux64
sed -i "s/LAdir = /LAdir = \/opt\/openblas\/${OPENBLAS_VERSION}/" Make.linux64
sed -i 's/LAinc = /LAinc = -I$(LAdir)\/include/' Make.linux64
sed -i 's/LAlib = -lblas/LAlib = $(LAdir)\/lib\/libopenblas.a/' Make.linux64
sed -i 's/LINKER = mpif77/LINKER = mpicc/' Make.linux64
cp Make.linux64 ../
cd ../
export LDFLAGS="-L${OPENBLAS_INSTALL_DIR}/lib"
./configure --prefix="${HPL_INSTALL_DIR}"
make arch='linux64'
make install
cd /tmp
# Remove HPL build directory and source tarball
rm -rf "hpl-${HPL_VERSION}"
rm "hpl-${HPL_VERSION}.tar.gz"
# Cleanup
apt-get -y autoremove --purge
apt-get -y clean
# Update database for mlocate
updatedb
%files
%runscript
%test
definition-files/omb/Singularity.omb-5.7-ubuntu-18.04-openmpi-4.0.4 deleted 100644 → 0
+ 0
− 115
View file @ ddef565d
Bootstrap: shub
From: mkandes/naked-singularity:ubuntu-18.04-openmpi-4.0.4
%labels
APPLICATION_NAME OSU Micro-Benchmarks
APPLICATION_VERSION 5.7
APPLICATION_URL http://mvapich.cse.ohio-state.edu/benchmarks
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20210305
%setup
%environment
# Set OMB major and minor version numbers, root and
# installation directories
export OMB_ROOT_URL='http://mvapich.cse.ohio-state.edu/download/mvapich'
export OMB_MAJOR='5'
export OMB_MINOR='7'
export OMB_VERSION="${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:${PATH}"
%post -c /bin/bash
# Set operating system mirror URL
export MIRRORURL='http://us.archive.ubuntu.com/ubuntu'
# Set operating system version
export OSVERSION='bionic'
# Set system locale
export LC_ALL='C'
# Set debian frontend interface
export DEBIAN_FRONTEND='noninteractive'
# Set Mellanox OFED version, operating system, and hardware platform
export MLNX_ROOT_URL='http://www.mellanox.com/downloads/ofed'
export MLNX_OFED_VERSION='4.7-3.2.9.0'
export MLNX_OS_VERSION='ubuntu18.04'
export MLNX_PLATFORM='x86_64'
# Set OpenMPI major, minor, and revision numbers, root and
# installation directories
export OMPI_ROOT_URL='https://download.open-mpi.org/release/open-mpi'
export OMPI_MAJOR='4'
export OMPI_MINOR='0'
export OMPI_REVISION='4'
export OMPI_VERSION="${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
definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.0.4 deleted 100644 → 0
+ 0
− 134
View file @ ddef565d
Bootstrap: shub
From: mkandes/naked-singularity:ubuntu-18.04
%labels
APPLICATION_NAME ubuntu + openmpi
APPLICATION_VERSION 18.04 + 4.0.4
APPLICATION_URL https://www.open-mpi.org
AUTHOR_NAME Marty Kandes
AUTHOR_EMAIL mkandes@sdsc.edu
LAST_UPDATED 20210223
%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='0'
export OMPI_REVISION='4'
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='0'
export OMPI_REVISION='4'
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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