Add Ubuntu 18.04 + OpenMPI 4.0.4 definition file

Updated the existing base Ubuntu 18.04 + OpenMPI 3.1.6 definition file
to OpenMPI 4.0.4, which is currently the default version of OpenMPI
deployed on Expanse at SDSC.

definition-files/ubuntu/Singularity.ubuntu-18.04-openmpi-4.0.4

+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 number, operating system, and hardware
+    # platform
+    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 versions, root and
+    # installation directories
+    export OPENMPI_MAJOR_VERSION=4
+    export OPENMPI_MINOR_VERSION=0
+    export OPENMPI_REVISION_VERSION=4
+    export OPENMPI_VERSION="${OPENMPI_MAJOR_VERSION}.${OPENMPI_MINOR_VERSION}.${OPENMPI_REVISION_VERSION}"
+    export OPENMPI_ROOT_DIR='/opt/openmpi'
+    export OPENMPI_INSTALL_DIR="${OPENMPI_ROOT_DIR}/${OPENMPI_VERSION}"
+
+    # Set paths to OpenMPI binaries and libraries
+    export PATH="${OPENMPI_INSTALL_DIR}/bin:${PATH}"
+    export LD_LIBRARY_PATH="${OPENMPI_INSTALL_DIR}/lib:${LD_LIBRARY_PATH}"
+
+%post -c /bin/bash
+
+    # Set operating system mirror URL
+    export MIRRORURL='http://us.archive.ubuntu.com/ubuntu'
+
+    # Set operating system version
+    export OSVERSION='bionic'
+
+    # Set system locale
+    export LC_ALL='C'
+
+    # Set debian frontend interface
+    export DEBIAN_FRONTEND='noninteractive'
+
+    # Upgrade all software packages to their latest versions
+    apt-get -y update && apt-get -y upgrade
+
+    # Install all dependencies and/or prerequisites for Mellanox OFED
+    apt-get -y install bison
+    apt-get -y install chrpath
+    apt-get -y install debhelper
+    apt-get -y install dpatch
+    apt-get -y install flex
+    apt-get -y install graphviz
+    apt-get -y install libnl-3-dev
+    apt-get -y install libnl-route-3-200
+    apt-get -y install tcl-dev
+    apt-get -y install tk-dev
+    apt-get -y install swig
+
+    cd /tmp
+
+    # Set Mellanox OFED version number, operating system, and hardware
+    # platform
+    export MLNX_OFED_VERSION='4.7-3.2.9.0'
+    export MLNX_OS_VERSION='ubuntu18.04'
+    export MLNX_PLATFORM='x86_64'
+
+    # Download and install Mellanox OFED drivers and supporting
+    # libraries for userspace access to Ethernet, RDMA, and Infiniband. 
+    # https://docs.mellanox.com/pages/releaseview.action?pageId=15049785
+    wget "http://www.mellanox.com/downloads/ofed/MLNX_OFED-${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}-${MLNX_PLATFORM}.tgz"
+
+    # Install additional tools
+    apt-get -y install numactl
+    apt-get -y install libnuma-dev
+
+    # Install OpenMPI dependencies
+    apt-get -y install zlib1g-dev
+
+    cd /tmp
+
+    # Set OpenMPI major, minor, and revision versions, root and
+    # installation directories
+    export OPENMPI_MAJOR_VERSION=4
+    export OPENMPI_MINOR_VERSION=0
+    export OPENMPI_REVISION_VERSION=4
+    export OPENMPI_VERSION="${OPENMPI_MAJOR_VERSION}.${OPENMPI_MINOR_VERSION}.${OPENMPI_REVISION_VERSION}"
+    export OPENMPI_ROOT_DIR='/opt/openmpi'
+    export OPENMPI_INSTALL_DIR="${OPENMPI_ROOT_DIR}/${OPENMPI_VERSION}"
+
+    # Download, build, and install OpenMPI
+    wget "https://download.open-mpi.org/release/open-mpi/v${OPENMPI_MAJOR_VERSION}.${OPENMPI_MINOR_VERSION}/openmpi-${OPENMPI_VERSION}.tar.gz"
+    tar -xf "openmpi-${OPENMPI_VERSION}.tar.gz"
+    cd "openmpi-${OPENMPI_VERSION}"
+    ./configure --prefix="${OPENMPI_INSTALL_DIR}"
+    make all install
+
+    cd /tmp
+
+    # Remove OpenMPI build directory and source tarball
+    rm -rf "openmpi-${OPENMPI_VERSION}"
+    rm "openmpi-${OPENMPI_VERSION}.tar.gz"
+
+    # Cleanup
+    apt-get -y autoremove --purge
+    apt-get -y clean
+
+    # Update database for mlocate
+    updatedb
+
+%files
+
+%runscript
+
+%test