EESSI-pilot-install-software.sh

#!/bin/bash

# Script to install EESSI pilot software stack (version set through init/eessi_defaults)

# see example parsing of command line arguments at
#   https://wiki.bash-hackers.org/scripting/posparams#using_a_while_loop
#   https://stackoverflow.com/questions/192249/how-do-i-parse-command-line-arguments-in-bash

display_help() {
  echo "usage: $0 [OPTIONS]"
  echo "  -g | --generic         -  instructs script to build for generic architecture target"
  echo "  -h | --help            -  display this usage information"
  echo "  -x | --http-proxy URL  -  provides URL for the environment variable http_proxy"
  echo "  -y | --https-proxy URL -  provides URL for the environment variable https_proxy"
}

POSITIONAL_ARGS=()

while [[ $# -gt 0 ]]; do
  case $1 in
    -g|--generic)
      EASYBUILD_OPTARCH="GENERIC"
      shift
      ;;
    -h|--help)
      display_help  # Call your function
      # no shifting needed here, we're done.
      exit 0
      ;;
    -x|--http-proxy)
      export http_proxy="$2"
      shift 2
      ;;
    -y|--https-proxy)
      export https_proxy="$2"
      shift 2
      ;;
    -*|--*)
      echo "Error: Unknown option: $1" >&2
      exit 1
      ;;
    *)  # No more options
      POSITIONAL_ARGS+=("$1") # save positional arg
      shift
      ;;
  esac
done

set -- "${POSITIONAL_ARGS[@]}"

TOPDIR=$(dirname $(realpath $0))

source $TOPDIR/scripts/utils.sh

# honor $TMPDIR if it is already defined, use /tmp otherwise
if [ -z $TMPDIR ]; then
    export WORKDIR=/tmp/$USER
else
    export WORKDIR=$TMPDIR/$USER
fi

TMPDIR=$(mktemp -d)

echo ">> Setting up environment..."

source $TOPDIR/init/minimal_eessi_env

if [ -d $EESSI_CVMFS_REPO ]; then
    echo_green "$EESSI_CVMFS_REPO available, OK!"
else
    fatal_error "$EESSI_CVMFS_REPO is not available!"
fi

# make sure we're in Prefix environment by checking $SHELL
if [[ ${SHELL} = ${EPREFIX}/bin/bash ]]; then
    echo_green ">> It looks like we're in a Gentoo Prefix environment, good!"
else
    fatal_error "Not running in Gentoo Prefix environment, run '${EPREFIX}/startprefix' first!"
fi

# avoid that pyc files for EasyBuild are stored in EasyBuild installation directory
export PYTHONPYCACHEPREFIX=$TMPDIR/pycache

DETECTION_PARAMETERS=''
GENERIC=0
EB='eb'
if [[ "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
    echo_yellow ">> GENERIC build requested, taking appropriate measures!"
    DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
    GENERIC=1
    EB='eb --optarch=GENERIC'
fi

echo ">> Determining software subdirectory to use for current build host..."
if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
  export EESSI_SOFTWARE_SUBDIR_OVERRIDE=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
  echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
else
  echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
fi

# Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
# $EESSI_SILENT - don't print any messages
# $EESSI_BASIC_ENV - give a basic set of environment variables
EESSI_SILENT=1 EESSI_BASIC_ENV=1 source $TOPDIR/init/eessi_environment_variables

if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
    fatal_error "Failed to determine software subdirectory?!"
elif [[ "${EESSI_SOFTWARE_SUBDIR}" != "${EESSI_SOFTWARE_SUBDIR_OVERRIDE}" ]]; then
    fatal_error "Values for EESSI_SOFTWARE_SUBDIR_OVERRIDE (${EESSI_SOFTWARE_SUBDIR_OVERRIDE}) and EESSI_SOFTWARE_SUBDIR (${EESSI_SOFTWARE_SUBDIR}) differ!"
else
    echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
fi

echo ">> Initializing Lmod..."
source $EPREFIX/usr/share/Lmod/init/bash
ml_version_out=$TMPDIR/ml.out
ml --version &> $ml_version_out
if [[ $? -eq 0 ]]; then
    echo_green ">> Found Lmod ${LMOD_VERSION}"
else
    fatal_error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
fi

echo ">> Configuring EasyBuild..."
source $TOPDIR/configure_easybuild

echo ">> Setting up \$MODULEPATH..."
# make sure no modules are loaded
module --force purge
# ignore current $MODULEPATH entirely
module unuse $MODULEPATH
module use $EASYBUILD_INSTALLPATH/modules/all
if [[ -z ${MODULEPATH} ]]; then
    fatal_error "Failed to set up \$MODULEPATH?!"
else
    echo_green ">> MODULEPATH set up: ${MODULEPATH}"
fi

echo "EESSI_CVMFS_REPO=${EESSI_CVMFS_REPO}"

REQ_EB_VERSION='4.7.1'
echo "REQ_EB_VERSION=${REQ_EB_VERSION}"
module avail 2>&1 | grep -i easybuild

echo ">> Checking for EasyBuild module..."
ml_av_easybuild_out=$TMPDIR/ml_av_easybuild.out
module avail 2>&1 | grep -i easybuild/${REQ_EB_VERSION} &> ${ml_av_easybuild_out}
if [[ $? -eq 0 ]]; then
    echo_green ">> EasyBuild module found!"
else
    echo_yellow ">> No EasyBuild module yet, installing it..."

    EB_TMPDIR=${TMPDIR}/ebtmp
    echo ">> Temporary installation (in ${EB_TMPDIR})..."
    pip_install_out=${TMPDIR}/pip_install.out
    pip3 install --prefix $EB_TMPDIR easybuild &> ${pip_install_out}

    # keep track of original $PATH and $PYTHONPATH values, so we can restore them
    ORIG_PATH=$PATH
    ORIG_PYTHONPATH=$PYTHONPATH

    echo ">> Final installation in ${EASYBUILD_INSTALLPATH}..."
    export PATH=${EB_TMPDIR}/bin:$PATH
    export PYTHONPATH=$(ls -d ${EB_TMPDIR}/lib/python*/site-packages):$PYTHONPATH
    eb_install_out=${TMPDIR}/eb_install.out
    ok_msg="Latest EasyBuild release installed, let's go!"
    fail_msg="Installing latest EasyBuild release failed, that's not good... (output: ${eb_install_out})"
    eb --install-latest-eb-release &> ${eb_install_out}
    check_exit_code $? "${ok_msg}" "${fail_msg}"

    eb --search EasyBuild-${REQ_EB_VERSION}.eb | grep EasyBuild-${REQ_EB_VERSION}.eb > /dev/null
    if [[ $? -eq 0 ]]; then
        ok_msg="EasyBuild v${REQ_EB_VERSION} installed, alright!"
        fail_msg="Installing EasyBuild v${REQ_EB_VERSION}, yikes! (output: ${eb_install_out})"
        eb EasyBuild-${REQ_EB_VERSION}.eb >> ${eb_install_out} 2>&1
        check_exit_code $? "${ok_msg}" "${fail_msg}"
    fi

    # restore origin $PATH and $PYTHONPATH values
    export PATH=${ORIG_PATH}
    export PYTHONPATH=${ORIG_PYTHONPATH}

    module avail easybuild/${REQ_EB_VERSION} &> ${ml_av_easybuild_out}
    if [[ $? -eq 0 ]]; then
        echo_green ">> EasyBuild module installed!"
    else
        fatal_error "EasyBuild/${REQ_EB_VERSION} module failed to install?! (output of 'pip install' in ${pip_install_out}, output of 'eb' in ${eb_install_out}, output of 'ml av easybuild' in ${ml_av_easybuild_out})"
    fi
fi

echo ">> Loading EasyBuild module..."
module load EasyBuild/$REQ_EB_VERSION
eb_show_system_info_out=${TMPDIR}/eb_show_system_info.out
$EB --show-system-info > ${eb_show_system_info_out}
if [[ $? -eq 0 ]]; then
    echo_green ">> EasyBuild seems to be working!"
    $EB --version | grep "${REQ_EB_VERSION}"
    if [[ $? -eq 0 ]]; then
        echo_green "Found EasyBuild version ${REQ_EB_VERSION}, looking good!"
    else
        $EB --version
        fatal_error "Expected to find EasyBuild version ${REQ_EB_VERSION}, giving up here..."
    fi
    $EB --show-config
else
    cat ${eb_show_system_info_out}
    fatal_error "EasyBuild not working?!"
fi

echo_green "All set, let's start installing some software in ${EASYBUILD_INSTALLPATH}..."

# add OpenBLAS: requires special handling for GENERIC CPU targets
# If we're building OpenBLAS for GENERIC, we need https://github.com/easybuilders/easybuild-easyblocks/pull/1946
# we need to specify --parallel 1 or run into weird linking issues supposedly
# introduced by GNU make v4.4, see for example
# https://github.com/xianyi/OpenBLAS/issues/3899 and https://github.com/xianyi/OpenBLAS/issues/3979
# a fix may be provided with https://github.com/xianyi/OpenBLAS/pull/3983
# the fix did not work, so only option seems to be --parallel 1
# another option seems to be to use make v4.3 as build dependency
if [[ $GENERIC -eq 1 ]]; then
    echo ">> Installing OpenBLAS..."
    ok_msg="Done with OpenBLAS (GENERIC architecture)!"
    fail_msg="Installation of OpenBLAS (GENERIC architecture) failed!"
    echo_yellow ">> Using https://github.com/easybuilders/easybuild-easyblocks/pull/1946 to build generic OpenBLAS."
    $EB --include-easyblocks easyblocks/o/openblas-pr1946-cc74e45.py OpenBLAS-0.3.15-GCC-10.3.0.eb --robot
    check_exit_code $? "${ok_msg}" "${fail_msg}"
fi

eb_install_easystack_out=${TMPDIR}/eb_install_easystack.out
${EB:-eb} --robot --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental | tee ${eb_install_easystack_out}

echo ">> Creating/updating Lmod cache on $(date) (nr 1) ..."
export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"
if [ ! -f $LMOD_RC ]; then
    python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH}
    check_exit_code $? "$LMOD_RC created" "Failed to create $LMOD_RC"
fi

$TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH}

$TOPDIR/check_missing_installations.sh

# TODO do not clean up by default (or provide a cmd line arg and when run
# from bot, do not clean up)
echo ">> Cleaning up ${TMPDIR}..."
rm -r ${TMPDIR}

exit 0