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 "  --build-logs-dir       -  location to copy EasyBuild logs to for failed builds"
  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"
  echo "  --shared-fs-path       -  path to directory on shared filesystem that can be used"
}

function copy_build_log() {
    # copy specified build log to specified directory, with some context added
    build_log=${1}
    build_logs_dir=${2}

    # also copy to build logs directory, if specified
    if [ ! -z "${build_logs_dir}" ]; then
        log_filename="$(basename ${build_log})"
        if [ ! -z "${SLURM_JOB_ID}" ]; then
            # use subdirectory for build log in context of a Slurm job
            build_log_path="${build_logs_dir}/jobs/${SLURM_JOB_ID}/${log_filename}"
        else
            build_log_path="${build_logs_dir}/non-jobs/${log_filename}"
        fi
        mkdir -p $(dirname ${build_log_path})
        cp -a ${build_log} ${build_log_path}
        chmod 0644 ${build_log_path}

        # add context to end of copied log file
        echo >> ${build_log_path}
        echo "Context from which build log was copied:" >> ${build_log_path}
        echo "- original path of build log: ${build_log}" >> ${build_log_path}
        echo "- working directory: ${PWD}" >> ${build_log_path}
        echo "- Slurm job ID: ${SLURM_OUT}" >> ${build_log_path}
        echo "- EasyBuild version: ${eb_version}" >> ${build_log_path}
        echo "- easystack file: ${easystack_file}" >> ${build_log_path}

        echo "EasyBuild log file ${build_log} copied to ${build_log_path} (with context appended)"
    fi
}

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="$2"
      shift 2
      ;;
    --build-logs-dir)
      export build_logs_dir="${2}"
      shift 2
      ;;
    --shared-fs-path)
      export shared_fs_path="${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

if [ ! -z "${shared_fs_path}" ]; then
    shared_eb_sourcepath=${shared_fs_path}/easybuild/sources
    echo ">> Using ${shared_eb_sourcepath} as shared EasyBuild source path"
    export EASYBUILD_SOURCEPATH=${shared_eb_sourcepath}:${EASYBUILD_SOURCEPATH}
fi

${EB} --show-config

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

# assume there's only one diff file that corresponds to the PR patch file
pr_diff=$(ls [0-9]*.diff | head -1)

# use PR patch file to determine in which easystack files stuff was added
for easystack_file in $(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eessi.*yml$' | egrep -v 'known-issues|missing'); do

    echo -e "Processing easystack file ${easystack_file}...\n\n"

    # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file
    eb_version=$(echo ${easystack_file} | sed 's/.*eb-\([0-9.]*\).*/\1/g')

    # load EasyBuild module (will be installed if it's not available yet)
    source ${TOPDIR}/load_easybuild_module.sh ${eb_version}

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

    if [ -f ${easystack_file} ]; then
        echo_green "Feeding easystack file ${easystack_file} to EasyBuild..."

        ${EB} --easystack ${TOPDIR}/${easystack_file} --robot
        ec=$?

        # copy EasyBuild log file if EasyBuild exited with an error
        if [ ${ec} -ne 0 ]; then
            eb_last_log=$(unset EB_VERBOSE; eb --last-log)
            # copy to current working directory
            cp -a ${eb_last_log} .
            echo "Last EasyBuild log file copied from ${eb_last_log} to ${PWD}"
            # copy to build logs dir (with context added)
            copy_build_log "${eb_last_log}" "${build_logs_dir}"
        fi

        $TOPDIR/check_missing_installations.sh ${TOPDIR}/${easystack_file}
    else
        fatal_error "Easystack file ${easystack_file} not found!"
    fi

done

### add packages here

echo ">> Creating/updating Lmod cache..."
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}

echo ">> Cleaning up ${TMPDIR}..."
rm -r ${TMPDIR}