container2module

#!/bin/bash
# Pull a container and install it as a module through EasyBuild
# Requirements:
#     skopeo - inspect container label without pulling
#     jq     - parse json
#
# Ruoshi Sun
# 2021-03-23 central container dir
# 2020-07-04

if [[ $# -lt 4 || $# -gt 5 ]]; then
    echo "Usage: `basename $0` URI_prefix user app tag [version]"
    echo "             URI_prefix = docker|library|shub|etc."
    echo "                   user = username of repository (if empty, put \"\")"
    echo "                    app = name of repository"
    echo "                    tag = tag of repository"
    echo "                version = Rivanna module version (default: tag)"
    echo
    echo "Pull command:"
    echo "apptainer pull app-version.sif URI_prefix://[user/]app:tag"
    exit 1
fi

# parse input
URI_PREFIX=$1
USER=$2
APP=$3
TAG=$4
[ $# -eq 4 ] && VERSION=$TAG || VERSION=$5

APPTAINER_VERSION=3.7.1
SKOPEO_VERSION=1.13.1

module purge

# constants
HERE=`pwd`

# functions
function exit_if_error {
    echo "+ $1"
    eval $1
    if [ $? -ne 0 ]; then
        echo "Error: $2"
        exit 1
    fi
}

function print_stage {
    echo -e "\033[1;34m==> $1\033[0m"
}

# URI
[ -z "$USER" ] && URI="${URI_PREFIX}://${APP}:${TAG}" || URI="${URI_PREFIX}://${USER}/${APP}:${TAG}"

# apptainer
SIF=${APP}-${VERSION}.sif
module load apptainer/$APPTAINER_VERSION easybuild

# check sources
print_stage "Checking sources"
cd $EASYBUILD_SOURCEPATH
SRCDIR=${APP::1}/${APP}
[ -d $SRCDIR ] || {
    print_stage "Creating directory $EASYBUILD_SOURCEPATH/$SRCDIR"
    mkdir -p $SRCDIR
}

cd $SRCDIR
if [ -e $SIF ]; then
    read -p "$SIF already exists. Overwrite? [y/N]" yn
    if [[ $yn =~ ^[Yy]$ ]]; then
        rm $SIF
    else
        SKIP_PULL=true
    fi
    EB_FORCE=true # Module may already exist. Set "eb -f"
fi

# check if container exists and store labels
print_stage "Checking URI"
module load skopeo >/dev/null 2>&1

INSPECT=$($CONTAINERDIR/skopeo-${SKOPEO_VERSION}.sif inspect $URI)
if [ $? -ne 0 ]; then
    echo "container $URI does not exist"
    exit 1
fi

module unload skopeo

# pull container as sif
if [ "$SKIP_PULL" = true ]; then
    print_stage "Pulling container [skipped]"
else
    print_stage "Pulling container"
    exit_if_error "apptainer pull $SIF $URI" "failed to pull container"
fi

module unload apptainer

# parse labels
print_stage "Parsing labels"
module load jq

declare -A LABEL
for i in homepage description moduleclass gpu; do
    LABEL[$i]=$(echo "$INSPECT" | jq -r ".Labels.$i")
done

module unload jq

# write easyconfig
EB=${APP}-${VERSION}-apptainer-${APPTAINER_VERSION}.eb 

print_stage "Writing easyconfig $HERE/$EB"
cd $HERE

DATE=$(date +%Y-%m-%d)
EB_HEADER="# $DATE generated by container2module script (Ruoshi Sun)"

[ "${LABEL[gpu]}" = true ] && USE_GPU="True" || USE_GPU="False"

cat >$EB <<EOF
$EB_HEADER

easyblock = 'EB_ApptainerImage'

name = '$APP'
version = '$VERSION'

homepage = '${LABEL[homepage]}'
description = """
${LABEL[description]}
"""

toolchain = {'name': 'apptainer', 'version': '$APPTAINER_VERSION'}

sources = ['%(name)s-%(version)s.sif']

use_gpu = $USE_GPU

skipsteps = ['sanitycheck']
EOF

if [ "$USE_GPU" = "True" ]; then
    cat >>$EB <<EOF
modluafooter = 'add_property("arch","gpu")'
EOF
fi

cat >>$EB <<EOF
moduleclass = '${LABEL[moduleclass]}'
EOF

cat $EB
echo
echo "Run: eb $EB"

## CONTAINERDIR set to None in .lua. Don't know why.
#echo "Inspect the above easyconfig."
#read -rsn1 -p "Press any key to start EasyBuild installation"
#echo
#
## EasyBuild installation
#print_stage "EasyBuild"
#if [ "$EB_FORCE" = true ]; then 
#    exit_if_error "eb $EB -f" "EasyBuild installation failed"
#else 
#    exit_if_error "eb $EB" "EasyBuild installation failed"
#fi
#
#echo
#echo -n "Done! "
#if command -v xxd &> /dev/null; then
#    echo "0000000: f09f 8e89 0a" | xxd -r
#else
#    echo
#fi