Run command in container of firedrake or firedrake-complex

firedrake-run

#!/bin/bash

set -e

TOOL=${TOOL:-docker}  # Set TOOL to 'docker' by default. Change it to 'podman' if needed.

BASE_IMAGE=${BASE_IMAGE:-firedrakeproject/firedrake}
RUN_ARGS=${RUN_ARGS:---rm}

if [[ "$TOOL" == "docker" ]]; then
    BUILD_ARGS="${BUILD_ARGS:---network=host}"
elif [[ "$TOOL" == "podman" ]]; then
    BUILD_ARGS="${BUILD_ARGS} --format docker"  # Use Docker format for Podman
else
    echo "Error: TOOL must be set to either 'docker' or 'podman'."
    exit 1
fi

usage() {
    PROG=$(basename "$0")
    echo
    echo "Usage: $PROG command [args...]"
    echo "Run a command inside the Firedrake container."
    echo
    echo "Examples (Scalar type: real):"
    echo "  $PROG python my-python-file.py"
    echo "  $PROG mpiexec -n 16 python my-python-file.py"
    echo
    echo "To use Podman instead of Docker:"
    echo "  TOOL=podman $PROG python my-python-file.py"
    echo "  TOOL=podman $PROG mpiexec -n 16 python my-python-file.py"
    echo
    echo "Run command with debug messages enabled:"
    echo "  DEBUG=Y $PROG python my-python-file.py"
    echo
    echo "Force a rebuild of the container image:"
    echo "  FORCE_BUILD=Y $PROG"
    echo
    if [[ "$TOOL" == "docker" ]]; then
        echo "Customize build arguments for '$TOOL build' (Default: '--network=host'):"
        echo "  FORCE_BUILD=Y BUILD_ARGS=\"--no-cache --network=host\" $PROG"
    else
        echo "Customize build arguments for '$TOOL build':"
        echo "  TOOL=podman FORCE_BUILD=Y BUILD_ARGS=\"--no-cache\" $PROG"
    fi
    echo
    echo "Example for complex scalar type:"
    echo "  BASE_IMAGE=firedrakeproject/firedrake-complex $PROG python my-python-file.py"
    echo
    exit 1
}

if [[ "x$1" =~ x-h|x--help ]]; then
    usage
fi

is_true () {
    _VAL=$(echo "${1:-N}" | tr '[:upper:]' '[:lower:]')
    [[ ${_VAL} =~ [1-9]|t|true|y|yes|on ]] && return 0  # true
    return 1  # false
}

print_msg () {
    MSG=$1
    TERM_WIDTH=${TERM_WIDTH:-$(tput cols)}
    PADDING_WIDTH=$(( (${TERM_WIDTH} - 2 - ${#MSG})/2 ))
    PADDING=$(for i in $(seq 1 ${PADDING_WIDTH}); do echo -n =; done)
    echo "$PADDING $MSG $PADDING"$([ $(( ${#MSG}%2 )) == 1 ]  && echo -n = || echo -n "")
}

TERM_WIDTH=80
FORCE_BUILD=$( is_true ${FORCE_BUILD} && echo Y || echo N)
DEBUG=$( is_true ${DEBUG:-$FORCE_BUILD} && echo "" || echo ":" )

${DEBUG} print_msg "DEBUG VARS BEGIN"
${DEBUG} echo -e "VARs:\n\tDEBUG: \"${DEBUG:-Y}\"\n\tFORCE_BUILD: \"$FORCE_BUILD\""
${DEBUG} print_msg "DEBUG VARS END"

if [[ "x$FDUTILS_COMMIT" != "x" ]]; then
    CHECKOUT_COMMIT="&& git checkout $FDUTILS_COMMIT"
fi

create_dockerfile () {
    _BASE_IMAGE=$1
    _DOCKERFILE=$2
    cat <<EOF > $_DOCKERFILE
FROM $_BASE_IMAGE

USER root
RUN echo -e "[safe]\n\tdirectory = *\n" >> /etc/gitconfig

USER firedrake
WORKDIR /home/firedrake

RUN bash -c ". /home/firedrake/firedrake/bin/activate && \\
    pip install pqdm gmsh siphash24 && \\
    git clone https://github.com/lrtfm/fdutils.git && \\
    cd fdutils $CHECKOUT_COMMIT && make develop"

RUN bash -c "sed -i.bak -e 's/^.*simplefilter.*$//g' firedrake/src/firedrake/firedrake/checkpointing.py"
EOF

    ${DEBUG} print_msg "THE DOCKER FILE BEGIN"
    ${DEBUG} cat $_DOCKERFILE
    ${DEBUG} print_msg "THE DOCKER FILE END"
}

if [[ "x$IMAGE" == "x" ]]; then
    BASE_NAME_NOTAG=${BASE_IMAGE//:*/}
    IMAGE_NAME=${BASE_NAME_NOTAG//*\//}-$(id -u -n)

    if ! ${TOOL} image inspect $BASE_IMAGE > /dev/null 2>&1; then
        ${TOOL} pull $BASE_IMAGE
    fi

    DATE_TAG=$(${TOOL} inspect -f '{{ .Created }}' $BASE_IMAGE | sed -E -e 's/(T| ).*//' -e 's/-//g')

    if ! ${TOOL} image inspect $IMAGE_NAME:$DATE_TAG > /dev/null 2>&1; then
        TARGET_EXIST="N"
    else
        TARGET_EXIST="Y"
    fi

    if [[ "$TARGET_EXIST" == "N" || "$FORCE_BUILD" == "Y" ]]; then
        TEMP_DOCKERFILE=$(mktemp .Dockerfile.XXXXXXXXXXXXXXXX)
        trap 'rm -f -- "$TEMP_DOCKERFILE"' EXIT
        create_dockerfile $BASE_IMAGE $TEMP_DOCKERFILE

        if [[ "$TARGET_EXIST" == "Y" ]]; then
            ${TOOL} tag $IMAGE_NAME:$DATE_TAG $IMAGE_NAME:$DATE_TAG-bak-$(date +%Y%m%d-%H%M%S)
        fi

        ${DEBUG} print_msg "BUILD BEGIN"
        echo "${TOOL} build $BUILD_ARGS -t $IMAGE_NAME:$DATE_TAG -f $TEMP_DOCKERFILE ."
        ${TOOL} build $BUILD_ARGS -t $IMAGE_NAME:$DATE_TAG -f $TEMP_DOCKERFILE .
        ${DEBUG} print_msg "BUILD END"
    fi
    IMAGE=$IMAGE_NAME:$DATE_TAG
fi

FD_INFO=$(${TOOL} run --rm $IMAGE bash -c 'echo $(id -u)\;$(id -g -n)\;$HOME\;$PATH\;')
IFS=';' read -r FD_UID FD_GNAME FD_HOME FD_PATH <<< "$FD_INFO"
[[ $(id -u) != ${FD_UID} ]] && FD_HOME=/work
FD_ENV=/home/firedrake/firedrake
FD_PATH=${FD_ENV}/bin:${FD_PATH}
SET_USER=${SET_USER:-$(id -u):$(id -g)}
ADD_GROUP=${ADD_GROUP:-$FD_GNAME}

${DEBUG} print_msg "THE CMD BEGIN"
${DEBUG} echo -ne "IMAGE:\n\t"; ${DEBUG} echo "$IMAGE"
${DEBUG} echo -ne "COMMAND:\n\t\x60"; ${DEBUG} echo -n "$@"; ${DEBUG} echo -e "\x27"
${DEBUG} echo -ne "HOME:\n\t"; ${DEBUG} echo "$FD_HOME"
${DEBUG} echo -ne "PATH:\n\t"; ${DEBUG} echo "$FD_PATH"
${DEBUG} echo -ne "SET_USER:\n\t"; ${DEBUG} echo "$SET_USER"
${DEBUG} echo -ne "ADD_GROUP:\n\t"; ${DEBUG} echo "$ADD_GROUP"
${DEBUG} print_msg "THE CMD END"

if [[ $# -eq 0 ]]; then
    usage
fi

if [[ "$TOOL" == "docker" ]]; then
    PERMISSION_ARGS="-u ${SET_USER} --group-add ${ADD_GROUP}"
elif [[ "$TOOL" == "podman" ]]; then
    PERMISSION_ARGS="--security-opt label=disable --userns keep-id:uid=1000,gid=1000"
fi

${TOOL} run ${RUN_ARGS} ${PERMISSION_ARGS} \
    -ti -v $(pwd):/work -w /work \
    -e HOME=${FD_HOME} \
    -e PATH=${FD_PATH} \
    -e VIRTUAL_ENV=${FD_ENV} \
    -e PYOP2_CACHE_DIR=/work/.cache \
    -e FIREDRAKE_TSFC_KERNEL_CACHE_DIR=/work/.cache \
    $IMAGE \
    "$@"

This aims to address inconsistent permission issues of the shared folders in the Firedrake container.

1. Download the script

   curl -O https://gist.githubusercontent.com/lrtfm/93d55c6d8d5bc92d2c7551dd0048fd4f/raw/firedrake-run
   

2. Add exec permission

   chmod +x firedrake-run
   

3. Now, you can run firedrake script

   ./firedrake-run python my-script.py