Run command in container of firedrake or firedrake-complex

firedrake-run

#!/bin/bash

set -e

if [[ $# -eq 0 || x$1 =~ x-h|x--help ]]; then
    PROG=$(basename $0)
    echo ""
    echo "Usage: $PROG command [args...]"
    echo "Run command in docker container of firedrake."
    echo ""
    echo "Examples (Scalar type: real):"
    echo ""
    echo "    $PROG python my-python-file.py"
    echo "    $PROG mpiexec -n 16 python my-python-file.py"
    echo ""
    echo "Examples (Scalar type: complex):"
    echo ""
    echo "    BASE_IMAGE=firedrakeproject/firedrake-complex $PROG python my-python-file.py"
    echo ""
    exit 1
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 git clone https://github.com/lrtfm/fdutils.git
RUN bash -c ". /home/firedrake/firedrake/bin/activate && pip install pqdm gmsh"
RUN bash -c ". /home/firedrake/firedrake/bin/activate && 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$IMAGE" == "x" ]]; then
    BASE_IMAGE=${BASE_IMAGE:-firedrakeproject/firedrake}
    BASE_NAME_NOTAG=${BASE_IMAGE//:*/}
    IMAGE_NAME=${BASE_NAME_NOTAG//*\//}-$(id -u -n)
    DATE_TAG=$(docker image ls --format "{{ .Tag }}" $IMAGE_NAME | sort -r | head -n1)
    if [[ "x$DATE_TAG" == "x" || "$FORCE_BUILD" == "Y" ]]; then
        TEMP_DOCKERFILE=$(mktemp .Dockerfile.XXXXXXXXXXXXXXXX)
        trap 'rm -f -- "$TEMP_DOCKERFILE"' EXIT
        create_dockerfile $BASE_IMAGE $TEMP_DOCKERFILE

        if ! docker image inspect $BASE_IMAGE > /dev/null 2>&1; then
            docker pull $BASE_IMAGE
        fi
        NEW_DATE_TAG=$(docker inspect -f '{{ .Created }}' $BASE_IMAGE | sed -e 's/T.*//' -e 's/-//g')
        if [[ "x$NEW_DATE_TAG" == "x$DATE_TAG" ]]; then
            docker tag $IMAGE_NAME:$DATE_TAG $IMAGE_NAME:$DATE_TAG-bak-$(date +%Y%m%d-%H%M%S)
        else
            DATE_TAG=$NEW_DATE_TAG
        fi
        docker build $BUILD_ARGS -t $IMAGE_NAME:$DATE_TAG -f $TEMP_DOCKERFILE .
    fi
    IMAGE=$IMAGE_NAME:$DATE_TAG
fi

FD_INFO=$(docker 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"

docker run --rm -ti -v $(pwd):/work -w /work \
    -u ${SET_USER} --group-add ${ADD_GROUP} \
    -e HOME=${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