source/eic-shell/install.sh

0001 #!/bin/bash
0002
0003 ## Simple setup script that installs the container
0004 ## in your local environment under $PREFIX/local/lib
0005 ## and creates a simple top-level launcher script
0006 ## that launches the container for this working directory
0007 ## with the $EIC_SHELL_PREFIX variable pointing
0008 ## to the $PREFIX/local directory
0009
0010 ORGANIZATION="eicweb"
0011 CONTAINER="eic_xl"
0012 VERSION="nightly"
0013 PREFIX="$PWD"
0014
0015 function print_the_help {
0016   echo "USAGE:  ./install.sh [-p PREFIX] [-v VERSION]"
0017   echo "OPTIONAL ARGUMENTS:"
0018   echo "          -p,--prefix        Working directory to deploy the environment (D: $PREFIX)"
0019   echo "          -t,--tmpdir        Change tmp directory (D: $([[ -z "$TMPDIR" ]] && echo "/tmp" || echo "$TMPDIR"))"
0020   echo "          -n,--no-cvmfs      Disable check for local CVMFS (D: enabled)"
0021   echo "          -o,--organization  Organization (D: $ORGANIZATION) (requires cvmfs)"
0022   echo "          -c,--container     Container family (D: $CONTAINER)"
0023   echo "          -v,--version       Version to install (D: $VERSION)"
0024   echo "          -h,--help          Print this message"
0025   echo ""
0026   echo "  Set up containerized development environment."
0027   echo ""
0028   echo "EXAMPLE: ./install.sh"
0029   exit
0030 }
0031
0032 while [ $# -gt 0 ]; do
0033   key=$1
0034   case $key in
0035     -p|--prefix)
0036       PREFIX=$(realpath ${2?Missing argument. Use --help for more info.})
0037       shift
0038       shift
0039       ;;
0040     -t|--tmpdir)
0041       export TMPDIR=${2?Missing argument. Use --help for more info.}
0042       export APPTAINER_TMPDIR=${2?Missing argument. Use --help for more info.}
0043       export SINGULARITY_TMPDIR=${2?Missing argument. Use --help for more info.}
0044       shift
0045       shift
0046       ;;
0047     -n|--no-cvmfs)
0048       DISABLE_CVMFS_USAGE=true
0049       shift
0050       ;;
0051     -c|--container)
0052       CONTAINER=${2?Missing argument. Use --help for more info.}
0053       shift
0054       shift
0055       ;;
0056     -v|--version)
0057       VERSION=${2?Missing argument. Use --help for more info.}
0058       shift
0059       shift
0060       ;;
0061     -h|--help)
0062       print_the_help
0063       exit 0
0064       ;;
0065     *)
0066       echo "ERROR: unknown argument: $key"
0067       echo "use --help for more info"
0068       exit 1
0069       ;;
0070   esac
0071 done
0072
0073 ## create prefix if needed
0074 mkdir -p $PREFIX || exit 1
0075 pushd $PREFIX
0076
0077 if [ ! -d $PREFIX ]; then
0078   echo "ERROR: not a valid directory: $PREFIX"
0079   echo "use --help for more info"
0080   exit 1
0081 fi
0082
0083 echo "Setting up development environment for eicweb/$CONTAINER:$VERSION"
0084
0085 mkdir -p $PREFIX/local/lib || exit 1
0086
0087 function install_singularity() {
0088   SINGULARITY=
0089   ## check for an apptainer install
0090   ## default to apptainer if found
0091   if [ $(type -P apptainer ) ]; then
0092     SINGULARITY=$(which apptainer)
0093     SINGULARITY_VERSION=`$SINGULARITY --version`
0094   fi
0095   if [ -z "$SINGULARITY" ]; then
0096     ## check for a singularity install
0097     ## default to singularity if new enough
0098     if [ $(type -P singularity ) ]; then
0099       SINGULARITY=$(which singularity)
0100       SINGULARITY_VERSION=$($SINGULARITY --version)
0101       if [ ${SINGULARITY_VERSION:0:1} = 2 ]; then
0102         ## too old, look for something else
0103         SINGULARITY=
0104       fi
0105     fi
0106   fi
0107   if [ -z "$SINGULARITY" ]; then
0108     ## first priority: a known good install (this one is on JLAB)
0109     if [ -d "/apps/singularity/3.7.1/bin/" ]; then
0110       SINGULARITY="/apps/singularity/3.7.1/bin/singularity"
0111     ## whatever is in the path is next
0112     elif [ $(type -P singularity ) ]; then
0113       SINGULARITY=$(which singularity)
0114     ## cvmfs apptainer is last resort (sandbox mode can cause issues)
0115     elif [ -f "/cvmfs/oasis.opensciencegrid.org/mis/apptainer/bin/apptainer" ]; then
0116       SINGULARITY="/cvmfs/oasis.opensciencegrid.org/mis/apptainer/bin/apptainer"
0117     ## cvmfs singularity is last resort (sandbox mode can cause issues)
0118     elif [ -f "/cvmfs/oasis.opensciencegrid.org/mis/singularity/bin/singularity" ]; then
0119       SINGULARITY="/cvmfs/oasis.opensciencegrid.org/mis/singularity/bin/singularity"
0120     ## not good...
0121     else
0122       echo "ERROR: no apptainer or singularity found, please make sure you have apptainer or singularity in your \$PATH"
0123       exit 1
0124     fi
0125   fi
0126   echo " - Found apptainer/singularity at $SINGULARITY"
0127
0128   ## get singularity version
0129   ## we only care if is 2.x or not, so we can use singularity --version
0130   ## which returns 2.xxxxx for version 2
0131   SINGULARITY_VERSION=`$SINGULARITY --version`
0132   SIF=
0133   if [ ${SINGULARITY_VERSION:0:1} = 2 ]; then
0134     SIF="$PREFIX/local/lib/${CONTAINER}-${VERSION}.simg"
0135
0136     echo "WARNING: your singularity version $SINGULARITY_VERSION is ancient, we strongly recommend using version 3.x"
0137     echo "We will attempt to use a fall-back SIMG image to be used with this singularity version"
0138     if [ -f /gpfs02/eic/athena/${CONTAINER}-${VERSION}.simg ]; then
0139       ln -sf /gpfs02/eic/athena/${CONTAINER}-${VERSION}.simg ${SIF}
0140     else
0141       echo "Attempting last-resort singularity pull for old image"
0142       echo "This may take a few minutes..."
0143       INSIF=`basename ${SIF}`
0144       singularity pull --name "${INSIF}" docker://eicweb/$CONTAINER:$VERSION
0145       mv ${INSIF} $SIF
0146       chmod +x ${SIF}
0147       unset INSIF
0148     fi
0149   ## we are in sane territory, yay!
0150   else
0151     ## check if we can just use cvmfs for the image
0152     SIF="$PREFIX/local/lib/${CONTAINER}-${VERSION}.sif"
0153     if [ -z "$DISABLE_CVMFS_USAGE" -a -d /cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION} ]; then
0154       SIF="$PREFIX/local/lib/${CONTAINER}-${VERSION}"
0155       ## need to cleanup in this case, else it will try to make a subdirectory
0156       rm -rf ${SIF}
0157       ln -sf /cvmfs/singularity.opensciencegrid.org/${ORGANIZATION}/${CONTAINER}:${VERSION} ${SIF}
0158     elif [ -f /cvmfs/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ]; then
0159       ln -sf /cvmfs/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ${SIF}
0160     elif [ -f /gpfs02/cvmfst0/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ]; then
0161       ln -sf /gpfs02/cvmfst0/eic.opensciencegrid.org/singularity/athena/${CONTAINER}_v${VERSION}.sif ${SIF}
0162     ## check if we have an internal CI image we will use for testing purposes
0163     elif [ -f $PWD/.gitlab-ci/${CONTAINER}-${VERSION}.sif ]; then
0164       ln -sf $PWD/.gitlab-ci/${CONTAINER}-${VERSION}.sif ${SIF}
0165     ## if not, download the container to the system
0166     else
0167       ## get the python installer and run the old-style install
0168       ## work in temp directory
0169       tmp_dir=$(mktemp -d -t ci-XXXXXXXXXX)
0170       pushd $tmp_dir
0171       wget https://eic.github.io/eic-shell/install.py
0172       chmod +x install.py
0173       ./install.py -f -c $CONTAINER -v $VERSION .
0174       INSIF=lib/`basename ${SIF}`
0175       mv $INSIF $SIF
0176       chmod +x ${SIF}
0177       ## cleanup
0178       popd
0179       rm -rf $tmp_dir
0180       unset INSIF
0181     fi
0182   fi
0183
0184   echo $SIF
0185   ls $SIF 2>&1 > /dev/null && GOOD_SIF=1
0186   if [ -z "$SIF" -o -z "$GOOD_SIF" ]; then
0187     echo "ERROR: no singularity image found"
0188     exit 1
0189   else
0190     echo " - Deployed ${CONTAINER} image: $SIF"
0191   fi
0192
0193   ## We want to make sure the root directory of the install directory
0194   ## is always bound. We also check for the existence of a few standard
0195   ## locations (/scratch /volatile /cache) and bind those too if found
0196   echo " - Determining additional bind paths"
0197   BINDPATH=$(echo ${SINGULARITY_BINDPATH},${APPTAINER_BINDPATH} | tr ',' '\n' | sort -u | tr '\n' ',' | sed 's/^,//;s/,$//')
0198   echo "   --> system bindpath: $BINDPATH"
0199   PREFIX_ROOT="/$(realpath $PREFIX | cut -d "/" -f2)"
0200   for dir in /w /work /media /scratch /volatile /cache /cvmfs /gpfs /gpfs01 /gpfs02 $PREFIX_ROOT; do
0201     ## only add directories once (match full path entries in comma-separated BINDPATH)
0202     if [[ ",$BINDPATH," == *,"$dir",* ]]; then
0203       continue
0204     fi
0205     if [ -d $dir ]; then
0206       echo "   --> $dir"
0207       BINDPATH=${dir}${BINDPATH:+,$BINDPATH}
0208     fi
0209   done
0210
0211   ## create a new top-level eic-shell launcher script
0212   ## that sets the EIC_SHELL_PREFIX and then starts apptainer/singularity
0213 cat << EOF > eic-shell
0214 #!/bin/bash
0215
0216 ## capture environment setup for upgrades
0217 ORGANIZATION=$ORGANIZATION
0218 CONTAINER=$CONTAINER
0219 TMPDIR=$TMPDIR
0220 VERSION=$VERSION
0221 PREFIX=$PREFIX
0222 DISABLE_CVMFS_USAGE=${DISABLE_CVMFS_USAGE}
0223
0224 function print_the_help {
0225   echo "USAGE:  ./eic-shell [OPTIONS] [ -- COMMAND ]"
0226   echo "OPTIONAL ARGUMENTS:"
0227   echo "          -u,--upgrade       Upgrade the container to the latest version"
0228   echo "          -n,--no-cvmfs      Disable check for local CVMFS when updating. (D: enabled)"
0229   echo "          -o,--organization  Organization (D: \$ORGANIZATION) (requires cvmfs)"
0230   echo "          -c,--container     Container family (D: \$CONTAINER) (requires cvmfs)"
0231   echo "          -v,--version       Version to install (D: \$VERSION) (requires cvmfs)"
0232   echo "          -h,--help          Print this message"
0233   echo ""
0234   echo "  Start the eic-shell containerized software environment (Apptainer/Singularity version)."
0235   echo ""
0236   echo "ENVIRONMENT VARIABLES:"
0237   echo "          SINGULARITY        Path to the singularity executable (D: detected during installation)"
0238   echo "          SINGULARITY_OPTIONS  Additional options to pass to singularity exec (D: none)"
0239   echo ""
0240   echo "EXAMPLES: "
0241   echo "  - Start an interactive shell: ./eic-shell"
0242   echo "  - Upgrade the container:      ./eic-shell --upgrade"
0243   echo "  - Use different version:      ./eic-shell --version \$(date +%y.%m).0-stable"
0244   echo "  - Execute a single command:   ./eic-shell -- <COMMAND>"
0245   echo "  - Use custom singularity:     SINGULARITY=/path/to/singularity ./eic-shell"
0246   echo "  - Pass singularity options:   SINGULARITY_OPTIONS='--nv' ./eic-shell"
0247   echo ""
0248   exit
0249 }
0250
0251 UPGRADE=
0252
0253 while [ \$# -gt 0 ]; do
0254   key=\$1
0255   case \$key in
0256     -u|--upgrade)
0257       UPGRADE=1
0258       shift
0259       ;;
0260     -n|--no-cvmfs)
0261       DISABLE_CVMFS_USAGE=true
0262       shift
0263       ;;
0264     -c|--container)
0265       CONTAINER=\${2?Missing argument. Use --help for more info.}
0266       export SIF=/cvmfs/singularity.opensciencegrid.org/\${ORGANIZATION}/\${CONTAINER}:\${VERSION}
0267       shift
0268       shift
0269       ;;
0270     -v|--version)
0271       VERSION=\${2?Missing argument. Use --help for more info.}
0272       export SIF=/cvmfs/singularity.opensciencegrid.org/\${ORGANIZATION}/\${CONTAINER}:\${VERSION}
0273       shift
0274       shift
0275       ;;
0276     -h|--help)
0277       print_the_help
0278       exit 0
0279       ;;
0280     --)
0281       shift
0282       break
0283       ;;
0284     *)
0285       echo "ERROR: unknown argument: \$key"
0286       echo "use --help for more info"
0287       exit 1
0288       ;;
0289   esac
0290 done
0291
0292 if [ ! -z \${UPGRADE} ]; then
0293   echo "Upgrading eic-shell..."
0294   if [ -z "\$DISABLE_CVMFS_USAGE" -a -d /cvmfs/singularity.opensciencegrid.org/\${ORGANIZATION}/\${CONTAINER}:\${VERSION} ]; then
0295     echo ""
0296     echo "Note: You cannot manually update the container as you are using the CVMFS version."
0297     echo "      The container will automatically update every 24 hours."
0298     echo "      You can override this by setting the '--no-cvmfs' flag, which will"
0299     echo "      instantiate a local version."
0300     echo "      This is only recommended for expert usage."
0301     echo ""
0302     echo "This will only upgrade the eic-shell script itself."
0303     echo ""
0304   fi
0305   FLAGS="-p \${PREFIX} -v \${VERSION}"
0306   if [ ! -z \${TMPDIR} ]; then
0307     FLAGS="\${FLAGS} -t \${TMPDIR}"
0308   fi
0309   if [ ! -z \${DISABLE_CVMFS_USAGE} ]; then
0310     FLAGS="\${FLAGS} --no-cvmfs"
0311   fi
0312   curl -L https://github.com/eic/eic-shell/raw/main/install.sh \
0313     | bash -s -- \${FLAGS}
0314   echo "eic-shell upgrade sucessful"
0315   exit 0
0316 fi
0317
0318 export EIC_SHELL_PREFIX=$PREFIX/local
0319 export APPTAINER_BINDPATH=$BINDPATH
0320 export SINGULARITY_BINDPATH=$BINDPATH
0321 \${SINGULARITY:-$SINGULARITY} exec \${SINGULARITY_OPTIONS:-} \${SIF:-$SIF} eic-shell \$@
0322 EOF
0323
0324   chmod +x eic-shell
0325
0326   echo " - Created custom eic-shell excecutable"
0327 }
0328
0329 function install_docker() {
0330   ## check for docker install
0331   DOCKER=$(which docker)
0332   if [ -z ${DOCKER} ]; then
0333     echo "ERROR: no docker install found, docker is required for the docker-based install"
0334   fi
0335   echo " - Found docker at ${DOCKER}"
0336
0337   IMG=eicweb/${CONTAINER}:${VERSION}
0338   docker pull ${IMG}
0339   echo " - Deployed ${CONTAINER} image: ${IMG}"
0340
0341   ## We want to make sure the root directory of the install directory
0342   ## is always bound. We also check for the existence of a few standard
0343   ## locations (/Volumes /Users /tmp) and bind those too if found
0344   echo " - Determining mount paths"
0345   PREFIX_ROOT="/$(realpath $PREFIX | cut -d "/" -f2)"
0346   MOUNT=""
0347   echo "   --> $PREFIX_ROOT"
0348   for dir in /Volumes /Users /tmp; do
0349     ## only add directories once
0350     if [[ ${MOUNT} =~ $(basename $dir) ]]; then
0351       continue
0352     fi
0353     if [ -d $dir ]; then
0354       echo "   --> $dir"
0355       MOUNT="$MOUNT -v $dir:$dir"
0356     fi
0357   done
0358   echo " - Docker mount directive: '$MOUNT'"
0359   PLATFORM_FLAG=''
0360   if [ `uname -m` = 'arm64' ]; then
0361     PLATFORM_FLAG='--platform linux/amd64'
0362     echo " - Additional platform flag to run on arm64"
0363   fi
0364
0365   ## create a new top-level eic-shell launcher script
0366   ## that sets the EIC_SHELL_PREFIX and then starts docker
0367 cat << EOF > eic-shell
0368 #!/bin/bash
0369
0370 ## capture environment setup for upgrades
0371 CONTAINER=$CONTAINER
0372 TMPDIR=$TMPDIR
0373 VERSION=$VERSION
0374 PREFIX=$PREFIX
0375 DISABLE_CVMFS_USAGE=${DISABLE_CVMFS_USAGE}
0376
0377 function print_the_help {
0378   echo "USAGE:  ./eic-shell [OPTIONS] [ -- COMMAND ]"
0379   echo "OPTIONAL ARGUMENTS:"
0380   echo "          -u,--upgrade    Upgrade the container to the latest version"
0381   echo "          --noX           Disable X11 forwarding on macOS"
0382   echo "          -h,--help       Print this message"
0383   echo ""
0384   echo "  Start the eic-shell containerized software environment (Docker version)."
0385   echo ""
0386   echo "EXAMPLES: "
0387   echo "  - Start an interactive shell: ./eic-shell"
0388   echo "  - Upgrade the container:      ./eic-shell --upgrade"
0389   echo "  - Execute a single command:   ./eic-shell -- <COMMAND>"
0390   echo ""
0391   exit
0392 }
0393
0394 UPGRADE=
0395 NOX=
0396 while [ \$# -gt 0 ]; do
0397   key=\$1
0398   case \$key in
0399     -u|--upgrade)
0400       UPGRADE=1
0401       shift
0402       ;;
0403     --noX)
0404       NOX=1
0405       shift
0406       ;;
0407      -h|--help)
0408       print_the_help
0409       exit 0
0410       ;;
0411     --)
0412       shift
0413       break
0414       ;;
0415     *)
0416       echo "ERROR: unknown argument: \$key"
0417       echo "use --help for more info"
0418       exit 1
0419       ;;
0420   esac
0421 done
0422
0423 if [ x\${DISPLAY} == "x" ] ; then
0424   echo "No X11 display detected, disabling X11" >&2
0425   NOX=1
0426 fi
0427
0428 if [ ! -z \${UPGRADE} ]; then
0429   echo "Upgrading eic-shell..."
0430   docker pull $IMG || exit 1
0431   echo "eic-shell upgrade sucessful"
0432   exit 0
0433 fi
0434 EOF
0435
0436   if [ `uname -s` = 'Darwin' ]; then
0437       echo 'if [ ! ${NOX} ]; then' >> eic-shell
0438       echo ' nolisten=`defaults find nolisten_tcp | grep nolisten | head -n 1 | awk ' "'{print" '$3}'"'" '|cut -b 1 `' >> eic-shell
0439       echo ' [[ $nolisten -ne 0 ]] && echo "For X support: In XQuartz settings --> Security --> enable \"Allow connections from network clients\" and restart (should be only once)." >&2' >> eic-shell
0440       ## getting the following single and double quotes, escapes and backticks right was a nightmare
0441       ## But with a heredoc it was worse
0442       echo '  xhost +localhost >&2' >> eic-shell
0443       echo '  dispnum=`ps -e |grep Xquartz | grep listen | grep -v xinit |awk ' "'{print" '$5}'"'" '`' >> eic-shell
0444       echo '  XSTUFF="-e DISPLAY=host.docker.internal${dispnum} -v /tmp/.X11-unix:/tmp/.X11-unix"' >> eic-shell
0445       echo 'fi' >> eic-shell
0446   fi
0447   ## -it on a terminal; -i for piped stdin; none for captured output (-t adds CRLF, -i blocks)
0448   echo 'STDIO=; [ -t 0 ] || STDIO=-i; [ -t 0 ] && [ -t 1 ] && STDIO=-it' >> eic-shell
0449   ## the entrypoint runs bash -c "$@": one argument is the command string,
0450   ## several are shell-quoted into one
0451   echo 'CMD=; case $# in 0) ;; 1) CMD=$1 ;; *) CMD=$(printf "%q " "$@") ;; esac' >> eic-shell
0452   echo "docker run $PLATFORM_FLAG \${DOCKER_OPTIONS:-} $MOUNT \$XSTUFF -w=$PWD \$STDIO --rm -e EIC_SHELL_PREFIX=$PREFIX/local $IMG eic-shell \${CMD:+\"\$CMD\"}" >> eic-shell
0453
0454   chmod +x eic-shell
0455   echo " - Created custom eic-shell excecutable"
0456 }
0457
0458 ## detect OS
0459 OS=`uname -s`
0460 CPU=`uname -m`
0461 case ${OS} in
0462   Linux)
0463     echo " - Detected OS: Linux"
0464     echo " - Detected CPU: $CPU"
0465     if [ "$CPU" = "arm64" ]; then
0466       install_docker
0467     else
0468       install_singularity
0469     fi
0470     ;;
0471   Darwin)
0472     echo " - Detected OS: MacOS"
0473     echo " - Detected CPU: $CPU"
0474     install_docker
0475     ;;
0476   *)
0477     echo "ERROR: OS '${OS}' not currently supported"
0478     exit 1
0479     ;;
0480 esac
0481
0482 popd
0483 echo "Environment setup succesfull"
0484 echo "You can start the development environment by running './eic-shell'"