diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh index 6c08a95757..e64798532e 100755 --- a/EESSI-install-software.sh +++ b/EESSI-install-software.sh @@ -204,29 +204,34 @@ ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12 # use PR patch file to determine in which easystack files stuff was added changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') -if [ -z ${changed_easystacks} ]; then +if [ -z "${changed_easystacks}" ]; then echo "No missing installations, party time!" # Ensure the bot report success, as there was nothing to be build here else - for easystack_file in ${changed_easystacks}; do - + + # first process rebuilds, if any, then easystack files for new installations + # "|| true" is used to make sure that the grep command always returns success + rebuild_easystacks=$(echo "${changed_easystacks}" | (grep "/rebuilds/" || true)) + new_easystacks=$(echo "${changed_easystacks}" | (grep -v "/rebuilds/" || true)) + for easystack_file in ${rebuild_easystacks} ${new_easystacks}; 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} - + ${EB} --show-config - + echo_green "All set, let's start installing some software with EasyBuild v${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) @@ -236,12 +241,12 @@ else # 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} ${TOPDIR}/${pr_diff} else fatal_error "Easystack file ${easystack_file} not found!" fi - + done fi diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh new file mode 100755 index 0000000000..446a156cb8 --- /dev/null +++ b/EESSI-remove-software.sh @@ -0,0 +1,125 @@ +#!/bin/bash +# +# Script to remove part of the EESSI 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 " -g | --generic - instructs script to build for generic architecture target" + echo " -h | --help - display this usage information" +} + +POSITIONAL_ARGS=() + +while [[ $# -gt 0 ]]; do + case $1 in + -g|--generic) + DETECTION_PARAMETERS="--generic" + shift + ;; + -h|--help) + display_help # Call your function + # no shifting needed here, we're done. + exit 0 + ;; + -*|--*) + 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 $0)) + +export TMPDIR=$(mktemp -d /tmp/eessi-remove.XXXXXXXX) + +source $TOPDIR/scripts/utils.sh + +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 + +echo ">> Setting up environment..." + +source $TOPDIR/init/bash + +if [ -d $EESSI_CVMFS_REPO ]; then + echo_green "$EESSI_CVMFS_REPO available, OK!" +else + fatal_error "$EESSI_CVMFS_REPO is not available!" +fi + +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 ">> Configuring EasyBuild..." +EB="eb" +source $TOPDIR/configure_easybuild + +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) + +# if this script is run as root, use PR patch file to determine if software needs to be removed first +if [ $EUID -eq 0 ]; then + changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing' | grep "/rebuilds/") + if [ -z ${changed_easystacks_rebuilds} ]; then + echo "No software needs to be removed." + else + for easystack_file in ${changed_easystacks_rebuilds}; do + # determine version of EasyBuild module to load based on EasyBuild version included in name of easystack file + eb_version=$(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} + + if [ -f ${easystack_file} ]; then + echo_green "Software rebuild(s) requested in ${easystack_file}, so determining which existing installation have to be removed..." + # we need to remove existing installation directories first, + # so let's figure out which modules have to be rebuilt by doing a dry-run and grepping "someapp/someversion" for the relevant lines (with [R]) + # * [R] $CFGS/s/someapp/someapp-someversion.eb (module: someapp/someversion) + rebuild_apps=$(eb --allow-use-as-root-and-accept-consequences --dry-run-short --rebuild --easystack ${easystack_file} | grep "^ \* \[R\]" | grep -o "module: .*[^)]" | awk '{print $2}') + for app in ${rebuild_apps}; do + app_dir=${EASYBUILD_INSTALLPATH}/software/${app} + app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua + echo_yellow "Removing ${app_dir} and ${app_module}..." + rm -rf ${app_dir} + rm -rf ${app_module} + done + else + fatal_error "Easystack file ${easystack_file} not found!" + fi + done + fi +else + fatal_error "This script can only be run by root!" +fi diff --git a/bot/build.sh b/bot/build.sh index 7eb15f319d..12c849205d 100755 --- a/bot/build.sh +++ b/bot/build.sh @@ -168,12 +168,58 @@ COMMON_ARGS+=("--mode" "run") # make sure to use the same parent dir for storing tarballs of tmp PREVIOUS_TMP_DIR=${PWD}/previous_tmp +# prepare arguments to install_software_layer.sh (specific to build step) +declare -a BUILD_STEP_ARGS=() +declare -a INSTALL_SCRIPT_ARGS=() +declare -a REMOVAL_SCRIPT_ARGS=() +if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then + INSTALL_SCRIPT_ARGS+=("--generic") + REMOVAL_SCRIPT_ARGS+=("--generic") +fi +[[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}") +[[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}") + +# determine if the removal step has to be run +# assume there's only one diff file that corresponds to the PR patch file +pr_diff=$(ls [0-9]*.diff | head -1) +# the true at the end of the next command is important: grep will expectedly return 1 if there is no easystack file being added under rebuilds, +# but due to "set -e" the entire script would otherwise fail +changed_easystacks_rebuilds=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | (grep "/rebuilds/" || true)) +if [[ -z "${changed_easystacks_rebuilds}" ]]; then + echo "This PR does not add any easystack files in a rebuilds subdirectory, so let's skip the removal step." +else + # prepare directory to store tarball of tmp for removal and build steps + TARBALL_TMP_REMOVAL_STEP_DIR=${PREVIOUS_TMP_DIR}/removal_step + mkdir -p ${TARBALL_TMP_REMOVAL_STEP_DIR} + + # prepare arguments to eessi_container.sh specific to remove step + declare -a REMOVAL_STEP_ARGS=() + REMOVAL_STEP_ARGS+=("--save" "${TARBALL_TMP_REMOVAL_STEP_DIR}") + REMOVAL_STEP_ARGS+=("--storage" "${STORAGE}") + # add fakeroot option in order to be able to remove software, see: + # https://github.com/EESSI/software-layer/issues/312 + REMOVAL_STEP_ARGS+=("--fakeroot") + + # create tmp file for output of removal step + removal_outerr=$(mktemp remove.outerr.XXXX) + + echo "Executing command to remove software:" + echo "./eessi_container.sh ${COMMON_ARGS[@]} ${REMOVAL_STEP_ARGS[@]}" + echo " -- ./EESSI-remove-software.sh \"${REMOVAL_SCRIPT_ARGS[@]}\" \"$@\" 2>&1 | tee -a ${removal_outerr}" + ./eessi_container.sh "${COMMON_ARGS[@]}" "${REMOVAL_STEP_ARGS[@]}" \ + -- ./EESSI-remove-software.sh "${REMOVAL_SCRIPT_ARGS[@]}" "$@" 2>&1 | tee -a ${removal_outerr} + + # make sure that the build step resumes from the same temporary directory + # this is important, as otherwise the removed software will still be there + REMOVAL_TMPDIR=$(grep ' as tmp directory ' ${removal_outerr} | cut -d ' ' -f 2) + BUILD_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}") +fi + # prepare directory to store tarball of tmp for build step TARBALL_TMP_BUILD_STEP_DIR=${PREVIOUS_TMP_DIR}/build_step mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR} # prepare arguments to eessi_container.sh specific to build step -declare -a BUILD_STEP_ARGS=() BUILD_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}") BUILD_STEP_ARGS+=("--storage" "${STORAGE}") # add options required to handle NVIDIA support @@ -182,14 +228,6 @@ if [[ ! -z ${SHARED_FS_PATH} ]]; then BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections") fi -# prepare arguments to install_software_layer.sh (specific to build step) -declare -a INSTALL_SCRIPT_ARGS=() -if [[ ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} =~ .*/generic$ ]]; then - INSTALL_SCRIPT_ARGS+=("--generic") -fi -[[ ! -z ${BUILD_LOGS_DIR} ]] && INSTALL_SCRIPT_ARGS+=("--build-logs-dir" "${BUILD_LOGS_DIR}") -[[ ! -z ${SHARED_FS_PATH} ]] && INSTALL_SCRIPT_ARGS+=("--shared-fs-path" "${SHARED_FS_PATH}") - # create tmp file for output of build step build_outerr=$(mktemp build.outerr.XXXX) @@ -211,8 +249,14 @@ declare -a TARBALL_STEP_ARGS=() TARBALL_STEP_ARGS+=("--save" "${TARBALL_TMP_TARBALL_STEP_DIR}") # determine temporary directory to resume from -BUILD_TMPDIR=$(grep ' as tmp directory ' ${build_outerr} | cut -d ' ' -f 2) -TARBALL_STEP_ARGS+=("--resume" "${BUILD_TMPDIR}") +if [[ -z ${REMOVAL_TMPDIR} ]]; then + # no rebuild step was done, so the tarball step should resume from the build directory + BUILD_TMPDIR=$(grep ' as tmp directory ' ${build_outerr} | cut -d ' ' -f 2) + TARBALL_STEP_ARGS+=("--resume" "${BUILD_TMPDIR}") +else + # a removal step was done, so resume from its temporary directory (which was also used for the build step) + TARBALL_STEP_ARGS+=("--resume" "${REMOVAL_TMPDIR}") +fi timestamp=$(date +%s) # to set EESSI_VERSION we need to source init/eessi_defaults now diff --git a/eessi_container.sh b/eessi_container.sh index e84912951c..5b41f4832a 100755 --- a/eessi_container.sh +++ b/eessi_container.sh @@ -73,6 +73,7 @@ display_help() { echo " -a | --access {ro,rw} - ro (read-only), rw (read & write) [default: ro]" echo " -c | --container IMG - image file or URL defining the container to use" echo " [default: docker://ghcr.io/eessi/build-node:debian11]" + echo " -f | --fakeroot - run the container with --fakeroot [default: false]" echo " -g | --storage DIR - directory space on host machine (used for" echo " temporary data) [default: 1. TMPDIR, 2. /tmp]" echo " -h | --help - display this usage information [default: false]" @@ -113,6 +114,7 @@ display_help() { ACCESS="ro" CONTAINER="docker://ghcr.io/eessi/build-node:debian11" #DRY_RUN=0 +FAKEROOT=0 VERBOSE=0 STORAGE= LIST_REPOS=0 @@ -140,6 +142,10 @@ while [[ $# -gt 0 ]]; do # DRY_RUN=1 # shift 1 # ;; + -f|--fakeroot) + FAKEROOT=1 + shift 1 + ;; -g|--storage) STORAGE="$2" shift 2 @@ -466,6 +472,11 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then fi fi +# Configure the fakeroot setting for the container +if [[ ${FAKEROOT} -eq 1 ]]; then + ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot") +fi + # set up repository config (always create directory repos_cfg and populate it with info when # arg -r|--repository is used) mkdir -p ${EESSI_TMPDIR}/repos_cfg