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Merge pull request #21 from boegel/pilot_2020.09
add script for installing 2020.09 pilot stack
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‎.github/workflows/tests.yml‎

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# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
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name: Tests
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on: [push, pull_request]
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jobs:
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build:
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runs-on: ubuntu-18.04
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strategy:
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matrix:
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python: [3.6, 3.7, 3.8]
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fail-fast: false
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steps:
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- uses: actions/checkout@v2
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- name: set up Python
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uses: actions/setup-python@v1
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with:
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python-version: ${{matrix.python}}
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architecture: x64
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- name: install Python packages
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run: |
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pip install archspec
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- name: test eessi_software_subdir.py script
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run: |
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./eessi_software_subdir.py | tee out
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grep '^x86_64/' out
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egrep '/intel/|/amd/' out

‎EESSI-pilot-2020.09.sh‎

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#!/bin/bash
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#
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# Script to install EESSI pilot software stack (version 2020.09)
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#
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TOPDIR=$(dirname $(realpath $0))
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function echo_green() {
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echo -e "\e[32m$1\e[0m"
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}
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function echo_red() {
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echo -e "\e[31m$1\e[0m"
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}
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function echo_yellow() {
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echo -e "\e[33m$1\e[0m"
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}
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function error() {
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echo_red "ERROR: $1" >&2
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exit 1
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}
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TMPDIR=$(mktemp -d)
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echo ">> Setting up environment..."
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export CVMFS_REPO="/cvmfs/pilot.eessi-hpc.org"
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export EESSI_PILOT_VERSION="2020.09"
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export ARCH=$(uname -m)
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export EESSI_PREFIX=${CVMFS_REPO}/${EESSI_PILOT_VERSION}
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export EPREFIX=${EESSI_PREFIX}/compat/${ARCH}
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DETECTION_PARAMETERS=''
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GENERIC=0
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EB='eb'
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if [[ "$1" == "--generic" || "$EASYBUILD_OPTARCH" == "GENERIC" ]]; then
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echo_yellow ">> GENERIC build requested, taking appropriate measures!"
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DETECTION_PARAMETERS="$DETECTION_PARAMETERS --generic"
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GENERIC=1
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EB='eb --optarch=GENERIC'
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fi
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# make sure that $PATH starts with $CVMFS_REPO
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# (if not, we're not running in the environment set up by 'startprefix')
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if [[ $PATH = ${CVMFS_REPO}* ]]; then
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echo_green ">> It looks like we're in a Gentoo Prefix environment, good!"
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else
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error "Not running in Gentoo Prefix environment, run '${EPREFIX}/startprefix' first!"
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fi
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echo ">> Initializing Lmod..."
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source $EPREFIX/usr/lmod/lmod/init/bash
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ml_version_out=$TMPDIR/ml.out
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ml --version &> $ml_version_out
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if [[ $? -eq 0 ]]; then
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echo_green ">> Found Lmod ${LMOD_VERSION}"
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else
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error "Failed to initialize Lmod?! (see output in ${ml_version_out}"
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fi
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echo ">> Determining software subdirectory to use for current build host..."
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export EESSI_SOFTWARE_SUBDIR=$(python3 $TOPDIR/eessi_software_subdir.py $DETECTION_PARAMETERS)
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if [[ -z ${EESSI_SOFTWARE_SUBDIR} ]]; then
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error "Failed to determine software subdirectory?!"
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else
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echo_green ">> Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory!"
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fi
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echo ">> Configuring EasyBuild..."
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export EASYBUILD_PREFIX=/tmp/${USER}/easybuild
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export EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_SOFTWARE_SUBDIR}
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export EASYBUILD_SOURCEPATH=/tmp/$USER/easybuild/sources:${EESSI_SOURCEPATH}
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# just ignore OS dependencies for now, see https://github.com/easybuilders/easybuild-framework/issues/3430
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export EASYBUILD_IGNORE_OSDEPS=1
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export EASYBUILD_SYSROOT=${EPREFIX}
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export EASYBUILD_DEBUG=1
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export EASYBUILD_TRACE=1
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export EASYBUILD_ZIP_LOGS=bzip2
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export EASYBUILD_RPATH=1
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export EASYBUILD_FILTER_ENV_VARS=LD_LIBRARY_PATH
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DEPS_TO_FILTER=Autoconf,Automake,Autotools,binutils,bzip2,gettext,libreadline,libtool,M4,ncurses,XZ,zlib
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# For aarch64 we need to also filter out Yasm.
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# See https://github.com/easybuilders/easybuild-easyconfigs/issues/11190
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if [[ "$ARCH" == "aarch64" ]]; then
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DEPS_TO_FILTER="${DEPS_TO_FILTER},Yasm"
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fi
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export EASYBUILD_FILTER_DEPS=$DEPS_TO_FILTER
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export EASYBUILD_MODULE_EXTENSIONS=1
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echo ">> Setting up \$MODULEPATH..."
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# make sure no modules are loaded
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module --force purge
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# ignore current $MODULEPATH entirely
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module unuse $MODULEPATH
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module use $EASYBUILD_INSTALLPATH/modules/all
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if [[ -z ${MODULEPATH} ]]; then
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error "Failed to set up \$MODULEPATH?!"
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else
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echo_green ">> MODULEPATH set up: ${MODULEPATH}"
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fi
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echo ">> Checking for EasyBuild module..."
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ml_av_easybuild_out=$TMPDIR/ml_av_easybuild.out
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module avail easybuild &> ${ml_av_easybuild_out}
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if [[ $? -eq 0 ]]; then
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echo_green ">> EasyBuild module found!"
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else
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echo_yellow ">> No EasyBuild module yet, installing it..."
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eb_bootstrap_out=${TMPDIR}/eb_bootstrap.out
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workdir=${TMPDIR}/easybuild_bootstrap
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mkdir -p ${workdir}
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cd ${workdir}
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curl --silent -OL https://raw.githubusercontent.com/easybuilders/easybuild-framework/develop/easybuild/scripts/bootstrap_eb.py
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python3 bootstrap_eb.py ${EASYBUILD_INSTALLPATH} &> ${eb_bootstrap_out}
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cd - > /dev/null
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module avail easybuild &> ${ml_av_easybuild_out}
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if [[ $? -eq 0 ]]; then
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echo_green ">> EasyBuild module installed!"
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else
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error "EasyBuild module failed to install?! (output of bootstrap script in ${eb_bootstrap_out}, output of 'ml av easybuild' in ${ml_av_easybuild_out})"
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fi
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fi
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echo ">> Loading EasyBuild module..."
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module load EasyBuild
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$EB --version
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if [[ $? -eq 0 ]]; then
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echo_green ">> Looking good!"
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$EB --show-config
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else
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error "EasyBuild not working?!"
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fi
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echo_green "All set, let's start installing some software in ${EASYBUILD_INSTALLPATH}..."
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export GCC_EC="GCC-9.3.0.eb"
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echo ">> Starting slow with ${GCC_EC}..."
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$EB ${GCC_EC} --robot
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if [[ $? -eq 0 ]]; then
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echo_green "${GCC_EC} installed, yippy! Off to a good start..."
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else
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error "Installation of ${GCC_EC} failed!"
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fi
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# side-step to fix missing build dependency for Perl,
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/11200
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export PERL_EC="Perl-5.30.2-GCCcore-9.3.0.eb"
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echo ">> Taking a small side step to install ${PERL_EC}..."
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$EB --from-pr 11368 makeinfo-6.7-GCCcore-9.3.0.eb --robot && $EB --from-pr 11200 --robot
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if [[ $? -eq 0 ]]; then
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echo_green "${PERL_EC} installed via easyconfigs PR #11200, that was just a small side step, don't worry..."
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else
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error "Installation of ${PERL_EC} failed!"
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fi
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# side-step to fix installation of CMake with zlib included in --filter-deps
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# see https://github.com/easybuilders/easybuild-easyblocks/pull/2187
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echo ">> Installing CMake with fixed easyblock..."
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$EB CMake-3.16.4-GCCcore-9.3.0.eb --include-easyblocks-from-pr 2187 --robot
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if [[ $? -eq 0 ]]; then
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echo_green "CMake installation done, glad that worked out!"
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else
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error "Installation of CMake failed, pfft..."
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fi
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# required to make sure that libraries like zlib that are listed in --filter-deps can be found by pkg-config
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# FIXME: fix this in EasyBuild framework!
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# see https://github.com/easybuilders/easybuild-framework/pull/3451
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export PKG_CONFIG_PATH=$EPREFIX/usr/lib64/pkgconfig
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# FIXME custom installation of Qt5 with patch required to build with Gentoo's zlib
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# see https://github.com/easybuilders/easybuild-easyconfigs/pull/11385
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echo ">> Installing Qt5 with extra patch to use zlib provided by Gentoo..."
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$EB --from-pr 11385 --robot
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if [[ $? -eq 0 ]]; then
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echo_green "Done with custom Qt5!"
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else
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error "Installation of custom Qt5 failed, grrr..."
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fi
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echo ">> Installing OpenBLAS, Python 3 and Qt5..."
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# If we're building OpenBLAS for GENERIC, we need https://github.com/easybuilders/easybuild-easyblocks/pull/1946
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if [[ $GENERIC -eq 1 ]]; then
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echo_yellow ">> Using https://github.com/easybuilders/easybuild-easyblocks/pull/1946 to build generic OpenBLAS."
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$EB --include-easyblocks-from-pr 1946 OpenBLAS-0.3.9-GCC-9.3.0.eb Python-3.8.2-GCCcore-9.3.0.eb Qt5-5.14.1-GCCcore-9.3.0.eb --robot
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else
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$EB OpenBLAS-0.3.9-GCC-9.3.0.eb Python-3.8.2-GCCcore-9.3.0.eb Qt5-5.14.1-GCCcore-9.3.0.eb --robot
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fi
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if [[ $? -eq 0 ]]; then
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echo_green "Done with OpenBLAS, Python 3 and Qt5!"
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else
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error "Installation of OpenBLAS, Python 3 and Qt5 failed!"
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fi
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# FIXME: customized installation of OpenMPI, that supports high speed interconnects properly...
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# see https://github.com/EESSI/software-layer/issues/14
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echo ">> Installing properly configured OpenMPI..."
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$EB --from-pr 11387 OpenMPI-4.0.3-GCC-9.3.0.eb --include-easyblocks-from-pr 2188 --robot
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if [[ $? -eq 0 ]]; then
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echo_green "OpenMPI installed, w00!"
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else
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error "Installation of OpenMPI failed, that's not good..."
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fi
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# FIXME custom instalation LAME with patch required to build on top of ncurses provided by Gentoo
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echo ">> Installing LAME with patch..."
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$EB --from-pr 11388 LAME-3.100-GCCcore-9.3.0.eb --robot
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if [[ $? -eq 0 ]]; then
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echo_green "LAME installed, yippy!"
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else
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error "Installation of LAME failed, oops..."
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fi
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echo ">> Installing GROMACS and OpenFOAM (twice!)..."
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$EB GROMACS-2020.1-foss-2020a-Python-3.8.2.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb --robot
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if [[ $? -eq 0 ]]; then
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echo_green "GROMACS and OpenFOAM installed, wow!"
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else
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error "Installation of GROMACS and OpenFOAM failed, we were so close..."
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fi
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echo ">> Installing R 4.0.0 (better be patient)..."
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$EB R-4.0.0-foss-2020a.eb --robot --include-easyblocks-from-pr 2189
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if [[ $? -eq 0 ]]; then
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echo_green "R installed, wow!"
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else
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error "Installation of R failed, so sad..."
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fi
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echo ">> Installing Bioconductor 3.11 bundle..."
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$EB R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb --robot
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if [[ $? -eq 0 ]]; then
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echo_green "Bioconductor installed, enjoy!"
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else
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error "Installation of Bioconductor failed, that's annoying..."
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fi
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echo ">> Cleaning up ${TMPDIR}..."
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rm -r ${TMPDIR}

‎eessi_software_subdir.py‎

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#!/usr/bin/env python3
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#
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# Determine EESSI software subdirectory to use for current build host, using archspec
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#
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import os
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import argparse
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import archspec.cpu
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parser = argparse.ArgumentParser(description='Determine EESSI software subdirectory to use for current build host.')
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parser.add_argument('--generic', dest='generic', action='store_true',
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default=False, help='Use generic for CPU name.')
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args = parser.parse_args()
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host_cpu = archspec.cpu.host()
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vendors = {
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'GenuineIntel': 'intel',
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'AuthenticAMD': 'amd',
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}
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vendor = vendors.get(host_cpu.vendor)
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if args.generic:
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parts = (host_cpu.family.name, 'generic')
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elif vendor:
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parts = (host_cpu.family.name, vendor, host_cpu.name)
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else:
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parts = (host_cpu.family.name, host_cpu.name)
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print(os.path.join(*parts))

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