testing EESSI/bot PR#182 & EESSI/fs PR#146

.github/workflows/test_eessi.yml

@@ -31,7 +31,19 @@ jobs:
               cvmfs_http_proxy: DIRECT
               cvmfs_repositories: pilot.eessi-hpc.org
 
-        - name: Test check_missing_installations.sh script
+#        - name: Test check_missing_installations.sh script
+#          run: |
+#              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+#              module load EasyBuild
+#              eb --version
+#              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+#              export EESSI_OS_TYPE=linux
+#              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
+#              env | grep ^EESSI | sort
+#              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
+#              ./check_missing_installations.sh
+
+        - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
               source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
@@ -40,4 +52,21 @@ jobs:
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
-              ./check_missing_installations.sh
+              echo "modify eessi-${{matrix.EESSI_VERSION}}.yml by adding a missing package (GCC/8.3.0)"
+              echo "  GCC:" >> eessi-${{matrix.EESSI_VERSION}}.yml
+              echo "    toolchains:" >> eessi-${{matrix.EESSI_VERSION}}.yml
+              echo "      SYSTEM:" >> eessi-${{matrix.EESSI_VERSION}}.yml
+              echo "        versions: '8.3.0'" >> eessi-${{matrix.EESSI_VERSION}}.yml
+              tail -n 4 eessi-${{matrix.EESSI_VERSION}}.yml
+              # note, check_missing_installations.sh exits 1 if a package was
+              # missing, which is intepreted as false (exit code based, not
+              # boolean logic), hence when the script exits 0 if no package was
+              # missing it is interpreted as true, thus the test did not capture
+              # the missing package
+              if ./check_missing_installations.sh; then
+                echo "did NOT capture missing package; test FAILED"
+                exit 1
+              else
+                echo "captured missing package; test PASSED"
+                exit 0
+              fi

EESSI-pilot-install-software.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-#
+
 # Script to install EESSI pilot software stack (version set through init/eessi_defaults)
 
 # see example parsing of command line arguments at
@@ -137,7 +137,11 @@ else
     echo_green ">> MODULEPATH set up: ${MODULEPATH}"
 fi
 
-REQ_EB_VERSION='4.5.0'
+echo "EESSI_CVMFS_REPO=${EESSI_CVMFS_REPO}"
+
+REQ_EB_VERSION='4.7.1'
+echo "REQ_EB_VERSION=${REQ_EB_VERSION}"
+module avail 2>&1 | grep -i easybuild
 
 echo ">> Checking for EasyBuild module..."
 ml_av_easybuild_out=$TMPDIR/ml_av_easybuild.out
@@ -165,10 +169,6 @@ else
     eb --install-latest-eb-release &> ${eb_install_out}
     check_exit_code $? "${ok_msg}" "${fail_msg}"
 
-    # restore origin $PATH and $PYTHONPATH values
-    export PATH=${ORIG_PATH}
-    export PYTHONPATH=${ORIG_PYTHONPATH}
-
     eb --search EasyBuild-${REQ_EB_VERSION}.eb | grep EasyBuild-${REQ_EB_VERSION}.eb > /dev/null
     if [[ $? -eq 0 ]]; then
         ok_msg="EasyBuild v${REQ_EB_VERSION} installed, alright!"
@@ -177,6 +177,10 @@ else
         check_exit_code $? "${ok_msg}" "${fail_msg}"
     fi
 
+    # restore origin $PATH and $PYTHONPATH values
+    export PATH=${ORIG_PATH}
+    export PYTHONPATH=${ORIG_PYTHONPATH}
+
     module avail easybuild/${REQ_EB_VERSION} &> ${ml_av_easybuild_out}
     if [[ $? -eq 0 ]]; then
         echo_green ">> EasyBuild module installed!"
@@ -206,232 +210,27 @@ fi
 
 echo_green "All set, let's start installing some software in ${EASYBUILD_INSTALLPATH}..."
 
-# install Java with fixed custom easyblock that uses patchelf to ensure right glibc is picked up,
-# see https://github.com/EESSI/software-layer/issues/123
-# and https://github.com/easybuilders/easybuild-easyblocks/pull/2557
-ok_msg="Java installed, off to a good (?) start!"
-fail_msg="Failed to install Java, woopsie..."
-$EB Java-11.eb --robot --include-easyblocks-from-pr 2557
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-# install GCC for foss/2020a
-export GCC_EC="GCC-9.3.0.eb"
-echo ">> Starting slow with ${GCC_EC}..."
-ok_msg="${GCC_EC} installed, yippy! Off to a good start..."
-fail_msg="Installation of ${GCC_EC} failed!"
-# pull in easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14453,
-# which includes patch to fix build of GCC 9.3 when recent kernel headers are in place
-$EB ${GCC_EC} --robot --from-pr 14453 GCCcore-9.3.0.eb
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-# install CMake with custom easyblock that patches CMake when --sysroot is used
-echo ">> Install CMake with fixed easyblock to take into account --sysroot"
-ok_msg="CMake installed!"
-fail_msg="Installation of CMake failed, what the ..."
-$EB CMake-3.16.4-GCCcore-9.3.0.eb --robot --include-easyblocks-from-pr 2248
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
+# add OpenBLAS: requires special handling for GENERIC CPU targets
 # If we're building OpenBLAS for GENERIC, we need https://github.com/easybuilders/easybuild-easyblocks/pull/1946
-echo ">> Installing OpenBLAS..."
-ok_msg="Done with OpenBLAS!"
-fail_msg="Installation of OpenBLAS failed!"
+# we need to specify --parallel 1 or run into weird linking issues supposedly
+# introduced by GNU make v4.4, see for example
+# https://github.com/xianyi/OpenBLAS/issues/3899 and https://github.com/xianyi/OpenBLAS/issues/3979
+# a fix may be provided with https://github.com/xianyi/OpenBLAS/pull/3983
+# the fix did not work, so only option seems to be --parallel 1
+# another option seems to be to use make v4.3 as build dependency
 if [[ $GENERIC -eq 1 ]]; then
+    echo ">> Installing OpenBLAS..."
+    ok_msg="Done with OpenBLAS (GENERIC architecture)!"
+    fail_msg="Installation of OpenBLAS (GENERIC architecture) failed!"
     echo_yellow ">> Using https://github.com/easybuilders/easybuild-easyblocks/pull/1946 to build generic OpenBLAS."
-    openblas_include_easyblocks_from_pr="--include-easyblocks-from-pr 1946"
-else
-    openblas_include_easyblocks_from_pr=''
-fi
-$EB $openblas_include_easyblocks_from_pr OpenBLAS-0.3.9-GCC-9.3.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing OpenMPI..."
-ok_msg="OpenMPI installed, w00!"
-fail_msg="Installation of OpenMPI failed, that's not good..."
-$EB OpenMPI-4.0.3-GCC-9.3.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-# install Python
-echo ">> Install Python 2.7.18 and Python 3.8.2..."
-ok_msg="Python 2.7.18 and 3.8.2 installed, yaay!"
-fail_msg="Installation of Python failed, oh no..."
-$EB Python-2.7.18-GCCcore-9.3.0.eb Python-3.8.2-GCCcore-9.3.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Perl..."
-ok_msg="Perl installed, making progress..."
-fail_msg="Installation of Perl failed, this never happens..."
-# use enhanced Perl easyblock from https://github.com/easybuilders/easybuild-easyblocks/pull/2640
-# to avoid trouble when using long installation prefix (for example with EESSI pilot 2021.12 on skylake_avx512...)
-$EB Perl-5.30.2-GCCcore-9.3.0.eb --robot --include-easyblocks-from-pr 2640
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Qt5..."
-ok_msg="Qt5 installed, phieuw, that was a big one!"
-fail_msg="Installation of Qt5 failed, that's frustrating..."
-$EB Qt5-5.14.1-GCCcore-9.3.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-# skip test step when installing SciPy-bundle on aarch64,
-# to dance around problem with broken numpy tests;
-# cfr. https://github.com/easybuilders/easybuild-easyconfigs/issues/11959
-echo ">> Installing SciPy-bundle"
-ok_msg="SciPy-bundle installed, yihaa!"
-fail_msg="SciPy-bundle installation failed, bummer..."
-SCIPY_EC=SciPy-bundle-2020.03-foss-2020a-Python-3.8.2.eb
-if [[ "$(uname -m)" == "aarch64" ]]; then
-  $EB $SCIPY_EC --robot --skip-test-step
-else
-  $EB $SCIPY_EC --robot
-fi
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing GROMACS..."
-ok_msg="GROMACS installed, wow!"
-fail_msg="Installation of GROMACS failed, damned..."
-$EB GROMACS-2020.1-foss-2020a-Python-3.8.2.eb GROMACS-2020.4-foss-2020a-Python-3.8.2.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-# note: compiling OpenFOAM is memory hungry (16GB is not enough with 8 cores)!
-# 32GB is sufficient to build with 16 cores
-echo ">> Installing OpenFOAM (twice!)..."
-ok_msg="OpenFOAM installed, now we're talking!"
-fail_msg="Installation of OpenFOAM failed, we were so close..."
-$EB OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-if [ ! "${EESSI_CPU_FAMILY}" = "ppc64le" ]; then
-    echo ">> Installing QuantumESPRESSO..."
-    ok_msg="QuantumESPRESSO installed, let's go quantum!"
-    fail_msg="Installation of QuantumESPRESSO failed, did somebody observe it?!"
-    $EB QuantumESPRESSO-6.6-foss-2020a.eb --robot
+    $EB --include-easyblocks easyblocks/o/openblas-pr1946-cc74e45.py OpenBLAS-0.3.15-GCC-10.3.0.eb --robot
     check_exit_code $? "${ok_msg}" "${fail_msg}"
 fi
 
-echo ">> Installing R 4.0.0 (better be patient)..."
-ok_msg="R installed, wow!"
-fail_msg="Installation of R failed, so sad..."
-$EB R-4.0.0-foss-2020a.eb --robot --parallel-extensions-install --experimental
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Bioconductor 3.11 bundle..."
-ok_msg="Bioconductor installed, enjoy!"
-fail_msg="Installation of Bioconductor failed, that's annoying..."
-$EB R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing TensorFlow 2.3.1..."
-ok_msg="TensorFlow 2.3.1 installed, w00!"
-fail_msg="Installation of TensorFlow failed, why am I not surprised..."
-$EB TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb --robot --include-easyblocks-from-pr 2218
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Horovod 0.21.3..."
-ok_msg="Horovod installed! Go do some parallel training!"
-fail_msg="Horovod installation failed. There comes the headache..."
-$EB Horovod-0.21.3-foss-2020a-TensorFlow-2.3.1-Python-3.8.2.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-if [ ! "${EESSI_CPU_FAMILY}" = "ppc64le" ]; then
-
-    echo ">> Installing code-server 3.7.3..."
-    ok_msg="code-server 3.7.3 installed, now you can use VS Code!"
-    fail_msg="Installation of code-server failed, that's going to be hard to fix..."
-    $EB code-server-3.7.3.eb --robot
-    check_exit_code $? "${ok_msg}" "${fail_msg}"
-fi
+eb_install_easystack_out=${TMPDIR}/eb_install_easystack.out
+${EB:-eb} --robot --easystack eessi-${EESSI_PILOT_VERSION}.yml --experimental | tee ${eb_install_easystack_out}
 
-echo ">> Installing RStudio-Server 1.3.1093..."
-ok_msg="RStudio-Server installed, enjoy!"
-fail_msg="Installation of RStudio-Server failed, might be OS deps..."
-$EB RStudio-Server-1.3.1093-foss-2020a-Java-11-R-4.0.0.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing OSU-Micro-Benchmarks 5.6.3..."
-ok_msg="OSU-Micro-Benchmarks installed, yihaa!"
-fail_msg="Installation of OSU-Micro-Benchmarks failed, that's unexpected..."
-$EB OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb -r
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Spark 3.1.1..."
-ok_msg="Spark installed, set off the fireworks!"
-fail_msg="Installation of Spark failed, no fireworks this time..."
-$EB Spark-3.1.1-foss-2020a-Python-3.8.2.eb -r
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing IPython 7.15.0..."
-ok_msg="IPython installed, launch your Jupyter Notebooks!"
-fail_msg="Installation of IPython failed, that's unexpected..."
-$EB IPython-7.15.0-foss-2020a-Python-3.8.2.eb -r
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing WRF 3.9.1.1..."
-ok_msg="WRF installed, it's getting hot in here!"
-fail_msg="Installation of WRF failed, that's unexpected..."
-OMPI_MCA_pml=ucx UCX_TLS=tcp $EB WRF-3.9.1.1-foss-2020a-dmpar.eb -r --include-easyblocks-from-pr 2648
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing R 4.1.0 (better be patient)..."
-ok_msg="R installed, wow!"
-fail_msg="Installation of R failed, so sad..."
-$EB --from-pr 14821 X11-20210518-GCCcore-10.3.0.eb -r && $EB --from-pr 16011 R-4.1.0-foss-2021a.eb --robot --parallel-extensions-install --experimental
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing Nextflow 22.10.1..."
-ok_msg="Nextflow installed, the work must flow..."
-fail_msg="Installation of Nextflow failed, that's unexpected..."
-$EB -r --from-pr 16531 Nextflow-22.10.1.eb
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing OSU-Micro-Benchmarks/5.7.1-gompi-2021a..."
-ok_msg="OSU-Micro-Benchmarks installed, yihaa!"
-fail_msg="Installation of OSU-Micro-Benchmarks failed, that's unexpected..."
-$EB OSU-Micro-Benchmarks-5.7.1-gompi-2021a.eb -r
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-echo ">> Installing EasyBuild 4.5.1..."
-ok_msg="EasyBuild v4.5.1 installed"
-fail_msg="EasyBuild v4.5.1 failed to install"
-$EB --from-pr 14545 --include-easyblocks-from-pr 2805
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-LMOD_IGNORE_CACHE=1 module swap EasyBuild/4.5.1
-check_exit_code $? "Swapped to EasyBuild/4.5.1" "Couldn't swap to EasyBuild/4.5.1"
-
-echo ">> Installing SciPy-bundle with foss/2021a..."
-ok_msg="SciPy-bundle with foss/2021a installed, welcome to the modern age"
-fail_msg="Installation of SciPy-bundle with foss/2021a failed, back to the stone age..."
-# use GCCcore easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14454
-# which includes patch to fix installation with recent Linux kernel headers
-$EB --from-pr 14454 GCCcore-10.3.0.eb --robot
-# use enhanced Perl easyblock from https://github.com/easybuilders/easybuild-easyblocks/pull/2640
-# to avoid trouble when using long installation prefix (for example with EESSI pilot 2021.12 on skylake_avx512...)
-$EB Perl-5.32.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2640
-# use enhanced CMake easyblock to patch CMake's UnixPaths.cmake script if --sysroot is set
-# from https://github.com/easybuilders/easybuild-easyblocks/pull/2248
-$EB CMake-3.20.1-GCCcore-10.3.0.eb --robot --include-easyblocks-from-pr 2248
-# use Rust easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/14584
-# that includes patch to fix bootstrap problem when using alternate sysroot
-$EB --from-pr 14584 Rust-1.52.1-GCCcore-10.3.0.eb --robot
-# use OpenBLAS easyconfig from https://github.com/easybuilders/easybuild-easyconfigs/pull/15885
-# which includes a patch to fix installation on POWER
-$EB $openblas_include_easyblocks_from_pr --from-pr 15885 OpenBLAS-0.3.15-GCC-10.3.0.eb --robot
-# ignore failing FlexiBLAS tests when building on POWER;
-# some tests are failing due to a segmentation fault due to "invalid memory reference",
-# see also https://github.com/easybuilders/easybuild-easyconfigs/pull/12476;
-# using -fstack-protector-strong -fstack-clash-protection should fix that,
-# but it doesn't for some reason when building for ppc64le/generic...
-if [ "${EESSI_SOFTWARE_SUBDIR}" = "ppc64le/generic" ]; then
-    $EB FlexiBLAS-3.0.4-GCC-10.3.0.eb --ignore-test-failure
-else
-    $EB FlexiBLAS-3.0.4-GCC-10.3.0.eb
-fi
-
-$EB SciPy-bundle-2021.05-foss-2021a.eb --robot
-check_exit_code $? "${ok_msg}" "${fail_msg}"
-
-### add packages here
-
-echo ">> Creating/updating Lmod cache..."
+echo ">> Creating/updating Lmod cache on $(date) (nr 1) ..."
 export LMOD_RC="${EASYBUILD_INSTALLPATH}/.lmod/lmodrc.lua"
 if [ ! -f $LMOD_RC ]; then
     python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH}
@@ -442,5 +241,9 @@ $TOPDIR/update_lmod_cache.sh ${EPREFIX} ${EASYBUILD_INSTALLPATH}
 
 $TOPDIR/check_missing_installations.sh
 
+# TODO do not clean up by default (or provide a cmd line arg and when run
+# from bot, do not clean up)
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
+
+exit 0

OpenBLAS-0.3.15-GCC-10.3.0.eb

@@ -0,0 +1,39 @@
+name = 'OpenBLAS'
+version = '0.3.15'
+
+homepage = 'https://xianyi.github.com/OpenBLAS/'
+description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version."
+
+toolchain = {'name': 'GCC', 'version': '10.3.0'}
+
+source_urls = [
+    # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble
+    'https://www.netlib.org/lapack/timing/',
+    'https://github.com/xianyi/OpenBLAS/archive/',
+]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    ('large.tgz', '.'),
+    ('timing.tgz', '.'),
+    'OpenBLAS-%(version)s_icelake-detection.patch',
+    'OpenBLAS-%(version)s_fix-aarch64.patch',
+    'OpenBLAS-%(version)s_workaround-gcc-miscompilation.patch',
+]
+checksums = [
+    '30a99dec977594b387a17f49904523e6bc8dd88bd247266e83485803759e4bbe',  # v0.3.15.tar.gz
+    'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1',  # large.tgz
+    '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af',  # timing.tgz
+    'aa96e1c3b1532dbafe4b6e8591688ef200e99304a902851f342cb9d467219762',  # OpenBLAS-0.3.15_icelake-detection.patch
+    'ba7bd45af9fe0516f8c9b1cf047eec7b833996e481bc925d4fb2563865d3db38',  # OpenBLAS-0.3.15_fix-aarch64.patch
+    # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch
+    'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971',
+]
+
+builddependencies = [
+    ('make', '4.3'),
+]
+
+# extensive testing can be enabled by uncommenting the line below
+# runtest = 'PATH=.:$PATH lapack-timing'
+
+moduleclass = 'numlib'