[0KRunning with gitlab-runner 15.1.0 (76984217)[0;m
[0K on BB5 map runner pnPo3yJy[0;m
section_start:1665656354:resolve_secrets
[0K[0K[36;1mResolving secrets[0;m[0;m
section_end:1665656354:resolve_secrets
[0Ksection_start:1665656354:prepare_executor
[0K[0K[36;1mPreparing the "custom" executor[0;m[0;m
[0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2037859618, slurm job id
Runner ID 29, project root hpc, project name coreneuron
Pipeline ID 78682, build ref 59f7ae7378b08bc2295981f9124416ec8e3a8322, job ID 389600
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P78682, optional exclusive flag , optional cpus per task flag --cpus-per-task=8, optional qos flag
A slurm job will be created with name GL_J389600_PROD_P112_CP10_C22
Job parameters: memory=76G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 860343
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J389600_PROD_P112_CP10_C22 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P78682 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P78682 --ntasks=2 --jobid=860343 --cpus-per-task=8 --mem=76G
section_end:1665656357:prepare_executor
[0Ksection_start:1665656357:prepare_script
[0K[0K[36;1mPreparing environment[0;m[0;m
Running on r2i2n22 via bbpv1.epfl.ch...
section_end:1665656361:prepare_script
[0Ksection_start:1665656361:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m[0;m
[32;1mSkipping Git repository setup[0;m
[32;1mSkipping Git checkout[0;m
[32;1mSkipping Git submodules setup[0;m
section_end:1665656362:get_sources
[0Ksection_start:1665656362:restore_cache
[0K[0K[36;1mRestoring cache[0;m[0;m
[32;1mChecking cache for build:coreneuron:mod2c:intel:shared:debug-8-non_protected...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=49947 revision[0;m=58ba2b95 version[0;m=14.2.0
cache.zip is up to date [0;m
[32;1mSuccessfully extracted cache[0;m
section_end:1665656364:restore_cache
[0Ksection_start:1665656364:download_artifacts
[0K[0K[36;1mDownloading artifacts[0;m[0;m
[32;1mDownloading artifacts for spack_setup (389594)...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=50101 revision[0;m=58ba2b95 version[0;m=14.2.0
Downloading artifacts from coordinator... ok [0;m id[0;m=389594 responseStatus[0;m=200 OK token[0;m=A1cy2Xsa
section_end:1665656365:download_artifacts
[0Ksection_start:1665656365:step_script
[0K[0K[36;1mExecuting "step_script" stage of the job script[0;m[0;m
[0;33mWARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426[0;m
[32;1m$ SPACK_BUILD="${PWD}/spack-build"[0;m
[32;1m$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m
[32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m
[32;1m$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config[0;m
[32;1m$ mkdir ${SPACK_USER_CONFIG_PATH}[0;m
[32;1m$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command[0;m
[32;1m$ spack config blame config[0;m
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389600/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389600/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389600/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389600/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389600/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/config.yaml:2 ccache: True
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:2 install_tree:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:3 root: $user_cache_path/software
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:4 projections:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:5 all: install_{compiler.name}-{compiler.version}-{target}/{name}-{version}-{hash:6}
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:6 module_roots:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:7 tcl: $user_cache_path/modules
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:9 environments:
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:10 root: $user_cache_path/environments
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:88 concretization: separately
/gpfs/bbp.cscs.ch/ssd/apps/bsd//config/config.yaml:12 build_jobs: 8
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:19 # This is the path to the root of the Spack install tree.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:19 # You can use $spack here to refer to the root of the spack instance.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``).
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # Another option that prevents conflicts and potential permission issues is
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # home directory.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # builds directly inside Spack's instance without staging them in a
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # temporary space. Problems with specifying a path inside a Spack instance
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # are that it precludes its use as a system package and its ability to be
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # pip installable.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # In any case, if the username is not already in the path, Spack will append
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # the value of `$user` in an attempt to avoid potential conflicts between
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # The build stage can be purged with `spack clean --stage` and
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # `spack clean -a`, so it is important that the specified directory uniquely
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:38 # identifies Spack staging to avoid accidentally wiping out non-Spack work.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:118 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:123 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:128 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:136 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:145 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/J389594/spack/etc/spack/defaults/config.yaml:207 terminal_title: False
_builtin debug: False
[32;1m$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config[0;m
[32;1m$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"[0;m
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P78682/J389600_local_config)
[32;1m$ mkdir -p "${XDG_CONFIG_HOME}/git"[0;m
[32;1m$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"[0;m
[32;1m$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"[0;m
[32;1m$ cat "${XDG_CONFIG_HOME}/git/config"[0;m
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = ssh://git@bbpgitlab.epfl.ch/
[32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"[0;m
[32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m
Preparing to install coreneuron%intel +caliper~gpu~legacy-unit~nmodl~openmp+shared+tests~unified build_type=Debug ^hpe-mpi%gcc ^caliper%gcc+cuda cuda_arch=70
[32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m
==> Warning: Missing a source id for libsonata-report@1.1.1_lfp
[32;1m$ SPACK_INSTALLED_HASH=$(module load unstable python; echo "${JSON_SPEC}" | python -c "import json, sys; print(json.loads(sys.stdin.read())[\"spec\"][\"nodes\"][0][\"hash\"])")[0;m
[32;1m$ echo "Determined its hash will be ${SPACK_INSTALLED_HASH}"[0;m
Determined its hash will be udoqinvar6cp75viyxkh44mgzbht4q76
[32;1m$ SPACK_STAGE_DIR=${SPACK_BUILD}/spack-stage-${SPACK_PACKAGE}-develop-${SPACK_INSTALLED_HASH}[0;m
[32;1m$ SPACK_BUILD_DIR=${SPACK_STAGE_DIR}/spack-build-${SPACK_INSTALLED_HASH:0:7}[0;m
[32;1m$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src[0;m
[32;1m$ if [ ${SPACK_USE_CCACHE+x} ]; then[0;m
[32;1m$ module load unstable ccache[0;m
[32;1m$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})[0;m
[32;1m$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}[0;m
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682
[32;1m$ export CCACHE_MAXSIZE=512M[0;m
[32;1m$ export CCACHE_DIR="${TMPDIR}/ccache"[0;m
[32;1m$ mkdir -p ${CCACHE_DIR}[0;m
[32;1m$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then[0;m
[32;1m$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"[0;m
[32;1m$ fi[0;m
[32;1m$ ccache --zero-stats[0;m
Statistics zeroed
[32;1m$ ccache --show-stats --verbose[0;m
Summary:
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/860343/ccache
Primary config: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/860343/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Oct 13 12:20:20 2022
Hits: 0 / 0
Direct: 0 / 0
Preprocessed: 0 / 0
Misses: 0
Direct: 0
Preprocessed: 0
Primary storage:
Hits: 0 / 0
Misses: 0
Cache size (GB): 0.12 / 0.51 (24.19 %)
Files: 1825
[32;1m$ fi[0;m
[32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m
[32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m
==> Error: No installed spec matches the hash: 'udoqinvar6cp75viyxkh44mgzbht4q76'
[32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m
Input spec
--------------------------------
- coreneuron%intel+caliper~gpu~legacy-unit~nmodl~openmp+shared+tests~unified build_type=Debug
- ^caliper%gcc+cuda cuda_arch=70
- ^hpe-mpi%gcc
Concretized
--------------------------------
- udoqinv coreneuron@develop%intel@2021.4.0+caliper~codegenopt~gpu~ipo~ispc~knl~legacy-unit+mpi~nmodl~openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=Debug arch=linux-rhel7-skylake
- dwdch6b ^bison@3.8.2%intel@2021.4.0 arch=linux-rhel7-skylake
[^] rdrurry ^boost@1.79.0%intel@2021.4.0+atomic+chrono~clanglibcpp~container~context~coroutine+date_time~debug+exception~fiber+filesystem+graph~icu+iostreams+locale+log+math~mpi+multithreaded~numpy+pic+program_options~python+random+regex+serialization+shared+signals~singlethreaded+system~taggedlayout+test+thread+timer~versionedlayout+wave cxxstd=98 visibility=hidden arch=linux-rhel7-skylake
[^] pfqy3p5 ^caliper@2.7.0%gcc@11.2.0+adiak+cuda~fortran+gotcha~ipo+libdw~libpfm+libunwind+mpi+papi+sampler+shared~sosflow build_type=RelWithDebInfo cuda_arch=70 arch=linux-rhel7-skylake
[^] at3kmf2 ^adiak@0.2.1%gcc@11.2.0~ipo+mpi+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] 2qmvlfy ^cmake@3.21.4%gcc@11.2.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake
[^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake
[^] wu42aul ^cuda@11.6.1%gcc@11.2.0~allow-unsupported-compilers~dev arch=linux-rhel7-skylake
[^] p6adpyi ^elfutils@0.186%gcc@11.2.0~bzip2~debuginfod+nls~xz arch=linux-rhel7-skylake
[^] iu2b5hx ^gettext@0.21%gcc@11.2.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-rhel7-skylake
[^] 3rmq3zx ^bzip2@1.0.8%gcc@11.2.0~debug~pic+shared arch=linux-rhel7-skylake
[^] hxxlexb ^libiconv@1.16%gcc@11.2.0 libs=shared,static arch=linux-rhel7-skylake
[^] dnxqn2k ^libxml2@2.9.12%gcc@11.2.0~python arch=linux-rhel7-skylake
[^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake
[^] jzpqn5y ^xz@5.2.5%gcc@11.2.0~pic libs=shared,static arch=linux-rhel7-skylake
[^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake
[^] ams67cx ^ncurses@6.2%gcc@11.2.0~symlinks+termlib abi=none arch=linux-rhel7-skylake
[^] ir7xtbl ^tar@1.28%gcc@11.2.0 patches=08921fcbd732050c74ddf1de7d8ad95ffdbc09f8b4342456fa2f6a0dd02a957c,125cd6142fac2cc339e9aebfe79e40f90766022b8e8401532b1729e84fc148c2,5c314db58d005043bf407abaf25eb9823b9032a22fd12a0b142d4bf548130fa4,d428578be7fb99b831eb61e53b8d88a859afe08b479a21238180899707d79ce4 arch=linux-rhel7-skylake
- bmpk6ez ^m4@1.4.16%gcc@11.2.0+sigsegv arch=linux-rhel7-skylake
[^] gc2ivgg ^libunwind@1.5.0%gcc@11.2.0~block_signals~conservative_checks~cxx_exceptions~debug~debug_frame+docs~pic+tests+weak_backtrace~xz~zlib components=none libs=shared,static arch=linux-rhel7-skylake
[^] vcit7s5 ^papi@6.0.0.1%gcc@11.2.0~cuda+example~infiniband~lmsensors~nvml~powercap~rapl~rocm~rocm_smi~sde+shared~static_tools amdgpu_target=none arch=linux-rhel7-skylake
[^] 72xzp3v ^python@3.9.7%gcc@11.2.0+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib patches=0d98e93189bc278fbc37a50ed7f183bd8aaf249a8e1670a465f0db6bb4f8cf87,4c2457325f2b608b1b6a2c63087df8c26e07db3e3d493caf36a56f0ecf6fb768,f2fd060afc4b4618fe8104c4c5d771f36dc55b1db5a4623785a4ea707ec72fb4 arch=linux-rhel7-skylake
- s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls arch=linux-rhel7-skylake
- za4z336 ^libsonata-report@1.1.1_lfp%gcc@11.2.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] utj47fz ^hdf5@1.10.7%gcc@11.2.0+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] r74vcyb ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] 7lotjqk ^fmt@8.1.1%gcc@11.2.0~ipo+pic~shared build_type=RelWithDebInfo cxxstd=11 arch=linux-rhel7-skylake
- 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake
[^] 5fkun4i ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake
[32;1m$ spack ${SPACK_INSTALL_EXTRA_FLAGS} install -j${SLURM_CPUS_PER_TASK} --log-format=junit --log-file=${CI_PROJECT_DIR}/install.xml --keep-stage ${SPACK_FULL_SPEC} || install_failed=1[0;m
==> bison@3.8.2 : has external module in ['bison/3.8.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/bison-3.8.2-ej2cew (external bison-3.8.2-dwdch6bmdeclr2novthsywtrryotawwz)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.79.0-zoxhho (external boost-1.79.0-rdrurryqe5eahijb4xf6mbqfryg7ezod)
==> cmake@3.21.4 : has external module in ['cmake/3.21.4']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cmake-3.21.4-cdyb7k (external cmake-3.21.4-2qmvlfyylrv3t5ankluyr5cqey2nlfzd)
==> hpe-mpi@2.25.hmpt : has external module in ['hpe-mpi/2.25.hmpt']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/hpe-mpi-2.25.hmpt-4ukyxt (external hpe-mpi-2.25.hmpt-hyunzknktdzri34bx26bupkvapehonql)
==> cuda@11.6.1 : has external module in ['cuda/11.6.1']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.6.1-ngetva (external cuda-11.6.1-wu42aulcivrayjquerqpqvvjeadgosp2)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/bzip2-1.0.8-eu2d6e (external bzip2-1.0.8-3rmq3zxuntsiphthnvty6gtydbmbkwr5)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libiconv-1.16-hxxlex
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/pkgconf-1.8.0-ihxi5r
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/xz-5.2.5-jzpqn5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/zlib-1.2.11-mswjss (external zlib-1.2.11-evtnqzdtuvprwnbd2nljimpzywrhw4uo)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ncurses-6.2-nsve5x (external ncurses-6.2-ams67cxbq5vc7wiay2ndr2ksce2igbfw)
[+] /usr (external tar-1.28-ir7xtblauhq3vtkpjrl7ou3nzevcsi3u)
[+] /usr (external m4-1.4.16-bmpk6ezkxo3553jsm5thxh7ygtrom3dn)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libunwind-1.5.0-gc2ivg
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/papi-6.0.0.1-vcit7s
==> python@3.9.7 : has external module in ['python/3.9.7']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/python-3.9.7-yj5alh (external python-3.9.7-72xzp3vgzh5b424qevkfruhs3ajzqbiy)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/flex-2.6.3-3mtl7j (external flex-2.6.3-s4ueg72j7l6vkdyvfxj2tweo7v7s3otx)
==> ninja@1.10.2 : has external module in ['ninja/1.10.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ninja-1.10.2-eh33rh (external ninja-1.10.2-6ggc5yre7qddwxdjmn7sfptpdoiy4dtp)
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/fmt-8.1.1-7lotjq
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/reportinglib-2.5.6-5fkun4
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/adiak-0.2.1-at3kmf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libxml2-2.9.12-dnxqn2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/hdf5-1.10.7-utj47f
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-r74vcy
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/gettext-0.21-iu2b5h
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/software/install_gcc-11.2.0-skylake/libsonata-report-1.1.1_lfp-za4z33
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/elfutils-0.186-p6adpy
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/caliper-2.7.0-pfqy3p
==> Installing coreneuron-develop-udoqinvar6cp75viyxkh44mgzbht4q76
==> No binary for coreneuron-develop-udoqinvar6cp75viyxkh44mgzbht4q76 found: installing from source
==> Warning: Missing a source id for libsonata-report@1.1.1_lfp
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682, but it is owned by 0
==> No patches needed for coreneuron
==> coreneuron: Executing phase: 'cmake'
==> coreneuron: Executing phase: 'build'
==> coreneuron: Executing phase: 'install'
==> coreneuron: Successfully installed coreneuron-develop-udoqinvar6cp75viyxkh44mgzbht4q76
Fetch: 8.36s. Build: 1m 31.93s. Total: 1m 40.29s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P78682/software/install_intel-2021.4.0-skylake/coreneuron-develop-udoqin
[32;1m$ chmod -R g+rX "${SPACK_BUILD}"[0;m
[32;1m$ if [[ ${install_failed} == 1 ]]; then exit 1; fi[0;m
[32;1m$ if [ ${SPACK_USE_CCACHE+x} ]; then[0;m
[32;1m$ ccache --cleanup[0;m
[32;1m$ ccache --show-stats --verbose[0;m
Summary:
Cache directory: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/860343/ccache
Primary config: /gpfs/bbp.cscs.ch/ssd/slurmTmpFS/bbpcihpcproj12/860343/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Oct 13 12:23:40 2022
Hits: 107 / 117 (91.45 %)
Direct: 89 / 117 (76.07 %)
Preprocessed: 18 / 28 (64.29 %)
Misses: 10
Direct: 28
Preprocessed: 10
Uncacheable: 23
Primary storage:
Hits: 196 / 234 (83.76 %)
Misses: 38
Cache size (GB): 0.12 / 0.51 (24.20 %)
Files: 1845
Uncacheable:
Called for linking: 20
No input file: 3
[32;1m$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .[0;m
[32;1m$ fi[0;m
[32;1m$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt[0;m
[32;1m$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/[0;m
[32;1m$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')[0;m
[32;1m$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m
[32;1m$ num_failures=$(module load unstable python-dev; python -c "from lxml import etree; xml = etree.parse('${CI_PROJECT_DIR}/install.xml'); print(sum(1 for _ in xml.getroot().iter('failure')) + sum(1 for _ in xml.getroot().iter('error')))")[0;m
Autoloading python/3.9.7
Autoloading hpe-mpi/2.25.hmpt
[32;1m$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi[0;m
section_end:1665656621:step_script
[0Ksection_start:1665656621:archive_cache
[0K[0K[36;1mSaving cache for successful job[0;m[0;m
[32;1mCreating cache build:coreneuron:mod2c:intel:shared:debug-8-non_protected...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=62893 revision[0;m=58ba2b95 version[0;m=14.2.0
ccache.tar: found 1 matching files and directories[0;m
Archive is up to date! [0;m
[32;1mCreated cache[0;m
section_end:1665656624:archive_cache
[0Ksection_start:1665656624:upload_artifacts_on_success
[0K[0K[36;1mUploading artifacts for successful job[0;m[0;m
[32;1mUploading artifacts...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=62965 revision[0;m=58ba2b95 version[0;m=14.2.0
install.xml: found 1 matching files and directories[0;m
spack_build_info.env: found 1 matching files and directories[0;m
spack_clone_variables.env: found 1 matching files and directories[0;m
initial_environment.env: found 1 matching files and directories[0;m
spack-build-env.txt: found 1 matching files and directories[0;m
spack-build-out.txt: found 1 matching files and directories[0;m
spack-configure-args.txt: found 1 matching files and directories[0;m
Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=389600 responseStatus[0;m=201 Created token[0;m=A1cy2Xsa
[32;1mUploading artifacts...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=63011 revision[0;m=58ba2b95 version[0;m=14.2.0
install.xml: found 1 matching files and directories[0;m
Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=389600 responseStatus[0;m=201 Created token[0;m=A1cy2Xsa
[32;1mUploading artifacts...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=63109 revision[0;m=58ba2b95 version[0;m=14.2.0
spack_build_info.env: found 1 matching files and directories[0;m
spack_clone_variables.env: found 1 matching files and directories[0;m
Uploading artifacts as "dotenv" to coordinator... ok[0;m id[0;m=389600 responseStatus[0;m=201 Created token[0;m=A1cy2Xsa
section_end:1665656627:upload_artifacts_on_success
[0Ksection_start:1665656627:cleanup_file_variables
[0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m
section_end:1665656629:cleanup_file_variables
[0K[32;1mJob succeeded[0;m