Created
February 14, 2022 12:14
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/coreneuron/-/pipelines/37548 (:no_entry:) running on GitHub PR BlueBrain/CoreNeuron#737.
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836035:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836035:resolve_secrets [0Ksection_start:1644836035: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor507380051, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153654 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153654_PROD_P112_CP4_C5 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274610 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153654_PROD_P112_CP4_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274610 --cpus-per-task=8 --mem=76G | |
| section_end:1644836060:prepare_executor [0Ksection_start:1644836060:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n21 via bbpv1.epfl.ch... | |
| section_end:1644836064:prepare_script [0Ksection_start:1644836064: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:1644836066:get_sources [0Ksection_start:1644836066:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:coreneuron:mod2c:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=33039 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:1644836068:restore_cache [0Ksection_start:1644836068:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for spack_setup (153640)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=33103 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153640 responseStatus[0;m=200 OK token[0;m=YywzWeu7 | |
| section_end:1644836070:download_artifacts [0Ksection_start:1644836070: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/P37548/J153654/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for coreneuron is commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f" | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-bluebrain/packages/coreneuron/package.py b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| index 11516ab..49f7b1e 100644 | |
| --- a/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| +++ b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| @@ -20,7 +20,7 @@ class Coreneuron(CMakePackage): | |
| # This simplifies testing the gitlab-pipelines repository: | |
| git = "git@bbpgitlab.epfl.ch:hpc/coreneuron.git" | |
| - version('develop', branch='master') | |
| + version('develop', commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f") | |
| # 1.0.1 > 1.0.0.20210519 > 1.0 as far as Spack is concerned | |
| version('1.0.0.20220111', commit='64e56b7') | |
| version('1.0.0.20211020', commit='e265f9d') | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install coreneuron@develop%intel+tests~legacy-unit build_type=Debug | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be jlimlp3c43orxijl3zdr5c3mlicgrilx | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274610/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274610/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: Mon Feb 14 11:54:56 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): 0.15 / 0.51 (28.99 %) | |
| Files: 3120 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'jlimlp3c43orxijl3zdr5c3mlicgrilx' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - coreneuron@develop%intel~legacy-unit+tests build_type=Debug | |
| Concretized | |
| -------------------------------- | |
| - jlimlp3 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 | |
| [^] i4sftdn ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| - z3q5f3x ^cmake@3.21.4%intel@2021.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| - s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls arch=linux-rhel7-skylake | |
| [^] 3narjkw ^hpe-mpi@2.25.hmpt%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] 3yjvqc4 ^libsonata-report@1.0.0.20211007%intel@2021.4.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ofveh3j ^hdf5@1.10.7%intel@2021.4.0+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] xys6npz ^pkgconf@1.8.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] e7w5nez ^zlib@1.2.11%intel@2021.4.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] wk3uenv ^spdlog@1.9.2%intel@2021.4.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] f27a7nn ^python@3.9.7%intel@2021.4.0+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 | |
| [^] gdhqypa ^reportinglib@2.5.6%intel@2021.4.0~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-1.77.0-6x26ce (external boost-1.77.0-i4sftdnkvomfatxuakfaezmt3a3bcetc) | |
| ==> 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-z3q5f3xwpuibd3qbgdscqmu3efarbu42) | |
| ==> 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) | |
| ==> 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-3narjkwjh6i2jr3zl3g5wdjlqi52hkwh) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/pkgconf-1.8.0-xys6np | |
| [+] /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-e7w5nezpwf572epfhbosqfzboztysout) | |
| ==> 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) | |
| ==> 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-f27a7nnhppeztxijpispnaedcfo2vjxi) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/spdlog-1.9.2-wk3uen | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/reportinglib-2.5.6-gdhqyp | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/hdf5-1.10.7-ofveh3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/libsonata-report-1.0.0.20211007-3yjvqc | |
| ==> Installing coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx | |
| ==> No binary for coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx found: installing from source | |
| ==> No patches needed for coreneuron | |
| ==> coreneuron: Executing phase: 'cmake' | |
| ==> coreneuron: Executing phase: 'build' | |
| ==> coreneuron: Executing phase: 'install' | |
| ==> coreneuron: Successfully installed coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx | |
| Fetch: 9.33s. Build: 3m 57.44s. Total: 4m 6.77s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_intel-2021.4.0-skylake/coreneuron-develop-jlimlp | |
| [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: /nvme/bbpcihpcproj12/274610/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274610/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: Mon Feb 14 11:59:50 2022 | |
| Hits: 52 / 115 (45.22 %) | |
| Direct: 34 / 116 (29.31 %) | |
| Preprocessed: 18 / 82 (21.95 %) | |
| Misses: 63 | |
| Direct: 82 | |
| Preprocessed: 64 | |
| Uncacheable: 18 | |
| Primary storage: | |
| Hits: 144 / 232 (62.07 %) | |
| Misses: 88 | |
| Cache size (GB): 0.16 / 0.51 (31.81 %) | |
| Files: 3188 | |
| Uncacheable: | |
| Called for linking: 14 | |
| Compiler produced no output: 1 | |
| 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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_CORENEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644836391:step_script [0Ksection_start:1644836391:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:coreneuron:mod2c:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=40769 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Acoreneuron%3Amod2c%3Aintel-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644836399:archive_cache [0Ksection_start:1644836399: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=40851 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=153654 responseStatus[0;m=201 Created token[0;m=ssyq9Fsy | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=40890 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=153654 responseStatus[0;m=201 Created token[0;m=ssyq9Fsy | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=40933 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=153654 responseStatus[0;m=201 Created token[0;m=ssyq9Fsy | |
| section_end:1644836400:upload_artifacts_on_success [0Ksection_start:1644836400:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836401:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836415:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836415:resolve_secrets [0Ksection_start:1644836415: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor899322889, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153656 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153656_PROD_P112_CP13_C21 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274638 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153656_PROD_P112_CP13_C21 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274638 --cpus-per-task=8 --mem=76G | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i6n18 via bbpv1.epfl.ch... | |
| section_end:1644836439:prepare_script [0Ksection_start:1644836439: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:1644836439:get_sources [0Ksection_start:1644836439:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:coreneuron:nmodl:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=200307 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:1644836442:restore_cache [0Ksection_start:1644836442:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:nmodl (153644)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=200464 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153644 responseStatus[0;m=200 OK token[0;m=3dEDZKZK | |
| section_end:1644836443:download_artifacts [0Ksection_start:1644836443: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_PACKAGE_DEPENDENCIES="${SPACK_PACKAGE_DEPENDENCIES}^hpe-mpi%gcc"[0;m | |
| [32;1m$ 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/P37548/J153656/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for coreneuron is commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f" | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-bluebrain/packages/coreneuron/package.py b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| index 11516ab..49f7b1e 100644 | |
| --- a/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| +++ b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| @@ -20,7 +20,7 @@ class Coreneuron(CMakePackage): | |
| # This simplifies testing the gitlab-pipelines repository: | |
| git = "git@bbpgitlab.epfl.ch:hpc/coreneuron.git" | |
| - version('develop', branch='master') | |
| + version('develop', commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f") | |
| # 1.0.1 > 1.0.0.20210519 > 1.0 as far as Spack is concerned | |
| version('1.0.0.20220111', commit='64e56b7') | |
| version('1.0.0.20211020', commit='e265f9d') | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install coreneuron@develop%intel+nmodl+tests~legacy-unit build_type=Debug ^/cnhmkfzsucqnmy6dfxyfikno2yj57grf^hpe-mpi%gcc | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274638/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274638/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: Mon Feb 14 12:01:20 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): 0.17 / 0.51 (33.39 %) | |
| Files: 4227 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - coreneuron@develop%intel~legacy-unit+nmodl+tests build_type=Debug | |
| - ^hpe-mpi%gcc | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - hp7e7dx 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 | |
| [^] i4sftdn ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden 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 | |
| - s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 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-1.77.0-6x26ce (external boost-1.77.0-i4sftdnkvomfatxuakfaezmt3a3bcetc) | |
| ==> 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) | |
| ==> 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) | |
| ==> 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) | |
| [+] /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_externals/install_gcc-11.2.0-skylake/zlib-1.2.11-mswjss (external zlib-1.2.11-evtnqzdtuvprwnbd2nljimpzywrhw4uo) | |
| ==> 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) | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| ==> Installing coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y | |
| ==> No binary for coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y found: installing from source | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> No patches needed for coreneuron | |
| ==> coreneuron: Executing phase: 'cmake' | |
| ==> coreneuron: Executing phase: 'build' | |
| ==> coreneuron: Executing phase: 'install' | |
| ==> coreneuron: Successfully installed coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y | |
| Fetch: 3.89s. Build: 1m 52.11s. Total: 1m 56.00s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_intel-2021.4.0-skylake/coreneuron-develop-hp7e7d | |
| [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: /nvme/bbpcihpcproj12/274638/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274638/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: Mon Feb 14 12:04:04 2022 | |
| Hits: 31 / 94 (32.98 %) | |
| Direct: 31 / 95 (32.63 %) | |
| Preprocessed: 0 / 64 (0.00 %) | |
| Misses: 63 | |
| Direct: 64 | |
| Preprocessed: 64 | |
| Uncacheable: 16 | |
| Primary storage: | |
| Hits: 111 / 190 (58.42 %) | |
| Misses: 79 | |
| Cache size (GB): 0.19 / 0.51 (36.23 %) | |
| Files: 4304 | |
| Uncacheable: | |
| Called for linking: 12 | |
| Compiler produced no output: 1 | |
| 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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_CORENEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644836645:step_script [0Ksection_start:1644836645:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:coreneuron:nmodl:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=206482 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Acoreneuron%3Anmodl%3Aintel-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644836653:archive_cache [0Ksection_start:1644836653: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=206804 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=153656 responseStatus[0;m=201 Created token[0;m=NAxHmCYD | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=206850 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=153656 responseStatus[0;m=201 Created token[0;m=NAxHmCYD | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=206898 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=153656 responseStatus[0;m=201 Created token[0;m=NAxHmCYD | |
| section_end:1644836655:upload_artifacts_on_success [0Ksection_start:1644836655:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836655:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836414:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836414:resolve_secrets [0Ksection_start:1644836414: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor520286591, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153652 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153652_PROD_P112_CP12_C20 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274639 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153652_PROD_P112_CP12_C20 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274639 --cpus-per-task=8 --mem=76G | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i6n18 via bbpv1.epfl.ch... | |
| section_end:1644836439:prepare_script [0Ksection_start:1644836439: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:1644836439:get_sources [0Ksection_start:1644836439:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:coreneuron:nmodl:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=200266 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:1644836441:restore_cache [0Ksection_start:1644836441:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:nmodl (153644)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=200401 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153644 responseStatus[0;m=200 OK token[0;m=3dEDZKZK | |
| section_end:1644836442:download_artifacts [0Ksection_start:1644836442: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_PACKAGE_DEPENDENCIES="${SPACK_PACKAGE_DEPENDENCIES}^hpe-mpi%gcc"[0;m | |
| [32;1m$ 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/P37548/J153652/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for coreneuron is commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f" | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-bluebrain/packages/coreneuron/package.py b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| index 11516ab..49f7b1e 100644 | |
| --- a/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| +++ b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| @@ -20,7 +20,7 @@ class Coreneuron(CMakePackage): | |
| # This simplifies testing the gitlab-pipelines repository: | |
| git = "git@bbpgitlab.epfl.ch:hpc/coreneuron.git" | |
| - version('develop', branch='master') | |
| + version('develop', commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f") | |
| # 1.0.1 > 1.0.0.20210519 > 1.0 as far as Spack is concerned | |
| version('1.0.0.20220111', commit='64e56b7') | |
| version('1.0.0.20211020', commit='e265f9d') | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install coreneuron@develop%nvhpc+nmodl~openmp+gpu+tests~legacy-unit+sympy build_type=RelWithDebInfo ^/cnhmkfzsucqnmy6dfxyfikno2yj57grf^hpe-mpi%gcc | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be vqg67goxagdsf3kxjwwbdbz6jsbvmspa | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274639/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274639/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: Mon Feb 14 12:01:20 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): 0.11 / 0.51 (20.91 %) | |
| Files: 4494 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'vqg67goxagdsf3kxjwwbdbz6jsbvmspa' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - coreneuron@develop%nvhpc+gpu~legacy-unit+nmodl~openmp+sympy+tests build_type=RelWithDebInfo | |
| - ^hpe-mpi%gcc | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - vqg67go coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl~openmp~profile+report+shared+sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - 4ydwt2s ^bison@3.8.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] yjmsba6 ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden 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 | |
| [^] akxpgv2 ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| - udykfw5 ^flex@2.6.3%nvhpc@22.1+lex~nls arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - k3tfixc ^ninja@1.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 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-3.8.2-4ydwt2sjpk4f7vuqyxhxg23cea3k6sxs) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-yjmsba6vrk7ay2rbkah4htoniepm5yci) | |
| ==> 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) | |
| ==> cuda@11.5.1 : has external module in ['cuda/11.5.1'] | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.5.1-fyf4dd (external cuda-11.5.1-akxpgv2q5zrp36lxyjpeuzhsfk77n2mf) | |
| ==> 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-udykfw5i5twmy3lnuuzeemfkn3lvsldx) | |
| ==> 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) | |
| [+] /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_externals/install_gcc-11.2.0-skylake/zlib-1.2.11-mswjss (external zlib-1.2.11-evtnqzdtuvprwnbd2nljimpzywrhw4uo) | |
| ==> 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-k3tfixcs5ddog5pciqqucifnc2qadnyt) | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| ==> Installing coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa | |
| ==> No binary for coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa found: installing from source | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> No patches needed for coreneuron | |
| ==> coreneuron: Executing phase: 'cmake' | |
| ==> coreneuron: Executing phase: 'build' | |
| ==> coreneuron: Executing phase: 'install' | |
| ==> coreneuron: Successfully installed coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa | |
| Fetch: 3.83s. Build: 5m 21.75s. Total: 5m 25.58s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/coreneuron-develop-vqg67g | |
| [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: /nvme/bbpcihpcproj12/274639/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274639/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: Mon Feb 14 12:07:35 2022 | |
| Hits: 31 / 96 (32.29 %) | |
| Direct: 30 / 96 (31.25 %) | |
| Preprocessed: 1 / 66 (1.52 %) | |
| Misses: 65 | |
| Direct: 66 | |
| Preprocessed: 65 | |
| Uncacheable: 16 | |
| Primary storage: | |
| Hits: 107 / 192 (55.73 %) | |
| Misses: 85 | |
| Cache size (GB): 0.11 / 0.51 (21.98 %) | |
| Files: 4579 | |
| Uncacheable: | |
| Called for linking: 13 | |
| 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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_CORENEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644836856:step_script [0Ksection_start:1644836856:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:coreneuron:nmodl:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=208182 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Acoreneuron%3Anmodl%3Anvhpc%3Aacc-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644836862:archive_cache [0Ksection_start:1644836862: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=208285 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=153652 responseStatus[0;m=201 Created token[0;m=tyUVfAMJ | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=208322 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=153652 responseStatus[0;m=201 Created token[0;m=tyUVfAMJ | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=208362 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=153652 responseStatus[0;m=201 Created token[0;m=tyUVfAMJ | |
| section_end:1644836863:upload_artifacts_on_success [0Ksection_start:1644836863:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836864:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836414:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836414:resolve_secrets [0Ksection_start:1644836414: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor675580677, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153650 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153650_PROD_P112_CP0_C1 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=1:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274636 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153650_PROD_P112_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274636 --cpus-per-task=8 --mem=76G | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n21 via bbpv1.epfl.ch... | |
| section_end:1644836438:prepare_script [0Ksection_start:1644836438: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:1644836438:get_sources [0Ksection_start:1644836438:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:coreneuron:nmodl:nvhpc:omp-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=42350 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:1644836440:restore_cache [0Ksection_start:1644836440:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:nmodl (153644)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=42473 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153644 responseStatus[0;m=200 OK token[0;m=3dEDZKZK | |
| section_end:1644836441:download_artifacts [0Ksection_start:1644836441: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_PACKAGE_DEPENDENCIES="${SPACK_PACKAGE_DEPENDENCIES}^hpe-mpi%gcc"[0;m | |
| [32;1m$ 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/P37548/J153650/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for coreneuron is commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f" | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-bluebrain/packages/coreneuron/package.py b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| index 11516ab..49f7b1e 100644 | |
| --- a/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| +++ b/bluebrain/repo-bluebrain/packages/coreneuron/package.py | |
| @@ -20,7 +20,7 @@ class Coreneuron(CMakePackage): | |
| # This simplifies testing the gitlab-pipelines repository: | |
| git = "git@bbpgitlab.epfl.ch:hpc/coreneuron.git" | |
| - version('develop', branch='master') | |
| + version('develop', commit="3469f1e9e6bf04e5d0f9be59fd494b8f281f457f") | |
| # 1.0.1 > 1.0.0.20210519 > 1.0 as far as Spack is concerned | |
| version('1.0.0.20220111', commit='64e56b7') | |
| version('1.0.0.20211020', commit='e265f9d') | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install coreneuron@develop%nvhpc+nmodl+openmp+gpu+tests~legacy-unit~sympy build_type=RelWithDebInfo ^/cnhmkfzsucqnmy6dfxyfikno2yj57grf^hpe-mpi%gcc | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be jgejfgix5nb6yjvuzuy64sbdppdrl73a | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274636/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274636/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: Mon Feb 14 12:01:07 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 (23.59 %) | |
| Files: 4694 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'jgejfgix5nb6yjvuzuy64sbdppdrl73a' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - coreneuron@develop%nvhpc+gpu~legacy-unit+nmodl+openmp~sympy+tests build_type=RelWithDebInfo | |
| - ^hpe-mpi%gcc | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - jgejfgi coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl+openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - 4ydwt2s ^bison@3.8.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] yjmsba6 ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden 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 | |
| [^] akxpgv2 ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| - udykfw5 ^flex@2.6.3%nvhpc@22.1+lex~nls arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - k3tfixc ^ninja@1.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 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-3.8.2-4ydwt2sjpk4f7vuqyxhxg23cea3k6sxs) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-yjmsba6vrk7ay2rbkah4htoniepm5yci) | |
| ==> 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) | |
| ==> cuda@11.5.1 : has external module in ['cuda/11.5.1'] | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.5.1-fyf4dd (external cuda-11.5.1-akxpgv2q5zrp36lxyjpeuzhsfk77n2mf) | |
| ==> 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-udykfw5i5twmy3lnuuzeemfkn3lvsldx) | |
| ==> 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) | |
| [+] /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_externals/install_gcc-11.2.0-skylake/zlib-1.2.11-mswjss (external zlib-1.2.11-evtnqzdtuvprwnbd2nljimpzywrhw4uo) | |
| ==> 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-k3tfixcs5ddog5pciqqucifnc2qadnyt) | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| ==> Installing coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a | |
| ==> No binary for coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a found: installing from source | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> No patches needed for coreneuron | |
| ==> coreneuron: Executing phase: 'cmake' | |
| ==> coreneuron: Executing phase: 'build' | |
| ==> coreneuron: Executing phase: 'install' | |
| ==> coreneuron: Successfully installed coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a | |
| Fetch: 4.69s. Build: 5m 32.03s. Total: 5m 36.71s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/coreneuron-develop-jgejfg | |
| [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: /nvme/bbpcihpcproj12/274636/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274636/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: Mon Feb 14 12:07:41 2022 | |
| Hits: 31 / 97 (31.96 %) | |
| Direct: 30 / 97 (30.93 %) | |
| Preprocessed: 1 / 67 (1.49 %) | |
| Misses: 66 | |
| Direct: 67 | |
| Preprocessed: 66 | |
| Uncacheable: 17 | |
| Primary storage: | |
| Hits: 107 / 194 (55.15 %) | |
| Misses: 87 | |
| Cache size (GB): 0.13 / 0.51 (24.69 %) | |
| Files: 4781 | |
| Uncacheable: | |
| Called for linking: 14 | |
| 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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_CORENEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644836862:step_script [0Ksection_start:1644836862:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:coreneuron:nmodl:nvhpc:omp-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=59535 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Acoreneuron%3Anmodl%3Anvhpc%3Aomp-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644836868:archive_cache [0Ksection_start:1644836868: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=59919 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=153650 responseStatus[0;m=201 Created token[0;m=XTZc5TNK | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=60031 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=153650 responseStatus[0;m=201 Created token[0;m=XTZc5TNK | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=60069 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=153650 responseStatus[0;m=201 Created token[0;m=XTZc5TNK | |
| section_end:1644836869:upload_artifacts_on_success [0Ksection_start:1644836869:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836870:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836405:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836405:resolve_secrets [0Ksection_start:1644836405: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor194978728, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153664 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153664_PROD_P112_CP4_C5 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274640 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153664_PROD_P112_CP4_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=2:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274640 --cpus-per-task=8 --mem=76G | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i6n32 via bbpv1.epfl.ch... | |
| section_end:1644836438:prepare_script [0Ksection_start:1644836438: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:1644836438:get_sources [0Ksection_start:1644836438:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:neuron:mod2c:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=165992 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:1644836444:restore_cache [0Ksection_start:1644836444:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:mod2c:intel (153654)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=166079 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153654 responseStatus[0;m=200 OK token[0;m=ssyq9Fsy | |
| section_end:1644836445:download_artifacts [0Ksection_start:1644836445: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/P37548/J153664/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153664/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153664/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153664/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153664/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ SPACK_PACKAGE_REF="${ref}='${!var_name}'"[0;m | |
| [32;1m$ echo "Set SPACK_PACKAGE_REF=${SPACK_PACKAGE_REF} from ${var_name}=${!var_name}"[0;m | |
| Set SPACK_PACKAGE_REF=branch='master' from NEURON_BRANCH=master | |
| [32;1m$ break[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for neuron is branch='master' | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py | |
| index 0042131..0b144bf 100644 | |
| --- a/bluebrain/repo-patches/packages/neuron/package.py | |
| +++ b/bluebrain/repo-patches/packages/neuron/package.py | |
| @@ -34,7 +34,7 @@ class Neuron(CMakePackage): | |
| # Patch for recent CMake versions that don't identify NVHPC as PGI | |
| patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:") | |
| - version("develop", branch="master") | |
| + version("develop", branch='master') | |
| version("8.0.2", tag="8.0.2") | |
| version("8.0.1", tag="8.0.1") | |
| version("8.0.0", tag="8.0.0") | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install neuron@develop%intel+coreneuron+debug+tests~legacy-unit~rx3d model_tests=channel-benchmark,olfactory,tqperf-heavy ^/jlimlp3c43orxijl3zdr5c3mlicgrilx | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| ==> Warning: Missing a source id for neuron@develop | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be 7fdjpn6td6dhzjavug7glqebdkw2qfjy | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274640/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274640/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: Mon Feb 14 12:01:09 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): 0.46 / 0.51 (89.54 %) | |
| Files: 38477 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: '7fdjpn6td6dhzjavug7glqebdkw2qfjy' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - neuron@develop%intel+coreneuron+debug~legacy-unit~rx3d+tests model_tests=channel-benchmark,olfactory,tqperf-heavy | |
| [+] ^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 | |
| [^] ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] ^hpe-mpi@2.25.hmpt%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] ^libsonata-report@1.0.0.20211007%intel@2021.4.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^hdf5@1.10.7%intel@2021.4.0+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^pkgconf@1.8.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] ^zlib@1.2.11%intel@2021.4.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] ^spdlog@1.9.2%intel@2021.4.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^python@3.9.7%intel@2021.4.0+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 | |
| [^] ^reportinglib@2.5.6%intel@2021.4.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - 7fdjpn6 neuron@develop%intel@2021.4.0+binary+cmake~codechecks+coreneuron~cross-compile+debug~interviews~ipo+legacy-fr~legacy-unit+memacs+mod-compatibility+mpi+multisend~profile+pysetup+python~rx3d+shared+tests build_type=RelWithDebInfo model_tests=channel-benchmark,olfactory,tqperf-heavy patches=708cb04826b394a858069d93e8c08e1e81e914c23e1ef3da0486e8233834ff6c arch=linux-rhel7-skylake | |
| - dwdch6b ^bison@3.8.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| - z3q5f3x ^cmake@3.21.4%intel@2021.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| [+] jlimlp3 ^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 | |
| [^] i4sftdn ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] 3narjkw ^hpe-mpi@2.25.hmpt%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] 3yjvqc4 ^libsonata-report@1.0.0.20211007%intel@2021.4.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ofveh3j ^hdf5@1.10.7%intel@2021.4.0+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] xys6npz ^pkgconf@1.8.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] e7w5nez ^zlib@1.2.11%intel@2021.4.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] wk3uenv ^spdlog@1.9.2%intel@2021.4.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] f27a7nn ^python@3.9.7%intel@2021.4.0+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 | |
| [^] gdhqypa ^reportinglib@2.5.6%intel@2021.4.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls arch=linux-rhel7-skylake | |
| [^] bjxwlfq ^gettext@0.21%intel@2021.4.0+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-rhel7-skylake | |
| [^] dvyfbbf ^bzip2@1.0.8%intel@2021.4.0~debug~pic+shared arch=linux-rhel7-skylake | |
| [^] ka2cfu4 ^libiconv@1.16%intel@2021.4.0 libs=shared,static arch=linux-rhel7-skylake | |
| [^] w3ob7m2 ^libxml2@2.9.12%intel@2021.4.0~python arch=linux-rhel7-skylake | |
| [^] ahg6hq4 ^xz@5.2.5%intel@2021.4.0~pic libs=shared,static arch=linux-rhel7-skylake | |
| [^] q3rwuez ^ncurses@6.2%intel@2021.4.0~symlinks+termlib abi=none arch=linux-rhel7-skylake | |
| [^] 2fli66n ^tar@1.28%intel@2021.4.0 patches=08921fcbd732050c74ddf1de7d8ad95ffdbc09f8b4342456fa2f6a0dd02a957c,125cd6142fac2cc339e9aebfe79e40f90766022b8e8401532b1729e84fc148c2,5c314db58d005043bf407abaf25eb9823b9032a22fd12a0b142d4bf548130fa4,d428578be7fb99b831eb61e53b8d88a859afe08b479a21238180899707d79ce4 arch=linux-rhel7-skylake | |
| - 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] qj3vvxk ^py-mpi4py@3.1.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] 5flpilw ^py-setuptools@57.4.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] ipsbwzp ^py-numpy@1.19.5%intel@2021.4.0+blas+lapack patches=8a9d5d1b3f145c043b8b04869e7d46c6ff95c3f486d84f69693017c7e6190c7d arch=linux-rhel7-skylake | |
| [^] rl5ojfn ^intel-mkl@2020.4.304%intel@2021.4.0~ilp64+shared threads=none arch=linux-rhel7-skylake | |
| [^] taxuisw ^py-cython@0.29.24%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] tzmlo5v ^py-pytest@6.2.4%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] d5szgli ^py-attrs@21.2.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] huky5p4 ^py-iniconfig@1.1.1%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] wli7caj ^py-packaging@21.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] 3a3ralt ^py-pyparsing@2.4.7%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] rh6zvev ^py-pluggy@0.13.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] kpwupa3 ^py-setuptools-scm@6.3.2%intel@2021.4.0+toml arch=linux-rhel7-skylake | |
| [^] apu667d ^py-tomli@1.2.1%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] jesa65u ^py-pip@21.1.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] skrpmyr ^py-py@1.9.0%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] ktthpzx ^py-toml@0.10.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] tzl5sq5 ^py-pytest-cov@2.8.1%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] zkd7o6d ^py-coverage@5.5%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] 5abs2t7 ^readline@8.1%intel@2021.4.0 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) | |
| ==> 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-z3q5f3xwpuibd3qbgdscqmu3efarbu42) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-i4sftdnkvomfatxuakfaezmt3a3bcetc) | |
| ==> 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-3narjkwjh6i2jr3zl3g5wdjlqi52hkwh) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/pkgconf-1.8.0-xys6np | |
| [+] /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-e7w5nezpwf572epfhbosqfzboztysout) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/spdlog-1.9.2-wk3uen | |
| ==> 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-f27a7nnhppeztxijpispnaedcfo2vjxi) | |
| ==> 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) | |
| [+] /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-dvyfbbfdan33i7wyydyeskb3legztopm) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/libiconv-1.16-ka2cfu | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/xz-5.2.5-ahg6hq | |
| [+] /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-q3rwuezhc2j56kexunypjpejzketozmc) | |
| [+] /usr (external tar-1.28-2fli66nkkv35g34exwd2xifp5w3gtgo6) | |
| ==> 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_externals/install_gcc-11.2.0-skylake/intel-mkl-2020.4.304-rzr3hj (external intel-mkl-2020.4.304-rl5ojfngtc7sffwyz7v6ek6eceq53wed) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/readline-8.1-we2frg (external readline-8.1-5abs2t7f6dtgbejv6kjzd4gjwhdlr7qr) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/reportinglib-2.5.6-gdhqyp | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/hdf5-1.10.7-ofveh3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-setuptools-57.4.0-5flpil | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/libxml2-2.9.12-w3ob7m | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/libsonata-report-1.0.0.20211007-3yjvqc | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-cython-0.29.24-taxuis | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-toml-0.10.2-ktthpz | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-pip-21.1.2-jesa65 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-pyparsing-2.4.7-3a3ral | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-iniconfig-1.1.1-huky5p | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-coverage-5.5-zkd7o6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-mpi4py-3.1.2-qj3vvx | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-attrs-21.2.0-d5szgl | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/gettext-0.21-bjxwlf | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_intel-2021.4.0-skylake/coreneuron-develop-jlimlp | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-numpy-1.19.5-ipsbwz | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-tomli-1.2.1-apu667 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-packaging-21.0-wli7ca | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-setuptools-scm-6.3.2-kpwupa | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-py-1.9.0-skrpmy | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-pluggy-0.13.0-rh6zve | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-pytest-6.2.4-tzmlo5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-pytest-cov-2.8.1-tzl5sq | |
| ==> Installing neuron-develop-7fdjpn6td6dhzjavug7glqebdkw2qfjy | |
| ==> No binary for neuron-develop-7fdjpn6td6dhzjavug7glqebdkw2qfjy found: installing from source | |
| ==> Warning: Missing a source id for neuron@develop | |
| ==> Applied patch /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/bluebrain/repo-patches/packages/neuron/revert_Import3d_numerical_format.master.patch | |
| ==> neuron: Executing phase: 'cmake' | |
| ==> neuron: Executing phase: 'build' | |
| ==> neuron: Executing phase: 'install' | |
| ==> neuron: Successfully installed neuron-develop-7fdjpn6td6dhzjavug7glqebdkw2qfjy | |
| Fetch: 5.88s. Build: 10m 45.29s. Total: 10m 51.18s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_intel-2021.4.0-skylake/neuron-develop-7fdjpn | |
| [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: /nvme/bbpcihpcproj12/274640/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274640/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: Mon Feb 14 12:12:49 2022 | |
| Hits: 556 / 820 (67.80 %) | |
| Direct: 170 / 829 (20.51 %) | |
| Preprocessed: 386 / 653 (59.11 %) | |
| Misses: 264 | |
| Direct: 659 | |
| Preprocessed: 267 | |
| Uncacheable: 132 | |
| Primary storage: | |
| Hits: 1205 / 1652 (72.94 %) | |
| Misses: 447 | |
| Cache size (GB): 0.46 / 0.51 (89.77 %) | |
| Files: 37828 | |
| Cleanups: 2 | |
| Uncacheable: | |
| Autoconf compile/link: 7 | |
| Called for linking: 109 | |
| Called for preprocessing: 1 | |
| Compilation failed: 3 | |
| No input file: 6 | |
| Preprocessing failed: 6 | |
| [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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit d5f613917bfb0567fba43f3f111f3787aeb01f56 in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_NEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644837171:step_script [0Ksection_start:1644837171:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:neuron:mod2c:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=182701 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Aneuron%3Amod2c%3Aintel-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644837188:archive_cache [0Ksection_start:1644837188: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=182796 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=153664 responseStatus[0;m=201 Created token[0;m=z9ztgK9q | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=182836 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=153664 responseStatus[0;m=201 Created token[0;m=z9ztgK9q | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=182878 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=153664 responseStatus[0;m=201 Created token[0;m=z9ztgK9q | |
| section_end:1644837189:upload_artifacts_on_success [0Ksection_start:1644837189:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644837190:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836408:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836408:resolve_secrets [0Ksection_start:1644836408: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor709808366, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153658 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153658_PROD_P112_CP1_C2 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274637 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153658_PROD_P112_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=2:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274637 --cpus-per-task=8 --mem=76G | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n29 via bbpv1.epfl.ch... | |
| section_end:1644836438:prepare_script [0Ksection_start:1644836438: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:1644836438:get_sources [0Ksection_start:1644836438:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:neuron:mod2c:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=143119 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:1644836444:restore_cache [0Ksection_start:1644836444:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:mod2c:nvhpc:acc (153646)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=143190 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153646 responseStatus[0;m=200 OK token[0;m=LzhyaC-w | |
| section_end:1644836445:download_artifacts [0Ksection_start:1644836445: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/P37548/J153658/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153658/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153658/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153658/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153658/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ SPACK_PACKAGE_REF="${ref}='${!var_name}'"[0;m | |
| [32;1m$ echo "Set SPACK_PACKAGE_REF=${SPACK_PACKAGE_REF} from ${var_name}=${!var_name}"[0;m | |
| Set SPACK_PACKAGE_REF=branch='master' from NEURON_BRANCH=master | |
| [32;1m$ break[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for neuron is branch='master' | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py | |
| index 0042131..0b144bf 100644 | |
| --- a/bluebrain/repo-patches/packages/neuron/package.py | |
| +++ b/bluebrain/repo-patches/packages/neuron/package.py | |
| @@ -34,7 +34,7 @@ class Neuron(CMakePackage): | |
| # Patch for recent CMake versions that don't identify NVHPC as PGI | |
| patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:") | |
| - version("develop", branch="master") | |
| + version("develop", branch='master') | |
| version("8.0.2", tag="8.0.2") | |
| version("8.0.1", tag="8.0.1") | |
| version("8.0.0", tag="8.0.0") | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install neuron@develop%nvhpc+coreneuron+debug+tests~legacy-unit~rx3d model_tests=channel-benchmark,olfactory,tqperf-heavy ^/stctgospgustbslpq3fnxooxmjytgnr4 | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| ==> Warning: Missing a source id for neuron@develop | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be 6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274637/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274637/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: Mon Feb 14 12:01:09 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): 0.46 / 0.51 (89.27 %) | |
| Files: 43114 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: '6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - neuron@develop%nvhpc+coreneuron+debug~legacy-unit~rx3d+tests model_tests=channel-benchmark,olfactory,tqperf-heavy | |
| [+] ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi~nmodl+openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] ^hpe-mpi@2.25.hmpt%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] ^libsonata-report@1.0.0.20211007%nvhpc@22.1~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^hdf5@1.10.7%nvhpc@22.1+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^pkgconf@1.8.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] ^zlib@1.2.11%nvhpc@22.1+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] ^spdlog@1.9.2%nvhpc@22.1~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^python@3.9.7%nvhpc@22.1+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 | |
| [^] ^reportinglib@2.5.6%nvhpc@22.1~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - 6y2lcde neuron@develop%nvhpc@22.1+binary+cmake~codechecks+coreneuron~cross-compile+debug~interviews~ipo+legacy-fr~legacy-unit+memacs+mod-compatibility+mpi+multisend~profile+pysetup+python~rx3d+shared+tests build_type=RelWithDebInfo model_tests=channel-benchmark,olfactory,tqperf-heavy patches=708cb04826b394a858069d93e8c08e1e81e914c23e1ef3da0486e8233834ff6c arch=linux-rhel7-skylake | |
| - 4ydwt2s ^bison@3.8.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| - p7c65dg ^cmake@3.21.4%nvhpc@22.1~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| [+] stctgos ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi~nmodl+openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] yjmsba6 ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] akxpgv2 ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] m2kogdx ^hpe-mpi@2.25.hmpt%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] f4xlnor ^libsonata-report@1.0.0.20211007%nvhpc@22.1~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] vpj3yjx ^hdf5@1.10.7%nvhpc@22.1+cxx~fortran+hl~ipo~java+mpi+shared~szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] hrj5mom ^pkgconf@1.8.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] lhe3cog ^zlib@1.2.11%nvhpc@22.1+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] tvz76i6 ^spdlog@1.9.2%nvhpc@22.1~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] uflaxk5 ^python@3.9.7%nvhpc@22.1+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 | |
| [^] pmjml4k ^reportinglib@2.5.6%nvhpc@22.1~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - udykfw5 ^flex@2.6.3%nvhpc@22.1+lex~nls arch=linux-rhel7-skylake | |
| [^] vfnujnu ^gettext@0.21%nvhpc@22.1+bzip2+curses+git~libunistring+libxml2+tar+xz patches=6e530daaae14725d578d6cafbf7d523accc9ed29fd817bd421cf98a5f51e9e1b,bbe9f0539aa504966ac104224d25a9260faa1015ed3adda936467be9c7de4eae,fb27a3fb5e414bdc50ffebbbe2da986473df70a493caa4396226f51a67c55424 arch=linux-rhel7-skylake | |
| [^] otl4d6j ^bzip2@1.0.8%nvhpc@22.1~debug~pic+shared arch=linux-rhel7-skylake | |
| [^] mvuwafa ^libiconv@1.16%nvhpc@22.1 libs=shared,static arch=linux-rhel7-skylake | |
| [^] 26lquyb ^libxml2@2.9.12%nvhpc@22.1~python patches=05ff238cf435825ef835c7ae39376b52dc83d8caf19e962f0766c841386a305a,10a88ad47f9797cf7cf2d7d07241f665a3b6d1f31fa026728c8c2ae93e1664e9 arch=linux-rhel7-skylake | |
| [^] rxezt7x ^xz@5.2.5%nvhpc@22.1~pic libs=shared,static arch=linux-rhel7-skylake | |
| [^] cr5jl3g ^ncurses@6.2%nvhpc@22.1~symlinks+termlib abi=none arch=linux-rhel7-skylake | |
| [^] bibgukq ^tar@1.28%nvhpc@22.1 patches=08921fcbd732050c74ddf1de7d8ad95ffdbc09f8b4342456fa2f6a0dd02a957c,125cd6142fac2cc339e9aebfe79e40f90766022b8e8401532b1729e84fc148c2,5c314db58d005043bf407abaf25eb9823b9032a22fd12a0b142d4bf548130fa4,d428578be7fb99b831eb61e53b8d88a859afe08b479a21238180899707d79ce4 arch=linux-rhel7-skylake | |
| - k3tfixc ^ninja@1.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] jxdaxac ^py-mpi4py@3.1.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] xaaaqpd ^py-setuptools@57.4.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] x6cazf6 ^py-numpy@1.17.5%gcc@11.2.0+blas+lapack patches=cf407c1024b0878c4222dd352aa9dece412073bb15b138243a2893725434c7b6 arch=linux-rhel7-skylake | |
| [^] r5cvgru ^intel-mkl@2020.4.304%gcc@11.2.0~ilp64+shared threads=none arch=linux-rhel7-skylake | |
| [^] n6ppovr ^py-pytest@6.2.4%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] k3wz6yw ^py-attrs@21.2.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] dfpy4e5 ^py-iniconfig@1.1.1%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] z4gqy6i ^py-packaging@21.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] qcykqrv ^py-pyparsing@2.4.7%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] wknqzdd ^py-pluggy@0.13.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] rhv2lki ^py-setuptools-scm@6.3.2%nvhpc@22.1+toml arch=linux-rhel7-skylake | |
| [^] mfmfxyt ^py-tomli@1.2.1%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] c6xuo6g ^py-pip@21.1.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] upuklap ^py-py@1.9.0%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] llxjlbe ^py-toml@0.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] 2ikjjpw ^py-pytest-cov@2.8.1%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] mxzfhfa ^py-coverage@5.5%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] f5syxww ^readline@8.1%nvhpc@22.1 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-3.8.2-4ydwt2sjpk4f7vuqyxhxg23cea3k6sxs) | |
| ==> 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-p7c65dgnlldt4dvtftndybaiajfebff4) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-yjmsba6vrk7ay2rbkah4htoniepm5yci) | |
| ==> cuda@11.5.1 : has external module in ['cuda/11.5.1'] | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.5.1-fyf4dd (external cuda-11.5.1-akxpgv2q5zrp36lxyjpeuzhsfk77n2mf) | |
| ==> 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-m2kogdxs5o73igxd4yhhbjkgr2ap6wvc) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/pkgconf-1.8.0-hrj5mo | |
| [+] /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-lhe3cogyglvnx55jlcaejfsy7dul3kjz) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/spdlog-1.9.2-tvz76i | |
| ==> 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-uflaxk5ioqutxfb4n2de3l7kjijzx772) | |
| ==> 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-udykfw5i5twmy3lnuuzeemfkn3lvsldx) | |
| [+] /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-otl4d6j6tddp7axqefto6tjntdttmmss) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/libiconv-1.16-mvuwaf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/xz-5.2.5-rxezt7 | |
| [+] /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-cr5jl3g3vto754rzzoyn56p3gvk7gjjf) | |
| [+] /usr (external tar-1.28-bibgukqmswxll4tnstm7lipywlaflbku) | |
| ==> 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-k3tfixcs5ddog5pciqqucifnc2qadnyt) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/intel-mkl-2020.4.304-rzr3hj (external intel-mkl-2020.4.304-r5cvgrurdnt6y267arsmmmgqi75ouxd2) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/readline-8.1-we2frg (external readline-8.1-f5syxwwo67gnhz6fu446xuhaezblb2t7) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/reportinglib-2.5.6-pmjml4 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/hdf5-1.10.7-vpj3yj | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-setuptools-57.4.0-xaaaqp | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/libxml2-2.9.12-26lquy | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/libsonata-report-1.0.0.20211007-f4xlno | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-toml-0.10.2-llxjlb | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-pip-21.1.2-c6xuo6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-pyparsing-2.4.7-qcykqr | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-numpy-1.17.5-x6cazf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-mpi4py-3.1.2-jxdaxa | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-iniconfig-1.1.1-dfpy4e | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-coverage-5.5-mxzfhf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-attrs-21.2.0-k3wz6y | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/gettext-0.21-vfnujn | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/coreneuron-develop-stctgo | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-tomli-1.2.1-mfmfxy | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-packaging-21.0-z4gqy6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-setuptools-scm-6.3.2-rhv2lk | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-py-1.9.0-upukla | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-pluggy-0.13.0-wknqzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-pytest-6.2.4-n6ppov | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.1-skylake/py-pytest-cov-2.8.1-2ikjjp | |
| ==> Installing neuron-develop-6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u | |
| ==> No binary for neuron-develop-6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u found: installing from source | |
| ==> Warning: Missing a source id for neuron@develop | |
| ==> Applied patch /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/bluebrain/repo-patches/packages/neuron/revert_Import3d_numerical_format.master.patch | |
| ==> neuron: Executing phase: 'cmake' | |
| ==> neuron: Executing phase: 'build' | |
| ==> neuron: Executing phase: 'install' | |
| ==> neuron: Successfully installed neuron-develop-6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u | |
| Fetch: 4.13s. Build: 12m 24.27s. Total: 12m 28.40s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/neuron-develop-6y2lcd | |
| [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: /nvme/bbpcihpcproj12/274637/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274637/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: Mon Feb 14 12:14:28 2022 | |
| Hits: 555 / 819 (67.77 %) | |
| Direct: 170 / 828 (20.53 %) | |
| Preprocessed: 385 / 652 (59.05 %) | |
| Misses: 264 | |
| Direct: 658 | |
| Preprocessed: 267 | |
| Uncacheable: 123 | |
| Primary storage: | |
| Hits: 1204 / 1650 (72.97 %) | |
| Misses: 446 | |
| Cache size (GB): 0.45 / 0.51 (87.34 %) | |
| Files: 41114 | |
| Cleanups: 3 | |
| Uncacheable: | |
| Autoconf compile/link: 7 | |
| Called for linking: 100 | |
| Called for preprocessing: 1 | |
| Compilation failed: 3 | |
| No input file: 6 | |
| Preprocessing failed: 6 | |
| [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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit d5f613917bfb0567fba43f3f111f3787aeb01f56 in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_NEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644837270:step_script [0Ksection_start:1644837270:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:neuron:mod2c:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=168503 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Aneuron%3Amod2c%3Anvhpc%3Aacc-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644837286:archive_cache [0Ksection_start:1644837286: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=168850 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=153658 responseStatus[0;m=201 Created token[0;m=dzpyhSZr | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=168888 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=153658 responseStatus[0;m=201 Created token[0;m=dzpyhSZr | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=168930 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=153658 responseStatus[0;m=201 Created token[0;m=dzpyhSZr | |
| section_end:1644837288:upload_artifacts_on_success [0Ksection_start:1644837288:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644837289:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836657:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836657:resolve_secrets [0Ksection_start:1644836657: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor686026666, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153666 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153666_PROD_P112_CP10_C21 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274666 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153666_PROD_P112_CP10_C21 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=2:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274666 --cpus-per-task=8 --mem=76G | |
| section_end:1644836684:prepare_executor [0Ksection_start:1644836684:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n30 via bbpv1.epfl.ch... | |
| section_end:1644836687:prepare_script [0Ksection_start:1644836687: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:1644836688:get_sources [0Ksection_start:1644836688:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:neuron:nmodl:intel-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=285613 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:1644836694:restore_cache [0Ksection_start:1644836694:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:intel (153656)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=285953 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153656 responseStatus[0;m=200 OK token[0;m=NAxHmCYD | |
| section_end:1644836696:download_artifacts [0Ksection_start:1644836696: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/P37548/J153666/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ SPACK_PACKAGE_REF="${ref}='${!var_name}'"[0;m | |
| [32;1m$ echo "Set SPACK_PACKAGE_REF=${SPACK_PACKAGE_REF} from ${var_name}=${!var_name}"[0;m | |
| Set SPACK_PACKAGE_REF=branch='master' from NEURON_BRANCH=master | |
| [32;1m$ break[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for neuron is branch='master' | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py | |
| index 0042131..0b144bf 100644 | |
| --- a/bluebrain/repo-patches/packages/neuron/package.py | |
| +++ b/bluebrain/repo-patches/packages/neuron/package.py | |
| @@ -34,7 +34,7 @@ class Neuron(CMakePackage): | |
| # Patch for recent CMake versions that don't identify NVHPC as PGI | |
| patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:") | |
| - version("develop", branch="master") | |
| + version("develop", branch='master') | |
| version("8.0.2", tag="8.0.2") | |
| version("8.0.1", tag="8.0.1") | |
| version("8.0.0", tag="8.0.0") | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install neuron@develop%intel+coreneuron+debug+tests~legacy-unit~rx3d model_tests=channel-benchmark,olfactory,tqperf-heavy ^/hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| ==> Warning: Missing a source id for neuron@develop | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be glvms6vo6gkpnkjk6xwlpthjp6fh3pqs | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274666/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274666/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: Mon Feb 14 12:05:23 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): 0.47 / 0.51 (92.10 %) | |
| Files: 35077 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'glvms6vo6gkpnkjk6xwlpthjp6fh3pqs' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - neuron@develop%intel+coreneuron+debug~legacy-unit~rx3d+tests model_tests=channel-benchmark,olfactory,tqperf-heavy | |
| [+] ^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 | |
| [^] ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^libsonata-report@1.0.0.20211007%gcc@11.2.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - glvms6v neuron@develop%intel@2021.4.0+binary+cmake~codechecks+coreneuron~cross-compile+debug~interviews~ipo+legacy-fr~legacy-unit+memacs+mod-compatibility+mpi+multisend~profile+pysetup+python~rx3d+shared+tests build_type=RelWithDebInfo model_tests=channel-benchmark,olfactory,tqperf-heavy patches=708cb04826b394a858069d93e8c08e1e81e914c23e1ef3da0486e8233834ff6c arch=linux-rhel7-skylake | |
| - dwdch6b ^bison@3.8.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| - z3q5f3x ^cmake@3.21.4%intel@2021.4.0~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| [+] hp7e7dx ^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 | |
| [^] i4sftdn ^boost@1.77.0%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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 5fkun4i ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls 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 | |
| [^] jzpqn5y ^xz@5.2.5%gcc@11.2.0~pic libs=shared,static 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 | |
| - 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake | |
| [^] n6q4vfz ^py-mpi4py@3.1.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] gjm7kkq ^py-numpy@1.19.5%gcc@11.2.0+blas+lapack patches=8a9d5d1b3f145c043b8b04869e7d46c6ff95c3f486d84f69693017c7e6190c7d arch=linux-rhel7-skylake | |
| [^] r5cvgru ^intel-mkl@2020.4.304%gcc@11.2.0~ilp64+shared threads=none arch=linux-rhel7-skylake | |
| [^] h2fsi6i ^py-cython@0.29.24%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] q5n7ofc ^py-pytest-cov@2.8.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] fudvy5v ^py-coverage@5.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 5abs2t7 ^readline@8.1%intel@2021.4.0 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) | |
| ==> 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-z3q5f3xwpuibd3qbgdscqmu3efarbu42) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-i4sftdnkvomfatxuakfaezmt3a3bcetc) | |
| ==> 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) | |
| [+] /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_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_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| ==> 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) | |
| [+] /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/xz-5.2.5-jzpqn5 | |
| [+] /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) | |
| ==> 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_externals/install_gcc-11.2.0-skylake/intel-mkl-2020.4.304-rzr3hj (external intel-mkl-2020.4.304-r5cvgrurdnt6y267arsmmmgqi75ouxd2) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/readline-8.1-we2frg (external readline-8.1-5abs2t7f6dtgbejv6kjzd4gjwhdlr7qr) | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /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/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-coverage-5.5-fudvy5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpi4py-3.1.2-n6q4vf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-cython-0.29.24-h2fsi6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /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/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-numpy-1.19.5-gjm7kk | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-cov-2.8.1-q5n7of | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_intel-2021.4.0-skylake/coreneuron-develop-hp7e7d | |
| ==> Installing neuron-develop-glvms6vo6gkpnkjk6xwlpthjp6fh3pqs | |
| ==> No binary for neuron-develop-glvms6vo6gkpnkjk6xwlpthjp6fh3pqs found: installing from source | |
| ==> Warning: Missing a source id for neuron@develop | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> Error: Error: [('nrn/src/nrnpython', '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-build/spack-stage-neuron-develop-glvms6vo6gkpnkjk6xwlpthjp6fh3pqs/spack-src/src/nrnpython', "[Errno 28] No space left on device: '/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153666/spack-build/spack-stage-neuron-develop-glvms6vo6gkpnkjk6xwlpthjp6fh3pqs/spack-src/src/nrnpython'")] | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/lib/spack/spack/package.py:1387, in do_fetch: | |
| 1384 | |
| 1385 self.stage.create() | |
| 1386 err_msg = None if not self.manual_download else self.download_instr | |
| >> 1387 start_time = time.time() | |
| 1388 self.stage.fetch(mirror_only, err_msg=err_msg) | |
| 1389 self._fetch_time = time.time() - start_time | |
| 1390 | |
| [32;1m$ chmod -R g+rX "${SPACK_BUILD}"[0;m | |
| [32;1m$ if [[ ${install_failed} == 1 ]]; then exit 1; fi[0;m | |
| srun: error: r1i7n30: task 0: Exited with exit code 1 | |
| section_end:1644836787:step_script [0Ksection_start:1644836787:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=289683 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=153666 responseStatus[0;m=201 Created token[0;m=9Ue_L81m | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=289733 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=153666 responseStatus[0;m=201 Created token[0;m=9Ue_L81m | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=289775 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=153666 responseStatus[0;m=201 Created token[0;m=9Ue_L81m | |
| section_end:1644836788:upload_artifacts_on_failure [0Ksection_start:1644836788:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836789:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836867:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836867:resolve_secrets [0Ksection_start:1644836867: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor665190715, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153662 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153662_PROD_P112_CP11_C13 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274677 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153662_PROD_P112_CP11_C13 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=2:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274677 --cpus-per-task=8 --mem=76G | |
| section_end:1644836898:prepare_executor [0Ksection_start:1644836898:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n21 via bbpv1.epfl.ch... | |
| section_end:1644836900:prepare_script [0Ksection_start:1644836900: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:1644836901:get_sources [0Ksection_start:1644836901:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:neuron:nmodl:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=61193 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:1644836907:restore_cache [0Ksection_start:1644836907:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:nvhpc:acc (153652)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=61270 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153652 responseStatus[0;m=200 OK token[0;m=tyUVfAMJ | |
| section_end:1644836907:download_artifacts [0Ksection_start:1644836907: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/P37548/J153662/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153662/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153662/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153662/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153662/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ SPACK_PACKAGE_REF="${ref}='${!var_name}'"[0;m | |
| [32;1m$ echo "Set SPACK_PACKAGE_REF=${SPACK_PACKAGE_REF} from ${var_name}=${!var_name}"[0;m | |
| Set SPACK_PACKAGE_REF=branch='master' from NEURON_BRANCH=master | |
| [32;1m$ break[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for neuron is branch='master' | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py | |
| index 0042131..0b144bf 100644 | |
| --- a/bluebrain/repo-patches/packages/neuron/package.py | |
| +++ b/bluebrain/repo-patches/packages/neuron/package.py | |
| @@ -34,7 +34,7 @@ class Neuron(CMakePackage): | |
| # Patch for recent CMake versions that don't identify NVHPC as PGI | |
| patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:") | |
| - version("develop", branch="master") | |
| + version("develop", branch='master') | |
| version("8.0.2", tag="8.0.2") | |
| version("8.0.1", tag="8.0.1") | |
| version("8.0.0", tag="8.0.0") | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install neuron@develop%nvhpc+coreneuron+debug+tests~legacy-unit~rx3d model_tests=channel-benchmark,olfactory,tqperf-heavy ^/vqg67goxagdsf3kxjwwbdbz6jsbvmspa | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| ==> Warning: Missing a source id for neuron@develop | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be 2qm6t5rbh7lbu3qrc6stglq74d6emsen | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274677/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274677/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: Mon Feb 14 12:08:54 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): 0.46 / 0.51 (89.03 %) | |
| Files: 30909 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: '2qm6t5rbh7lbu3qrc6stglq74d6emsen' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - neuron@develop%nvhpc+coreneuron+debug~legacy-unit~rx3d+tests model_tests=channel-benchmark,olfactory,tqperf-heavy | |
| [+] ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl~openmp~profile+report+shared+sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^libsonata-report@1.0.0.20211007%gcc@11.2.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - 2qm6t5r neuron@develop%nvhpc@22.1+binary+cmake~codechecks+coreneuron~cross-compile+debug~interviews~ipo+legacy-fr~legacy-unit+memacs+mod-compatibility+mpi+multisend~profile+pysetup+python~rx3d+shared+tests build_type=RelWithDebInfo model_tests=channel-benchmark,olfactory,tqperf-heavy patches=708cb04826b394a858069d93e8c08e1e81e914c23e1ef3da0486e8233834ff6c arch=linux-rhel7-skylake | |
| - 4ydwt2s ^bison@3.8.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| - p7c65dg ^cmake@3.21.4%nvhpc@22.1~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| [+] vqg67go ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl~openmp~profile+report+shared+sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] yjmsba6 ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] akxpgv2 ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 5fkun4i ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - udykfw5 ^flex@2.6.3%nvhpc@22.1+lex~nls 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 | |
| [^] jzpqn5y ^xz@5.2.5%gcc@11.2.0~pic libs=shared,static 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 | |
| - k3tfixc ^ninja@1.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] n6q4vfz ^py-mpi4py@3.1.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] gjm7kkq ^py-numpy@1.19.5%gcc@11.2.0+blas+lapack patches=8a9d5d1b3f145c043b8b04869e7d46c6ff95c3f486d84f69693017c7e6190c7d arch=linux-rhel7-skylake | |
| [^] r5cvgru ^intel-mkl@2020.4.304%gcc@11.2.0~ilp64+shared threads=none arch=linux-rhel7-skylake | |
| [^] h2fsi6i ^py-cython@0.29.24%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] q5n7ofc ^py-pytest-cov@2.8.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] fudvy5v ^py-coverage@5.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] f5syxww ^readline@8.1%nvhpc@22.1 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-3.8.2-4ydwt2sjpk4f7vuqyxhxg23cea3k6sxs) | |
| ==> 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-p7c65dgnlldt4dvtftndybaiajfebff4) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-yjmsba6vrk7ay2rbkah4htoniepm5yci) | |
| ==> cuda@11.5.1 : has external module in ['cuda/11.5.1'] | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.5.1-fyf4dd (external cuda-11.5.1-akxpgv2q5zrp36lxyjpeuzhsfk77n2mf) | |
| ==> 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) | |
| [+] /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_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_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| ==> 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-udykfw5i5twmy3lnuuzeemfkn3lvsldx) | |
| [+] /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/xz-5.2.5-jzpqn5 | |
| [+] /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) | |
| ==> 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-k3tfixcs5ddog5pciqqucifnc2qadnyt) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/intel-mkl-2020.4.304-rzr3hj (external intel-mkl-2020.4.304-r5cvgrurdnt6y267arsmmmgqi75ouxd2) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/readline-8.1-we2frg (external readline-8.1-f5syxwwo67gnhz6fu446xuhaezblb2t7) | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /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/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-cython-0.29.24-h2fsi6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpi4py-3.1.2-n6q4vf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-coverage-5.5-fudvy5 | |
| [+] /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/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-numpy-1.19.5-gjm7kk | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-cov-2.8.1-q5n7of | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/coreneuron-develop-vqg67g | |
| ==> Installing neuron-develop-2qm6t5rbh7lbu3qrc6stglq74d6emsen | |
| ==> No binary for neuron-develop-2qm6t5rbh7lbu3qrc6stglq74d6emsen found: installing from source | |
| ==> Warning: Missing a source id for neuron@develop | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> Applied patch /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/bluebrain/repo-patches/packages/neuron/revert_Import3d_numerical_format.master.patch | |
| ==> neuron: Executing phase: 'cmake' | |
| ==> neuron: Executing phase: 'build' | |
| ==> neuron: Executing phase: 'install' | |
| ==> neuron: Successfully installed neuron-develop-2qm6t5rbh7lbu3qrc6stglq74d6emsen | |
| Fetch: 4.45s. Build: 49m 9.57s. Total: 49m 14.02s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/neuron-develop-2qm6t5 | |
| [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: /nvme/bbpcihpcproj12/274677/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274677/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: Mon Feb 14 12:59:01 2022 | |
| Hits: 584 / 801 (72.91 %) | |
| Direct: 163 / 810 (20.12 %) | |
| Preprocessed: 421 / 641 (65.68 %) | |
| Misses: 217 | |
| Direct: 647 | |
| Preprocessed: 220 | |
| Uncacheable: 120 | |
| Primary storage: | |
| Hits: 1057 / 1614 (65.49 %) | |
| Misses: 557 | |
| Cache size (GB): 0.45 / 0.51 (87.52 %) | |
| Files: 29891 | |
| Cleanups: 3 | |
| Uncacheable: | |
| Autoconf compile/link: 7 | |
| Called for linking: 97 | |
| Called for preprocessing: 1 | |
| Compilation failed: 3 | |
| No input file: 6 | |
| Preprocessing failed: 6 | |
| [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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit d5f613917bfb0567fba43f3f111f3787aeb01f56 in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_NEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644839942:step_script [0Ksection_start:1644839942:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:neuron:nmodl:nvhpc:acc-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=129884 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Aneuron%3Anmodl%3Anvhpc%3Aacc-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644839959:archive_cache [0Ksection_start:1644839959: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=130110 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=153662 responseStatus[0;m=201 Created token[0;m=yz6CrK9t | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=130147 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=153662 responseStatus[0;m=201 Created token[0;m=yz6CrK9t | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=130191 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=153662 responseStatus[0;m=201 Created token[0;m=yz6CrK9t | |
| section_end:1644839961:upload_artifacts_on_success [0Ksection_start:1644839961:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644839962:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836873:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836873:resolve_secrets [0Ksection_start:1644836873: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor736900649, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153660 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=8 | |
| A slurm job will be created with name GL_J153660_PROD_P112_CP0_C1 | |
| Job parameters: memory=76G, cpus_per_task=8, duration=2:00:00, constraint=cpu ntasks=2 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274679 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=2 --cpus-per-task=8 --mem=76G --job-name=GL_J153660_PROD_P112_CP0_C1 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=2:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=2 --jobid=274679 --cpus-per-task=8 --mem=76G | |
| section_end:1644836898:prepare_executor [0Ksection_start:1644836898:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n29 via bbpv1.epfl.ch... | |
| section_end:1644836900:prepare_script [0Ksection_start:1644836900: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:1644836901:get_sources [0Ksection_start:1644836901:restore_cache [0K[0K[36;1mRestoring cache[0;m[0;m | |
| [32;1mChecking cache for build:neuron:nmodl:nvhpc:omp-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=149416 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:1644836907:restore_cache [0Ksection_start:1644836907:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:nvhpc:omp (153650)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=149825 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153650 responseStatus[0;m=200 OK token[0;m=XTZc5TNK | |
| section_end:1644836907:download_artifacts [0Ksection_start:1644836907: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/P37548/J153660/spack-config/config.yaml:2 build_stage: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153660/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153660/spack-build | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153660/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153660/spack-source-cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 extensions: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 template_dirs: | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``). | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # home directory. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # pip installable. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces. | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:38 # | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/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/P37548/J153640/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/P37548/J153640/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/P37548/J153640/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:118 checksum: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:123 deprecated: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:128 dirty: False | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:136 build_language: C | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:145 locks: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300 | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True | |
| /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/etc/spack/defaults/config.yaml:207 terminal_title: False | |
| _builtin debug: False | |
| [32;1m$ if [ "${SPACK_EXPORT_SPECS}" ]; then[0;m | |
| [32;1m$ export XDG_CONFIG_HOME=${PWD}/local_config[0;m | |
| [32;1m$ 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$ cat "${XDG_CONFIG_HOME}/git/config"[0;m | |
| [url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"] | |
| insteadOf = git@bbpgitlab.epfl.ch: | |
| [32;1m$ for ref in tag commit branch; do[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ done[0;m | |
| [32;1m$ var_name="${SPACK_PACKAGE^^}_${ref^^}"[0;m | |
| [32;1m$ if [[ -n "${!var_name}" ]]; then[0;m | |
| [32;1m$ SPACK_PACKAGE_REF="${ref}='${!var_name}'"[0;m | |
| [32;1m$ echo "Set SPACK_PACKAGE_REF=${SPACK_PACKAGE_REF} from ${var_name}=${!var_name}"[0;m | |
| Set SPACK_PACKAGE_REF=branch='master' from NEURON_BRANCH=master | |
| [32;1m$ break[0;m | |
| [32;1m$ SPACK_PACKAGE_FILE="$(spack location -p ${SPACK_PACKAGE})/package.py"[0;m | |
| [32;1m$ if [ "${SPACK_PACKAGE_REF}" ]; then[0;m | |
| [32;1m$ echo New ref for ${SPACK_PACKAGE} is ${SPACK_PACKAGE_REF}[0;m | |
| New ref for neuron is branch='master' | |
| [32;1m$ sed -i -e "/^\s*version\s*(\s*\(['\"]\)develop\1/ { s/,\s*\(commit\|tag\|branch\)=\([\"']\)[^\"']\+\2//g; s#)#, ${SPACK_PACKAGE_REF})#; }" "${SPACK_PACKAGE_FILE}"[0;m | |
| [32;1m$ (cd $(dirname "${SPACK_PACKAGE_FILE}") && git diff "${SPACK_PACKAGE_FILE}")[0;m | |
| diff --git a/bluebrain/repo-patches/packages/neuron/package.py b/bluebrain/repo-patches/packages/neuron/package.py | |
| index 0042131..0b144bf 100644 | |
| --- a/bluebrain/repo-patches/packages/neuron/package.py | |
| +++ b/bluebrain/repo-patches/packages/neuron/package.py | |
| @@ -34,7 +34,7 @@ class Neuron(CMakePackage): | |
| # Patch for recent CMake versions that don't identify NVHPC as PGI | |
| patch("patch-v800-cmake-nvhpc.patch", when="@8.0.0%nvhpc^cmake@3.20:") | |
| - version("develop", branch="master") | |
| + version("develop", branch='master') | |
| version("8.0.2", tag="8.0.2") | |
| version("8.0.1", tag="8.0.1") | |
| version("8.0.0", tag="8.0.0") | |
| [32;1m$ fi[0;m | |
| [32;1m$ SPACK_FULL_SPEC="${SPACK_PACKAGE}@develop${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER}${SPACK_PACKAGE_SPEC}${SPACK_PACKAGE_DEPENDENCIES:+ }${SPACK_PACKAGE_DEPENDENCIES}"[0;m | |
| [32;1m$ echo "Preparing to install ${SPACK_FULL_SPEC}"[0;m | |
| Preparing to install neuron@develop%nvhpc+coreneuron+debug+tests~legacy-unit~rx3d model_tests=channel-benchmark,olfactory,tqperf-heavy ^/jgejfgix5nb6yjvuzuy64sbdppdrl73a | |
| [32;1m$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})[0;m | |
| ==> Warning: Missing a source id for neuron@develop | |
| [32;1m$ 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 ${SPACK_INSTALLED_HASH}"[0;m | |
| Determined its hash will be ccjdz33a47dcm6emvjsbg2kpa4job22w | |
| [32;1m$ 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=${CCACHE_BASEDIR}[0;m | |
| CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548 | |
| [32;1m$ 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: /nvme/bbpcihpcproj12/274679/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274679/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: Mon Feb 14 12:09:17 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): 0.46 / 0.51 (89.24 %) | |
| Files: 36831 | |
| [32;1m$ fi[0;m | |
| [32;1m$ module load unstable git ${SPACK_EXTRA_MODULES}[0;m | |
| [32;1m$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true[0;m | |
| ==> Error: No installed spec matches the hash: 'ccjdz33a47dcm6emvjsbg2kpa4job22w' | |
| [32;1m$ spack spec -Il ${SPACK_FULL_SPEC}[0;m | |
| Input spec | |
| -------------------------------- | |
| - neuron@develop%nvhpc+coreneuron+debug~legacy-unit~rx3d+tests model_tests=channel-benchmark,olfactory,tqperf-heavy | |
| [+] ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl+openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^libsonata-report@1.0.0.20211007%gcc@11.2.0~ipo+mpi build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] ^py-markupsafe@2.0.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^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 | |
| [^] ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| Concretized | |
| -------------------------------- | |
| - ccjdz33 neuron@develop%nvhpc@22.1+binary+cmake~codechecks+coreneuron~cross-compile+debug~interviews~ipo+legacy-fr~legacy-unit+memacs+mod-compatibility+mpi+multisend~profile+pysetup+python~rx3d+shared+tests build_type=RelWithDebInfo model_tests=channel-benchmark,olfactory,tqperf-heavy patches=708cb04826b394a858069d93e8c08e1e81e914c23e1ef3da0486e8233834ff6c arch=linux-rhel7-skylake | |
| - 4ydwt2s ^bison@3.8.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| - p7c65dg ^cmake@3.21.4%nvhpc@22.1~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake | |
| [+] jgejfgi ^coreneuron@develop%nvhpc@22.1~caliper~codegenopt+gpu~ipo~ispc~knl~legacy-unit+mpi+nmodl+openmp~profile+report+shared~sympy~sympyopt+tests~unified build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] yjmsba6 ^boost@1.77.0%nvhpc@22.1+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 patches=93f4aad8f88d1437e50d95a2d066390ef3753b99ef5de24f7a46bc083bd6df06 visibility=hidden arch=linux-rhel7-skylake | |
| [^] akxpgv2 ^cuda@11.5.1%nvhpc@22.1~dev arch=linux-rhel7-skylake | |
| [^] hyunzkn ^hpe-mpi@2.25.hmpt%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] exroq36 ^libsonata-report@1.0.0.20211007%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 | |
| [^] ihxi5rl ^pkgconf@1.8.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] evtnqzd ^zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-rhel7-skylake | |
| [^] x72vveu ^spdlog@1.9.2%gcc@11.2.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [+] cnhmkfz ^nmodl@develop%gcc@11.2.0~ipo~legacy-unit~python build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| [^] onq3mhg ^py-jinja2@3.0.1%gcc@11.2.0~i18n arch=linux-rhel7-skylake | |
| [^] 4ectow5 ^py-markupsafe@2.0.1%gcc@11.2.0 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 | |
| [^] 22arfs4 ^py-pytest@6.2.4%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ascbeii ^py-attrs@21.2.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] kvw3vhm ^py-iniconfig@1.1.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 7iyiygo ^py-packaging@21.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] c7qvw2q ^py-pyparsing@2.4.7%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] mazoiox ^py-pluggy@0.13.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] y7rfzdj ^py-py@1.9.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] v4z3s5e ^py-setuptools@57.4.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] w4gddqx ^py-toml@0.10.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] ci5oe5b ^py-pyyaml@5.3.1%gcc@11.2.0+libyaml arch=linux-rhel7-skylake | |
| [^] xj2wlac ^libyaml@0.2.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] xtett6q ^py-sympy@1.8%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] 5fkun4i ^reportinglib@2.5.6%gcc@11.2.0~ipo~profile+shared~tests build_type=RelWithDebInfo arch=linux-rhel7-skylake | |
| - udykfw5 ^flex@2.6.3%nvhpc@22.1+lex~nls 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 | |
| [^] jzpqn5y ^xz@5.2.5%gcc@11.2.0~pic libs=shared,static 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 | |
| - k3tfixc ^ninja@1.10.2%nvhpc@22.1 arch=linux-rhel7-skylake | |
| [^] n6q4vfz ^py-mpi4py@3.1.2%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] gjm7kkq ^py-numpy@1.19.5%gcc@11.2.0+blas+lapack patches=8a9d5d1b3f145c043b8b04869e7d46c6ff95c3f486d84f69693017c7e6190c7d arch=linux-rhel7-skylake | |
| [^] r5cvgru ^intel-mkl@2020.4.304%gcc@11.2.0~ilp64+shared threads=none arch=linux-rhel7-skylake | |
| [^] h2fsi6i ^py-cython@0.29.24%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] q5n7ofc ^py-pytest-cov@2.8.1%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] fudvy5v ^py-coverage@5.5%gcc@11.2.0 arch=linux-rhel7-skylake | |
| [^] f5syxww ^readline@8.1%nvhpc@22.1 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-3.8.2-4ydwt2sjpk4f7vuqyxhxg23cea3k6sxs) | |
| ==> 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-p7c65dgnlldt4dvtftndybaiajfebff4) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/boost-1.77.0-6x26ce (external boost-1.77.0-yjmsba6vrk7ay2rbkah4htoniepm5yci) | |
| ==> cuda@11.5.1 : has external module in ['cuda/11.5.1'] | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/cuda-11.5.1-fyf4dd (external cuda-11.5.1-akxpgv2q5zrp36lxyjpeuzhsfk77n2mf) | |
| ==> 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) | |
| [+] /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_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_applications/install_gcc-11.2.0-skylake/spdlog-1.9.2-x72vve | |
| ==> 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) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/libyaml-0.2.5-xj2wla | |
| ==> 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-udykfw5i5twmy3lnuuzeemfkn3lvsldx) | |
| [+] /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/xz-5.2.5-jzpqn5 | |
| [+] /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) | |
| ==> 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-k3tfixcs5ddog5pciqqucifnc2qadnyt) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/intel-mkl-2020.4.304-rzr3hj (external intel-mkl-2020.4.304-r5cvgrurdnt6y267arsmmmgqi75ouxd2) | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/readline-8.1-we2frg (external readline-8.1-f5syxwwo67gnhz6fu446xuhaezblb2t7) | |
| [+] /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/hdf5-1.10.7-utj47f | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyparsing-2.4.7-c7qvw2 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-attrs-21.2.0-ascbei | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-toml-0.10.2-w4gddq | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-iniconfig-1.1.1-kvw3vh | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pluggy-0.13.0-mazoio | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpmath-1.1.0-dzb2mf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-setuptools-57.4.0-v4z3s5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-py-1.9.0-y7rfzd | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-markupsafe-2.0.1-4ectow | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pyyaml-5.3.1-ci5oe5 | |
| [+] /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/libsonata-report-1.0.0.20211007-exroq3 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-packaging-21.0-7iyiyg | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.8-xtett6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-coverage-5.5-fudvy5 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-mpi4py-3.1.2-n6q4vf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-cython-0.29.24-h2fsi6 | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-jinja2-3.0.1-onq3mh | |
| [+] /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/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-6.2.4-22arfs | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-numpy-1.19.5-gjm7kk | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_gcc-11.2.0-skylake/nmodl-develop-cnhmkf | |
| [+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-pytest-cov-2.8.1-q5n7of | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/coreneuron-develop-jgejfg | |
| ==> Installing neuron-develop-ccjdz33a47dcm6emvjsbg2kpa4job22w | |
| ==> No binary for neuron-develop-ccjdz33a47dcm6emvjsbg2kpa4job22w found: installing from source | |
| ==> Warning: Missing a source id for neuron@develop | |
| ==> Warning: Missing a source id for nmodl@develop | |
| ==> Applied patch /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153640/spack/bluebrain/repo-patches/packages/neuron/revert_Import3d_numerical_format.master.patch | |
| ==> neuron: Executing phase: 'cmake' | |
| ==> neuron: Executing phase: 'build' | |
| ==> neuron: Executing phase: 'install' | |
| ==> neuron: Successfully installed neuron-develop-ccjdz33a47dcm6emvjsbg2kpa4job22w | |
| Fetch: 14.75s. Build: 20m 25.16s. Total: 20m 39.90s. | |
| [+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/software/install_nvhpc-22.1-skylake/neuron-develop-ccjdz3 | |
| [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: /nvme/bbpcihpcproj12/274679/ccache | |
| Primary config: /nvme/bbpcihpcproj12/274679/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: Mon Feb 14 12:32:00 2022 | |
| Hits: 547 / 801 (68.29 %) | |
| Direct: 160 / 810 (19.75 %) | |
| Preprocessed: 387 / 644 (60.09 %) | |
| Misses: 254 | |
| Direct: 650 | |
| Preprocessed: 257 | |
| Uncacheable: 120 | |
| Primary storage: | |
| Hits: 1020 / 1614 (63.20 %) | |
| Misses: 594 | |
| Cache size (GB): 0.46 / 0.51 (90.30 %) | |
| Files: 36799 | |
| Cleanups: 1 | |
| Uncacheable: | |
| Autoconf compile/link: 7 | |
| Called for linking: 97 | |
| Called for preprocessing: 1 | |
| Compilation failed: 3 | |
| No input file: 6 | |
| Preprocessing failed: 6 | |
| [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 ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ SPACK_PACKAGE_DEPENDENCIES=^/${SPACK_INSTALLED_HASH}[0;m | |
| [32;1m$ SPACK_PACKAGE_COMMIT=$(cd ${SPACK_SOURCE_DIR} && git rev-parse HEAD)[0;m | |
| [32;1m$ echo The develop version mapped onto commit ${SPACK_PACKAGE_COMMIT} in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_${SPACK_PACKAGE^^}_COMMIT.[0;m | |
| The develop version mapped onto commit d5f613917bfb0567fba43f3f111f3787aeb01f56 in this case, saving that to SPACK_PACKAGE_COMMIT and SPACK_NEURON_COMMIT. | |
| [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}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_${SPACK_PACKAGE^^}_COMMIT=${SPACK_PACKAGE_COMMIT}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ echo "SPACK_PACKAGE_DEPENDENCIES=${SPACK_PACKAGE_DEPENDENCIES}" >> ${CI_PROJECT_DIR}/spack_build_info.env[0;m | |
| [32;1m$ 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 py-virtualenv/16.7.6 | |
| Autoloading py-scipy/1.7.1 | |
| Autoloading py-numpy/1.19.5 | |
| Autoloading py-mpi4py/3.1.2 | |
| Autoloading hpe-mpi/2.25.hmpt | |
| Autoloading py-h5py/3.4.0 | |
| Autoloading hdf5/1.10.7 | |
| [32;1m$ echo "Returning the number of failed builds, ${num_failures}"[0;m | |
| Returning the number of failed builds, 0 | |
| [32;1m$ exit ${num_failures}[0;m | |
| section_end:1644838321:step_script [0Ksection_start:1644838321:archive_cache [0K[0K[36;1mSaving cache for successful job[0;m[0;m | |
| [32;1mCreating cache build:neuron:nmodl:nvhpc:omp-8...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=197581 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ccache.tar: found 1 matching files and directories[0;m | |
| Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/112/build%3Aneuron%3Anmodl%3Anvhpc%3Aomp-8[0;m | |
| [32;1mCreated cache[0;m | |
| section_end:1644838337:archive_cache [0Ksection_start:1644838337: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=198246 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=153660 responseStatus[0;m=201 Created token[0;m=VZPSXxs8 | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=198287 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=153660 responseStatus[0;m=201 Created token[0;m=VZPSXxs8 | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=198330 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=153660 responseStatus[0;m=201 Created token[0;m=VZPSXxs8 | |
| section_end:1644838339:upload_artifacts_on_success [0Ksection_start:1644838339:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644838339:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| ! |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836405:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836405:resolve_secrets [0Ksection_start:1644836405: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor485026225, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153676 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153676_PROD_P112_CP10_C13 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=cpu ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274635 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153676_PROD_P112_CP10_C13 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274635 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n30 via bbpv1.epfl.ch... | |
| section_end:1644836438:prepare_script [0Ksection_start:1644836438: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:1644836439:get_sources [0Ksection_start:1644836439:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:mod2c:intel (153654)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=257519 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153654 responseStatus[0;m=200 OK token[0;m=ssyq9Fsy | |
| section_end:1644836440:download_artifacts [0Ksection_start:1644836440: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n21 | |
| Build name: Linux-icpc | |
| Create new tag: 20220214-1101 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-build/spack-stage-coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx/spack-build-jlimlp3 | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 17: reporting_1 | |
| 1/17 Test #6: ring_TEST .......................... Passed 2.00 sec | |
| Start 7: ring_binqueue_TEST | |
| 2/17 Test #3: alignment_test ..................... Passed 2.21 sec | |
| 3/17 Test #4: queuing_test ....................... Passed 2.51 sec | |
| Start 8: ring_multisend_TEST | |
| 4/17 Test #1: cmd_interface_test ................. Passed 2.58 sec | |
| 5/17 Test #2: interleave_info_constructor_test ... Passed 2.71 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 6/17 Test #5: lfp_test ........................... Passed 2.89 sec | |
| 7/17 Test #17: reporting_1 ........................***Failed 4.59 sec | |
| num_mpi=2 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 12.5664, Min 12.3828, Avg 12.4746 | |
| Memory (MBs) : After MPI_Init : Max 12.8242, Min 12.6406, Avg 12.7324 | |
| Memory (MBs) : Before nrn_setup : Max 12.9492, Min 12.7617, Avg 12.8555 | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 1(g:1) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 259213, Host: r1i7n30, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-build/spack-stage-coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx/spack-build-jlimlp3/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host r1i7n30, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-build/spack-stage-coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx/spack-build-jlimlp3/bin/x86_64/special-core, Rank 1, Process 259213: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153654/spack-build/spack-stage-coreneuron-develop-jlimlp3c43orxijl3zdr5c3mlicgrilx/spack-build-jlimlp3/tests/integration/reporting_1 | |
| srun: error: r1i7n30: task 1: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274635.10 | |
| slurmstepd: error: *** STEP 274635.10 ON r1i7n30 CANCELLED AT 2022-02-14T12:01:14 *** | |
| srun: error: r1i7n30: task 0: Terminated | |
| srun: Force Terminated StepId=274635.10 | |
| Start 10: ring_permute1_TEST | |
| 8/17 Test #7: ring_binqueue_TEST ................. Passed 2.66 sec | |
| Start 11: ring_permute2_TEST | |
| 9/17 Test #8: ring_multisend_TEST ................ Passed 2.46 sec | |
| Start 12: ring_gap_TEST | |
| 10/17 Test #9: ring_spike_buffer_TEST ............. Passed 2.29 sec | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/17 Test #10: ring_permute1_TEST ................. Passed 2.59 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/17 Test #12: ring_gap_TEST ...................... Passed 4.82 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/17 Test #11: ring_permute2_TEST ................. Passed 5.25 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/17 Test #14: ring_gap_multisend_TEST ............ Passed 4.87 sec | |
| 15/17 Test #13: ring_gap_binqueue_TEST ............. Passed 7.13 sec | |
| 16/17 Test #15: ring_gap_permute1_TEST ............. Passed 3.24 sec | |
| 17/17 Test #16: ring_gap_permute2_TEST ............. Passed 3.17 sec | |
| 94% tests passed, 1 tests failed out of 17 | |
| Total Test time (real) = 13.14 sec | |
| The following tests FAILED: | |
| 17 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: r1i7n30: task 0: Exited with exit code 1 | |
| section_end:1644836483:step_script [0Ksection_start:1644836483:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=260354 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153676 responseStatus[0;m=201 Created token[0;m=Qg_XbJYw | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=260386 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153676 responseStatus[0;m=201 Created token[0;m=Qg_XbJYw | |
| section_end:1644836484:upload_artifacts_on_failure [0Ksection_start:1644836484:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836485:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836513:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836513:resolve_secrets [0Ksection_start:1644836513: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor355887584, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153670 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153670_PROD_P112_CP2_C0 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274645 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153670_PROD_P112_CP2_C0 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274645 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836539:prepare_executor [0Ksection_start:1644836539:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644836540:prepare_script [0Ksection_start:1644836540: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:1644836541:get_sources [0Ksection_start:1644836541:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:mod2c:nvhpc:acc:unified (153648)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=53087 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153648 responseStatus[0;m=200 OK token[0;m=zNF67sz- | |
| section_end:1644836542:download_artifacts [0Ksection_start:1644836542: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n30 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1102 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153648/spack-build/spack-stage-coreneuron-develop-oyd6hpfvzs36t5go6nq4cnbm6qyg4l2n/spack-build-oyd6hpf | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 19: reporting_1 | |
| 1/19 Test #1: cmd_interface_test ..................... Passed 2.22 sec | |
| 2/19 Test #5: lfp_test ............................... Passed 3.52 sec | |
| Start 7: ring_binqueue_TEST | |
| 3/19 Test #4: queuing_test ........................... Passed 3.55 sec | |
| 4/19 Test #3: alignment_test ......................... Passed 14.82 sec | |
| Start 8: ring_multisend_TEST | |
| 5/19 Test #7: ring_binqueue_TEST ..................... Passed 11.41 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 6/19 Test #2: interleave_info_constructor_test ....... Passed 15.07 sec | |
| 7/19 Test #6: ring_TEST .............................. Passed 15.17 sec | |
| Start 10: ring_permute1_TEST | |
| 8/19 Test #19: reporting_1 ............................***Failed 23.47 sec | |
| num_mpi=2 | |
| num_omp_thread=1 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 237.8516, Min 237.8008, Avg 237.8262 | |
| Memory (MBs) : After MPI_Init : Max 238.0430, Min 237.8516, Avg 237.9473 | |
| Memory (MBs) : Before nrn_setup : Max 238.1406, Min 238.0625, Avg 238.1016 | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 1(g:1) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 55267, Host: ldir01u05.bbp.epfl.ch, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153648/spack-build/spack-stage-coreneuron-develop-oyd6hpfvzs36t5go6nq4cnbm6qyg4l2n/spack-build-oyd6hpf/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host ldir01u05.bbp.epfl.ch, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153648/spack-build/spack-stage-coreneuron-develop-oyd6hpfvzs36t5go6nq4cnbm6qyg4l2n/spack-build-oyd6hpf/bin/x86_64/special-core, Rank 1, Process 55267: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153648/spack-build/spack-stage-coreneuron-develop-oyd6hpfvzs36t5go6nq4cnbm6qyg4l2n/spack-build-oyd6hpf/tests/integration/reporting_1 | |
| srun: error: ldir01u05: task 1: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274645.9 | |
| MPT: Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153648/spack-build/spack-stage-coreneuron-develop-oyd6hpfvzs36t5go6nq4cnbm6qyg4l2n/spack-build-oyd6hpf/bin/x86_64/special-core, Rank 0, Process 55265: Core dump on signal SIGABRT/SIGIOT(6) suppressed. | |
| srun: error: ldir01u05: task 0: Killed | |
| srun: Force Terminated StepId=274645.9 | |
| Start 11: ring_permute2_TEST | |
| 9/19 Test #10: ring_permute1_TEST ..................... Passed 21.85 sec | |
| Start 12: ring_gap_TEST | |
| 10/19 Test #9: ring_spike_buffer_TEST ................. Passed 22.18 sec | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/19 Test #8: ring_multisend_TEST .................... Passed 22.42 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/19 Test #11: ring_permute2_TEST ..................... Passed 21.98 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/19 Test #13: ring_gap_binqueue_TEST ................. Passed 329.06 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/19 Test #12: ring_gap_TEST .......................... Passed 333.51 sec | |
| Start 17: ring_permute2_cudaInterface_TEST | |
| 15/19 Test #15: ring_gap_permute1_TEST ................. Passed 325.35 sec | |
| Start 18: ring_gap_permute2_cudaInterface_TEST | |
| 16/19 Test #14: ring_gap_multisend_TEST ................ Passed 333.80 sec | |
| 17/19 Test #17: ring_permute2_cudaInterface_TEST ....... Passed 40.54 sec | |
| 18/19 Test #16: ring_gap_permute2_TEST ................. Passed 46.31 sec | |
| 19/19 Test #18: ring_gap_permute2_cudaInterface_TEST ... Passed 46.79 sec | |
| 95% tests passed, 1 tests failed out of 19 | |
| Total Test time (real) = 417.62 sec | |
| The following tests FAILED: | |
| 19 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: ldir01u05: task 0: Exited with exit code 1 | |
| section_end:1644836989:step_script [0Ksection_start:1644836989:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=65320 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153670 responseStatus[0;m=201 Created token[0;m=6rw7B9A2 | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=65353 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153670 responseStatus[0;m=201 Created token[0;m=6rw7B9A2 | |
| section_end:1644836990:upload_artifacts_on_failure [0Ksection_start:1644836990:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836991:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836409:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836409:resolve_secrets [0Ksection_start:1644836409: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor457116025, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153668 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153668_PROD_P112_CP11_C19 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274641 | |
| job state: PD | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153668_PROD_P112_CP11_C19 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274641 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836435:prepare_executor [0Ksection_start:1644836435:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644836436:prepare_script [0Ksection_start:1644836436: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:1644836437:get_sources [0Ksection_start:1644836437:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:mod2c:nvhpc:acc (153646)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=50742 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153646 responseStatus[0;m=200 OK token[0;m=LzhyaC-w | |
| section_end:1644836438:download_artifacts [0Ksection_start:1644836438: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n29 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1101 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153646/spack-build/spack-stage-coreneuron-develop-stctgospgustbslpq3fnxooxmjytgnr4/spack-build-stctgos | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 19: reporting_1 | |
| 1/19 Test #2: interleave_info_constructor_test ....... Passed 2.57 sec | |
| 2/19 Test #4: queuing_test ........................... Passed 3.20 sec | |
| Start 7: ring_binqueue_TEST | |
| 3/19 Test #3: alignment_test ......................... Passed 3.33 sec | |
| 4/19 Test #1: cmd_interface_test ..................... Passed 3.37 sec | |
| Start 8: ring_multisend_TEST | |
| 5/19 Test #5: lfp_test ............................... Passed 3.49 sec | |
| 6/19 Test #6: ring_TEST .............................. Passed 6.48 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 7/19 Test #7: ring_binqueue_TEST ..................... Passed 7.27 sec | |
| Start 10: ring_permute1_TEST | |
| 8/19 Test #8: ring_multisend_TEST .................... Passed 7.13 sec | |
| Start 11: ring_permute2_TEST | |
| 9/19 Test #9: ring_spike_buffer_TEST ................. Passed 7.63 sec | |
| Start 12: ring_gap_TEST | |
| 10/19 Test #19: reporting_1 ............................***Failed 15.74 sec | |
| num_mpi=2 | |
| num_omp_thread=1 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 237.8594, Min 237.8086, Avg 237.8340 | |
| Memory (MBs) : After MPI_Init : Max 238.0547, Min 237.8594, Avg 237.9570 | |
| Memory (MBs) : Before nrn_setup : Max 238.1445, Min 238.0664, Avg 238.1055 | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 0(g:0) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 51686, Host: ldir01u05.bbp.epfl.ch, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153646/spack-build/spack-stage-coreneuron-develop-stctgospgustbslpq3fnxooxmjytgnr4/spack-build-stctgos/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host ldir01u05.bbp.epfl.ch, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153646/spack-build/spack-stage-coreneuron-develop-stctgospgustbslpq3fnxooxmjytgnr4/spack-build-stctgos/bin/x86_64/special-core, Rank 0, Process 51686: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153646/spack-build/spack-stage-coreneuron-develop-stctgospgustbslpq3fnxooxmjytgnr4/spack-build-stctgos/tests/integration/reporting_1 | |
| srun: error: ldir01u05: task 0: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274641.10 | |
| MPT: Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153646/spack-build/spack-stage-coreneuron-develop-stctgospgustbslpq3fnxooxmjytgnr4/spack-build-stctgos/bin/x86_64/special-core, Rank 1, Process 51687: Core dump on signal SIGABRT/SIGIOT(6) suppressed. | |
| srun: error: ldir01u05: task 1: Killed | |
| srun: Force Terminated StepId=274641.10 | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/19 Test #10: ring_permute1_TEST ..................... Passed 10.36 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/19 Test #11: ring_permute2_TEST ..................... Passed 10.97 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/19 Test #12: ring_gap_TEST .......................... Passed 7.57 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/19 Test #13: ring_gap_binqueue_TEST ................. Passed 9.67 sec | |
| Start 17: ring_permute2_cudaInterface_TEST | |
| 15/19 Test #14: ring_gap_multisend_TEST ................ Passed 6.49 sec | |
| Start 18: ring_gap_permute2_cudaInterface_TEST | |
| 16/19 Test #15: ring_gap_permute1_TEST ................. Passed 10.19 sec | |
| 17/19 Test #16: ring_gap_permute2_TEST ................. Passed 10.08 sec | |
| 18/19 Test #17: ring_permute2_cudaInterface_TEST ....... Passed 7.65 sec | |
| 19/19 Test #18: ring_gap_permute2_cudaInterface_TEST ... Passed 7.79 sec | |
| 95% tests passed, 1 tests failed out of 19 | |
| Total Test time (real) = 35.14 sec | |
| The following tests FAILED: | |
| 19 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: ldir01u05: task 0: Exited with exit code 1 | |
| section_end:1644836500:step_script [0Ksection_start:1644836500:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=52661 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153668 responseStatus[0;m=201 Created token[0;m=-Y13uge2 | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=52694 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153668 responseStatus[0;m=201 Created token[0;m=-Y13uge2 | |
| section_end:1644836501:upload_artifacts_on_failure [0Ksection_start:1644836501:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836502:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836657:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836657:resolve_secrets [0Ksection_start:1644836657: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor323885275, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153679 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153679_PROD_P112_CP13_C25 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=cpu ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274667 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153679_PROD_P112_CP13_C25 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274667 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836684:prepare_executor [0Ksection_start:1644836684:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n21 via bbpv1.epfl.ch... | |
| section_end:1644836688:prepare_script [0Ksection_start:1644836688: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:1644836690:get_sources [0Ksection_start:1644836690:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:intel (153656)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=51932 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153656 responseStatus[0;m=200 OK token[0;m=NAxHmCYD | |
| section_end:1644836692:download_artifacts [0Ksection_start:1644836692: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i6n18 | |
| Build name: Linux-icpc | |
| Create new tag: 20220214-1105 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-build/spack-stage-coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y/spack-build-hp7e7dx | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 17: reporting_1 | |
| 1/17 Test #6: ring_TEST .......................... Passed 2.18 sec | |
| Start 7: ring_binqueue_TEST | |
| 2/17 Test #3: alignment_test ..................... Passed 2.27 sec | |
| 3/17 Test #4: queuing_test ....................... Passed 2.45 sec | |
| Start 8: ring_multisend_TEST | |
| 4/17 Test #2: interleave_info_constructor_test ... Passed 2.63 sec | |
| 5/17 Test #1: cmd_interface_test ................. Passed 2.83 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 6/17 Test #5: lfp_test ........................... Passed 3.00 sec | |
| 7/17 Test #17: reporting_1 ........................***Failed 5.09 sec | |
| num_mpi=2 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 12.3906, Min 12.2109, Avg 12.3008 | |
| Memory (MBs) : After MPI_Init : Max 12.6484, Min 12.4688, Avg 12.5586 | |
| Memory (MBs) : Before nrn_setup : Max 12.7656, Min 12.5859, Avg 12.6758 | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 0(g:0) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 53021, Host: r1i7n21, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-build/spack-stage-coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y/spack-build-hp7e7dx/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host r1i7n21, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-build/spack-stage-coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y/spack-build-hp7e7dx/bin/x86_64/special-core, Rank 0, Process 53021: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153656/spack-build/spack-stage-coreneuron-develop-hp7e7dx6ljmhh7s6hbo7c2wszfpbvk3y/spack-build-hp7e7dx/tests/integration/reporting_1 | |
| srun: error: r1i7n21: task 0: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274667.10 | |
| slurmstepd: error: *** STEP 274667.10 ON r1i7n21 CANCELLED AT 2022-02-14T12:05:27 *** | |
| srun: error: r1i7n21: task 1: Terminated | |
| srun: Force Terminated StepId=274667.10 | |
| Start 10: ring_permute1_TEST | |
| 8/17 Test #8: ring_multisend_TEST ................ Passed 2.75 sec | |
| Start 11: ring_permute2_TEST | |
| 9/17 Test #9: ring_spike_buffer_TEST ............. Passed 2.42 sec | |
| Start 12: ring_gap_TEST | |
| 10/17 Test #7: ring_binqueue_TEST ................. Passed 5.03 sec | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/17 Test #10: ring_permute1_TEST ................. Passed 2.57 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/17 Test #11: ring_permute2_TEST ................. Passed 4.12 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/17 Test #12: ring_gap_TEST ...................... Passed 4.29 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/17 Test #14: ring_gap_multisend_TEST ............ Passed 2.43 sec | |
| 15/17 Test #13: ring_gap_binqueue_TEST ............. Passed 3.89 sec | |
| 16/17 Test #15: ring_gap_permute1_TEST ............. Passed 2.48 sec | |
| 17/17 Test #16: ring_gap_permute2_TEST ............. Passed 2.32 sec | |
| 94% tests passed, 1 tests failed out of 17 | |
| Total Test time (real) = 11.88 sec | |
| The following tests FAILED: | |
| 17 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: r1i7n21: task 0: Exited with exit code 1 | |
| section_end:1644836735:step_script [0Ksection_start:1644836735:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=53984 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153679 responseStatus[0;m=201 Created token[0;m=Vv8GiRDY | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=54015 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153679 responseStatus[0;m=201 Created token[0;m=Vv8GiRDY | |
| section_end:1644836737:upload_artifacts_on_failure [0Ksection_start:1644836737:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644836740:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836867:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836867:resolve_secrets [0Ksection_start:1644836867: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor731265829, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153674 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153674_PROD_P112_CP12_C19 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274680 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153674_PROD_P112_CP12_C19 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274680 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836898:prepare_executor [0Ksection_start:1644836898:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644836900:prepare_script [0Ksection_start:1644836900: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:1644836901:get_sources [0Ksection_start:1644836901:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:nvhpc:acc (153652)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=61591 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153652 responseStatus[0;m=200 OK token[0;m=tyUVfAMJ | |
| section_end:1644836902:download_artifacts [0Ksection_start:1644836902: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i6n18 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1108 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build/spack-stage-coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa/spack-build-vqg67go | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 19: reporting_1 | |
| 1/19 Test #2: interleave_info_constructor_test ....... Passed 2.41 sec | |
| 2/19 Test #4: queuing_test ........................... Passed 2.55 sec | |
| Start 7: ring_binqueue_TEST | |
| 3/19 Test #3: alignment_test ......................... Passed 2.69 sec | |
| 4/19 Test #6: ring_TEST .............................. Passed 2.83 sec | |
| Start 8: ring_multisend_TEST | |
| 5/19 Test #1: cmd_interface_test ..................... Passed 2.92 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 6/19 Test #5: lfp_test ............................... Passed 3.74 sec | |
| 7/19 Test #8: ring_multisend_TEST .................... Passed 9.45 sec | |
| Start 10: ring_permute1_TEST | |
| 8/19 Test #19: reporting_1 ............................***Failed 12.92 sec | |
| num_mpi=2 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 237.2656, Min 235.3359, Avg 236.3008 | |
| Memory (MBs) : After MPI_Init : Max 237.2656, Min 235.3359, Avg 236.3008 | |
| Memory (MBs) : Before nrn_setup : Max 237.7070, Min 235.6602, Avg 236.6836 | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 1(g:1) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 63841, Host: ldir01u05.bbp.epfl.ch, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build/spack-stage-coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa/spack-build-vqg67go/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host ldir01u05.bbp.epfl.ch, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build/spack-stage-coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa/spack-build-vqg67go/bin/x86_64/special-core, Rank 1, Process 63841: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build/spack-stage-coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa/spack-build-vqg67go/tests/integration/reporting_1 | |
| srun: error: ldir01u05: task 1: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274680.10 | |
| MPT: Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153652/spack-build/spack-stage-coreneuron-develop-vqg67goxagdsf3kxjwwbdbz6jsbvmspa/spack-build-vqg67go/bin/x86_64/special-core, Rank 0, Process 63840: Core dump on signal SIGABRT/SIGIOT(6) suppressed. | |
| srun: error: ldir01u05: task 0: Killed | |
| srun: Force Terminated StepId=274680.10 | |
| Start 11: ring_permute2_TEST | |
| 9/19 Test #9: ring_spike_buffer_TEST ................. Passed 15.07 sec | |
| Start 12: ring_gap_TEST | |
| 10/19 Test #7: ring_binqueue_TEST ..................... Passed 31.99 sec | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/19 Test #10: ring_permute1_TEST ..................... Passed 30.45 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/19 Test #11: ring_permute2_TEST ..................... Passed 41.41 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/19 Test #12: ring_gap_TEST .......................... Passed 67.31 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/19 Test #13: ring_gap_binqueue_TEST ................. Passed 54.35 sec | |
| Start 17: ring_permute2_cudaInterface_TEST | |
| 15/19 Test #14: ring_gap_multisend_TEST ................ Passed 46.69 sec | |
| Start 18: ring_gap_permute2_cudaInterface_TEST | |
| 16/19 Test #15: ring_gap_permute1_TEST ................. Passed 35.24 sec | |
| 17/19 Test #16: ring_gap_permute2_TEST ................. Passed 8.24 sec | |
| 18/19 Test #17: ring_permute2_cudaInterface_TEST ....... Passed 5.84 sec | |
| 19/19 Test #18: ring_gap_permute2_cudaInterface_TEST ... Passed 7.97 sec | |
| 95% tests passed, 1 tests failed out of 19 | |
| Total Test time (real) = 97.43 sec | |
| The following tests FAILED: | |
| 19 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: ldir01u05: task 0: Exited with exit code 1 | |
| section_end:1644837028:step_script [0Ksection_start:1644837028:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=66037 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153674 responseStatus[0;m=201 Created token[0;m=vCrZWiVh | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=66069 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153674 responseStatus[0;m=201 Created token[0;m=vCrZWiVh | |
| section_end:1644837029:upload_artifacts_on_failure [0Ksection_start:1644837029:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644837030:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644836873:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644836873:resolve_secrets [0Ksection_start:1644836873: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor981013059, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153673 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153673_PROD_P112_CP13_C20 | |
| Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=8 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274678 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=8 --cpus-per-task=1 --mem=30750M --job-name=GL_J153673_PROD_P112_CP13_C20 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=8 --jobid=274678 --cpus-per-task=1 --mem=30750M | |
| section_end:1644836898:prepare_executor [0Ksection_start:1644836898:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644836900:prepare_script [0Ksection_start:1644836900: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:1644836901:get_sources [0Ksection_start:1644836901:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:coreneuron:nmodl:nvhpc:omp (153650)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=61660 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153650 responseStatus[0;m=200 OK token[0;m=XTZc5TNK | |
| section_end:1644836902:download_artifacts [0Ksection_start:1644836902: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n21 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1108 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build/spack-stage-coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a/spack-build-jgejfgi | |
| Start 1: cmd_interface_test | |
| Start 2: interleave_info_constructor_test | |
| Start 3: alignment_test | |
| Start 4: queuing_test | |
| Start 5: lfp_test | |
| Start 6: ring_TEST | |
| Start 19: reporting_1 | |
| 1/19 Test #3: alignment_test ......................... Passed 2.87 sec | |
| 2/19 Test #1: cmd_interface_test ..................... Passed 3.01 sec | |
| Start 7: ring_binqueue_TEST | |
| 3/19 Test #2: interleave_info_constructor_test ....... Passed 3.13 sec | |
| 4/19 Test #5: lfp_test ............................... Passed 3.56 sec | |
| Start 8: ring_multisend_TEST | |
| 5/19 Test #4: queuing_test ........................... Passed 3.57 sec | |
| 6/19 Test #6: ring_TEST .............................. Passed 12.46 sec | |
| Start 9: ring_spike_buffer_TEST | |
| 7/19 Test #19: reporting_1 ............................***Failed 12.76 sec | |
| num_mpi=2 | |
| num_omp_thread=1 | |
| Duke, Yale, and the BlueBrain Project -- Copyright 1984-2020 | |
| Version : 1.0 3469f1e9 (2022-02-14 11:51:47 +0100) | |
| Additional mechanisms from files | |
| exp2syn.mod expsyn.mod halfgap.mod hh.mod netstim.mod passive.mod pattern.mod stim.mod svclmp.mod | |
| Memory (MBs) : After mk_mech : Max 241.7578, Min 241.5859, Avg 241.6719 | |
| Memory (MBs) : After MPI_Init : Max 241.7578, Min 241.5859, Avg 241.6719 | |
| Memory (MBs) : Before nrn_setup : Max 242.0859, Min 241.9336, Avg 242.0098 | |
| no chkpnt line for 33 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT ERROR: Rank 0(g:0) received signal SIGABRT/SIGIOT(6). | |
| Process ID: 63920, Host: ldir01u05.bbp.epfl.ch, Program: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build/spack-stage-coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a/spack-build-jgejfgi/bin/x86_64/special-core | |
| MPT Version: HPE HMPT 2.25 10/22/21 03:18:39 | |
| MPT: --------stack traceback------- | |
| no chkpnt line for 31 | |
| ../spack-src/coreneuron/io/nrn_filehandler.cpp:96: Assertion 'n_scan == 1' failed. | |
| MPT: ImportError: No module named site | |
| MPT: -----stack traceback ends----- | |
| MPT: On host ldir01u05.bbp.epfl.ch, Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build/spack-stage-coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a/spack-build-jgejfgi/bin/x86_64/special-core, Rank 0, Process 63920: Dumping core on signal SIGABRT/SIGIOT(6) into directory /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build/spack-stage-coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a/spack-build-jgejfgi/tests/integration/reporting_1 | |
| srun: error: ldir01u05: task 0: Aborted (core dumped) | |
| srun: launch/slurm: _step_signal: Terminating StepId=274678.10 | |
| MPT: Program /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153650/spack-build/spack-stage-coreneuron-develop-jgejfgix5nb6yjvuzuy64sbdppdrl73a/spack-build-jgejfgi/bin/x86_64/special-core, Rank 1, Process 63921: Core dump on signal SIGABRT/SIGIOT(6) suppressed. | |
| srun: error: ldir01u05: task 1: Killed | |
| srun: Force Terminated StepId=274678.10 | |
| Start 10: ring_permute1_TEST | |
| 8/19 Test #7: ring_binqueue_TEST ..................... Passed 49.52 sec | |
| Start 11: ring_permute2_TEST | |
| 9/19 Test #8: ring_multisend_TEST .................... Passed 53.14 sec | |
| Start 12: ring_gap_TEST | |
| 10/19 Test #9: ring_spike_buffer_TEST ................. Passed 47.90 sec | |
| Start 13: ring_gap_binqueue_TEST | |
| 11/19 Test #10: ring_permute1_TEST ..................... Passed 47.60 sec | |
| Start 14: ring_gap_multisend_TEST | |
| 12/19 Test #11: ring_permute2_TEST ..................... Passed 14.01 sec | |
| Start 15: ring_gap_permute1_TEST | |
| 13/19 Test #12: ring_gap_TEST .......................... Passed 15.83 sec | |
| Start 16: ring_gap_permute2_TEST | |
| 14/19 Test #14: ring_gap_multisend_TEST ................ Passed 90.97 sec | |
| Start 17: ring_permute2_cudaInterface_TEST | |
| 15/19 Test #17: ring_permute2_cudaInterface_TEST ....... Passed 17.48 sec | |
| Start 18: ring_gap_permute2_cudaInterface_TEST | |
| 16/19 Test #13: ring_gap_binqueue_TEST ................. Passed 148.99 sec | |
| 17/19 Test #15: ring_gap_permute1_TEST ................. Passed 151.66 sec | |
| 18/19 Test #16: ring_gap_permute2_TEST ................. Passed 146.47 sec | |
| 19/19 Test #18: ring_gap_permute2_cudaInterface_TEST ... Passed 50.50 sec | |
| 95% tests passed, 1 tests failed out of 19 | |
| Total Test time (real) = 219.34 sec | |
| The following tests FAILED: | |
| 19 - reporting_1 (Failed) | |
| Errors while running CTest | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| srun: error: ldir01u05: task 0: Exited with exit code 1 | |
| section_end:1644837150:step_script [0Ksection_start:1644837150:upload_artifacts_on_failure [0K[0K[36;1mUploading artifacts for failed 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=66635 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 8 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153673 responseStatus[0;m=201 Created token[0;m=TJLRe2dT | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=66667 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153673 responseStatus[0;m=201 Created token[0;m=TJLRe2dT | |
| section_end:1644837151:upload_artifacts_on_failure [0Ksection_start:1644837151:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644837152:cleanup_file_variables [0K[31;1mERROR: Job failed: exit status 1 | |
| [0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644837194:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644837194:resolve_secrets [0Ksection_start:1644837194: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor394387164, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153687 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153687_PROD_P112_CP2_C5 | |
| Job parameters: memory=76G, cpus_per_task=1, duration=1:00:00, constraint=cpu ntasks=16 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| 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 274697 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=16 --cpus-per-task=1 --mem=76G --job-name=GL_J153687_PROD_P112_CP2_C5 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=16 --jobid=274697 --cpus-per-task=1 --mem=76G | |
| section_end:1644837227:prepare_executor [0Ksection_start:1644837227:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on r1i7n21 via bbpv1.epfl.ch... | |
| section_end:1644837230:prepare_script [0Ksection_start:1644837230: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:1644837231:get_sources [0Ksection_start:1644837231:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:neuron:mod2c:intel (153664)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=68969 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153664 responseStatus[0;m=200 OK token[0;m=z9ztgK9q | |
| section_end:1644837233:download_artifacts [0Ksection_start:1644837233: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i6n32 | |
| Build name: Linux-icpc | |
| Create new tag: 20220214-1115 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153664/spack-build/spack-stage-neuron-develop-7fdjpn6td6dhzjavug7glqebdkw2qfjy/spack-build-7fdjpn6 | |
| Start 33: external_ringtest::coreneuron_cpu_mpi_offline::preparation | |
| Start 40: testcorenrn_bbcore::coreneuron_cpu_offline::preparation | |
| Start 46: testcorenrn_deriv::coreneuron_cpu_offline::preparation | |
| Start 52: testcorenrn_gf::coreneuron_cpu_offline::preparation | |
| Start 57: testcorenrn_patstim::coreneuron_cpu_offline::preparation | |
| Start 63: testcorenrn_vecplay::coreneuron_cpu_offline::preparation | |
| Start 69: testcorenrn_vecevent::coreneuron_cpu_offline::preparation | |
| Start 75: testcorenrn_watch::coreneuron_cpu_offline::preparation | |
| 1/105 Test #46: testcorenrn_deriv::coreneuron_cpu_offline::preparation ............. Passed 4.51 sec | |
| Start 81: testcorenrn_conc::coreneuron_cpu_offline::preparation | |
| 2/105 Test #40: testcorenrn_bbcore::coreneuron_cpu_offline::preparation ............ Passed 4.84 sec | |
| Start 87: testcorenrn_kin::coreneuron_cpu_offline::preparation | |
| 3/105 Test #75: testcorenrn_watch::coreneuron_cpu_offline::preparation ............. Passed 14.85 sec | |
| Start 28: external_ringtest::neuron | |
| Start 36: testcorenrn_bbcore::neuron | |
| 4/105 Test #63: testcorenrn_vecplay::coreneuron_cpu_offline::preparation ........... Passed 15.45 sec | |
| Start 29: external_ringtest::neuron_mpi | |
| 5/105 Test #57: testcorenrn_patstim::coreneuron_cpu_offline::preparation ........... Passed 15.86 sec | |
| Start 30: external_ringtest::coreneuron_cpu_mpi_offline_saverestore | |
| 6/105 Test #69: testcorenrn_vecevent::coreneuron_cpu_offline::preparation .......... Passed 18.02 sec | |
| Start 102: olfactory-bulb-3d::neuron::preparation | |
| 7/105 Test #87: testcorenrn_kin::coreneuron_cpu_offline::preparation ............... Passed 13.38 sec | |
| Start 37: testcorenrn_bbcore::coreneuron_cpu_online | |
| 8/105 Test #81: testcorenrn_conc::coreneuron_cpu_offline::preparation .............. Passed 13.93 sec | |
| Start 38: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate | |
| 9/105 Test #52: testcorenrn_gf::coreneuron_cpu_offline::preparation ................ Passed 18.48 sec | |
| Start 31: external_ringtest::coreneuron_cpu_mpi | |
| 10/105 Test #102: olfactory-bulb-3d::neuron::preparation ............................. Passed 0.47 sec | |
| Start 104: olfactory-bulb-3d::coreneuron_cpu_online::preparation | |
| 11/105 Test #104: olfactory-bulb-3d::coreneuron_cpu_online::preparation .............. Passed 0.92 sec | |
| Start 25: reduced_dentate::neuron | |
| 12/105 Test #33: external_ringtest::coreneuron_cpu_mpi_offline::preparation ......... Passed 20.67 sec | |
| Start 32: external_ringtest::coreneuron_cpu_mpi_offline | |
| 13/105 Test #36: testcorenrn_bbcore::neuron ......................................... Passed 6.09 sec | |
| Start 39: testcorenrn_bbcore::coreneuron_cpu_offline | |
| 14/105 Test #28: external_ringtest::neuron .......................................... Passed 10.96 sec | |
| Start 42: testcorenrn_deriv::neuron | |
| 15/105 Test #39: testcorenrn_bbcore::coreneuron_cpu_offline ......................... Passed 6.03 sec | |
| Start 43: testcorenrn_deriv::coreneuron_cpu_online | |
| 16/105 Test #37: testcorenrn_bbcore::coreneuron_cpu_online .......................... Passed 13.94 sec | |
| Start 44: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate | |
| 17/105 Test #32: external_ringtest::coreneuron_cpu_mpi_offline ...................... Passed 12.87 sec | |
| Start 45: testcorenrn_deriv::coreneuron_cpu_offline | |
| Start 77: testcorenrn_conc::neuron | |
| 18/105 Test #29: external_ringtest::neuron_mpi ...................................... Passed 20.09 sec | |
| Start 48: testcorenrn_gf::neuron | |
| 19/105 Test #38: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate ......... Passed 23.46 sec | |
| Start 78: testcorenrn_conc::coreneuron_cpu_online | |
| 20/105 Test #45: testcorenrn_deriv::coreneuron_cpu_offline .......................... Passed 10.39 sec | |
| Start 79: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate | |
| 21/105 Test #42: testcorenrn_deriv::neuron .......................................... Passed 18.39 sec | |
| Start 80: testcorenrn_conc::coreneuron_cpu_offline | |
| 22/105 Test #25: reduced_dentate::neuron ............................................ Passed 26.44 sec | |
| Start 26: reduced_dentate::coreneuron_cpu | |
| 23/105 Test #77: testcorenrn_conc::neuron ........................................... Passed 14.47 sec | |
| Start 83: testcorenrn_kin::neuron | |
| 24/105 Test #31: external_ringtest::coreneuron_cpu_mpi .............................. Passed 30.29 sec | |
| Start 49: testcorenrn_gf::coreneuron_cpu_online | |
| 25/105 Test #43: testcorenrn_deriv::coreneuron_cpu_online ........................... Passed 21.93 sec | |
| Start 84: testcorenrn_kin::coreneuron_cpu_online | |
| 26/105 Test #48: testcorenrn_gf::neuron ............................................. Passed 13.95 sec | |
| Start 50: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate | |
| 27/105 Test #80: testcorenrn_conc::coreneuron_cpu_offline ........................... Passed 5.21 sec | |
| Start 85: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate | |
| 28/105 Test #44: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate .......... Passed 17.54 sec | |
| Start 86: testcorenrn_kin::coreneuron_cpu_offline | |
| 29/105 Test #78: testcorenrn_conc::coreneuron_cpu_online ............................ Passed 11.12 sec | |
| Start 93: channel_benchmark_hippo::neuron | |
| 30/105 Test #30: external_ringtest::coreneuron_cpu_mpi_offline_saverestore .......... Passed 40.21 sec | |
| Start 51: testcorenrn_gf::coreneuron_cpu_offline | |
| 31/105 Test #86: testcorenrn_kin::coreneuron_cpu_offline ............................ Passed 8.05 sec | |
| Start 94: channel_benchmark_hippo::coreneuron_cpu_online | |
| 32/105 Test #79: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate ........... Passed 16.04 sec | |
| Start 95: channel_benchmark_hippo::coreneuron_cpu_filemode | |
| 33/105 Test #83: testcorenrn_kin::neuron ............................................ Passed 11.83 sec | |
| Start 97: channel_benchmark_sscx::neuron | |
| 34/105 Test #51: testcorenrn_gf::coreneuron_cpu_offline ............................. Passed 12.15 sec | |
| Start 54: testcorenrn_patstim::neuron | |
| 35/105 Test #85: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate ............ Passed 22.01 sec | |
| Start 98: channel_benchmark_sscx::coreneuron_cpu_online | |
| 36/105 Test #84: testcorenrn_kin::coreneuron_cpu_online ............................. Passed 22.75 sec | |
| Start 99: channel_benchmark_sscx::coreneuron_cpu_filemode | |
| 37/105 Test #49: testcorenrn_gf::coreneuron_cpu_online .............................. Passed 28.96 sec | |
| Start 55: testcorenrn_patstim::coreneuron_cpu_offline_saverestore | |
| 38/105 Test #54: testcorenrn_patstim::neuron ........................................ Passed 25.28 sec | |
| Start 56: testcorenrn_patstim::coreneuron_cpu_offline | |
| 39/105 Test #50: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate ............. Passed 45.89 sec | |
| Start 59: testcorenrn_vecplay::neuron | |
| 40/105 Test #26: reduced_dentate::coreneuron_cpu .................................... Passed 54.14 sec | |
| Start 60: testcorenrn_vecplay::coreneuron_cpu_online | |
| Start 61: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate | |
| 41/105 Test #56: testcorenrn_patstim::coreneuron_cpu_offline ........................ Passed 8.52 sec | |
| Start 62: testcorenrn_vecplay::coreneuron_cpu_offline | |
| 42/105 Test #62: testcorenrn_vecplay::coreneuron_cpu_offline ........................ Passed 10.65 sec | |
| Start 71: testcorenrn_watch::neuron | |
| 43/105 Test #59: testcorenrn_vecplay::neuron ........................................ Passed 20.76 sec | |
| Start 72: testcorenrn_watch::coreneuron_cpu_online | |
| 44/105 Test #55: testcorenrn_patstim::coreneuron_cpu_offline_saverestore ............ Passed 48.21 sec | |
| Start 73: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate | |
| 45/105 Test #71: testcorenrn_watch::neuron .......................................... Passed 27.08 sec | |
| Start 74: testcorenrn_watch::coreneuron_cpu_offline | |
| 46/105 Test #93: channel_benchmark_hippo::neuron .................................... Passed 88.52 sec | |
| Start 1: testneuron | |
| 47/105 Test #60: testcorenrn_vecplay::coreneuron_cpu_online ......................... Passed 43.30 sec | |
| Start 89: testcorenrn_netstimdirect::direct_netstimdirect | |
| 48/105 Test #1: testneuron ......................................................... Passed 1.96 sec | |
| Start 2: ringtest | |
| 49/105 Test #74: testcorenrn_watch::coreneuron_cpu_offline .......................... Passed 10.54 sec | |
| Start 90: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate | |
| 50/105 Test #61: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate ........ Passed 55.50 sec | |
| Start 3: connect_dend | |
| Start 4: pynrn_tests::basic_tests | |
| 51/105 Test #2: ringtest ........................................................... Passed 13.33 sec | |
| Start 5: parallel_tests | |
| 52/105 Test #3: connect_dend ....................................................... Passed 5.10 sec | |
| Start 6: parallel_partrans | |
| 53/105 Test #72: testcorenrn_watch::coreneuron_cpu_online ........................... Passed 52.34 sec | |
| Start 7: parallel_netpar | |
| Start 8: parallel_bas | |
| 54/105 Test #73: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate .......... Passed 66.62 sec | |
| Start 9: coreneuron_modtests::fornetcon_py_cpu | |
| Start 10: coreneuron_modtests::direct_py_cpu | |
| 55/105 Test #89: testcorenrn_netstimdirect::direct_netstimdirect .................... Passed 58.30 sec | |
| Start 11: coreneuron_modtests::direct_hoc_cpu | |
| Start 12: coreneuron_modtests::spikes_py_cpu | |
| 56/105 Test #94: channel_benchmark_hippo::coreneuron_cpu_online ..................... Passed 157.90 sec | |
| Start 13: coreneuron_modtests::spikes_file_mode_py_cpu | |
| 57/105 Test #6: parallel_partrans .................................................. Passed 59.67 sec | |
| Start 14: coreneuron_modtests::fast_imem_py_cpu | |
| 58/105 Test #90: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate ... Passed 73.95 sec | |
| Start 15: coreneuron_modtests::datareturn_py_cpu | |
| Start 16: coreneuron_modtests::test_units_py_cpu | |
| 59/105 Test #7: parallel_netpar .................................................... Passed 57.81 sec | |
| Start 17: coreneuron_modtests::test_netmove_py_cpu | |
| 60/105 Test #5: parallel_tests ..................................................... Passed 70.26 sec | |
| Start 18: coreneuron_modtests::test_watchrange_py_cpu | |
| 61/105 Test #97: channel_benchmark_sscx::neuron ..................................... Passed 168.15 sec | |
| Start 19: coreneuron_modtests::test_psolve_py_cpu | |
| 62/105 Test #95: channel_benchmark_hippo::coreneuron_cpu_filemode ................... Passed 168.50 sec | |
| Start 20: coreneuron_modtests::test_natrans_py_cpu | |
| 63/105 Test #11: coreneuron_modtests::direct_hoc_cpu ................................ Passed 30.46 sec | |
| Start 24: external_nrntest | |
| 64/105 Test #99: channel_benchmark_sscx::coreneuron_cpu_filemode .................... Passed 162.60 sec | |
| Start 27: reduced_dentate::compare_results | |
| 65/105 Test #98: channel_benchmark_sscx::coreneuron_cpu_online ...................... Passed 162.75 sec | |
| Start 41: testcorenrn_bbcore::compare_results | |
| 66/105 Test #27: reduced_dentate::compare_results ................................... Passed 2.21 sec | |
| Start 47: testcorenrn_deriv::compare_results | |
| 67/105 Test #41: testcorenrn_bbcore::compare_results ................................ Passed 2.26 sec | |
| Start 53: testcorenrn_gf::compare_results | |
| 68/105 Test #9: coreneuron_modtests::fornetcon_py_cpu .............................. Passed 46.34 sec | |
| Start 58: testcorenrn_patstim::compare_results | |
| 69/105 Test #10: coreneuron_modtests::direct_py_cpu ................................. Passed 46.39 sec | |
| Start 64: testcorenrn_vecplay::compare_results | |
| 70/105 Test #12: coreneuron_modtests::spikes_py_cpu ................................. Passed 37.20 sec | |
| Start 76: testcorenrn_watch::compare_results | |
| 71/105 Test #47: testcorenrn_deriv::compare_results ................................. Passed 3.01 sec | |
| Start 82: testcorenrn_conc::compare_results | |
| 72/105 Test #53: testcorenrn_gf::compare_results .................................... Passed 3.02 sec | |
| Start 88: testcorenrn_kin::compare_results | |
| 73/105 Test #64: testcorenrn_vecplay::compare_results ............................... Passed 1.77 sec | |
| Start 91: testcorenrn_netstimdirect::compare_results | |
| 74/105 Test #58: testcorenrn_patstim::compare_results ............................... Passed 2.26 sec | |
| Start 96: channel_benchmark_hippo::compare_results | |
| 75/105 Test #76: testcorenrn_watch::compare_results ................................. Passed 1.98 sec | |
| Start 100: channel_benchmark_sscx::compare_results | |
| 76/105 Test #88: testcorenrn_kin::compare_results ................................... Passed 1.87 sec | |
| 77/105 Test #82: testcorenrn_conc::compare_results .................................. Passed 2.42 sec | |
| Start 21: coreneuron_modtests::spikes_mpi_py_cpu | |
| 78/105 Test #13: coreneuron_modtests::spikes_file_mode_py_cpu ....................... Passed 26.63 sec | |
| 79/105 Test #91: testcorenrn_netstimdirect::compare_results ......................... Passed 2.37 sec | |
| Start 22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu | |
| 80/105 Test #96: channel_benchmark_hippo::compare_results ........................... Passed 2.16 sec | |
| 81/105 Test #100: channel_benchmark_sscx::compare_results ............................ Passed 2.39 sec | |
| Start 23: coreneuron_modtests::inputpresyn_py_cpu | |
| 82/105 Test #18: coreneuron_modtests::test_watchrange_py_cpu ........................ Passed 23.08 sec | |
| 83/105 Test #14: coreneuron_modtests::fast_imem_py_cpu .............................. Passed 29.61 sec | |
| 84/105 Test #17: coreneuron_modtests::test_netmove_py_cpu ........................... Passed 25.42 sec | |
| 85/105 Test #8: parallel_bas ....................................................... Passed 91.13 sec | |
| Start 65: testcorenrn_vecevent::neuron | |
| 86/105 Test #22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu ................... Passed 20.73 sec | |
| 87/105 Test #16: coreneuron_modtests::test_units_py_cpu ............................. Passed 40.45 sec | |
| 88/105 Test #20: coreneuron_modtests::test_natrans_py_cpu ........................... Passed 38.39 sec | |
| Start 66: testcorenrn_vecevent::coreneuron_cpu_online | |
| 89/105 Test #21: coreneuron_modtests::spikes_mpi_py_cpu ............................. Passed 25.84 sec | |
| 90/105 Test #23: coreneuron_modtests::inputpresyn_py_cpu ............................ Passed 26.10 sec | |
| Start 67: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate | |
| 91/105 Test #15: coreneuron_modtests::datareturn_py_cpu ............................. Passed 47.48 sec | |
| 92/105 Test #19: coreneuron_modtests::test_psolve_py_cpu ............................ Passed 43.86 sec | |
| 93/105 Test #65: testcorenrn_vecevent::neuron ....................................... Passed 13.81 sec | |
| Start 34: external_ringtest::coreneuron_cpu_mpi_threads | |
| 94/105 Test #66: testcorenrn_vecevent::coreneuron_cpu_online ........................ Passed 14.41 sec | |
| Start 68: testcorenrn_vecevent::coreneuron_cpu_offline | |
| 95/105 Test #67: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate ....... Passed 14.29 sec | |
| Start 101: olfactory-bulb-3d::neuron | |
| 96/105 Test #68: testcorenrn_vecevent::coreneuron_cpu_offline ....................... Passed 4.35 sec | |
| Start 103: olfactory-bulb-3d::coreneuron_cpu_online | |
| 97/105 Test #34: external_ringtest::coreneuron_cpu_mpi_threads ...................... Passed 13.81 sec | |
| Start 35: external_ringtest::compare_results | |
| Start 70: testcorenrn_vecevent::compare_results | |
| 98/105 Test #70: testcorenrn_vecevent::compare_results .............................. Passed 1.32 sec | |
| 99/105 Test #35: external_ringtest::compare_results ................................. Passed 1.45 sec | |
| 100/105 Test #4: pynrn_tests::basic_tests ........................................... Passed 141.16 sec | |
| 101/105 Test #101: olfactory-bulb-3d::neuron .......................................... Passed 112.91 sec | |
| 102/105 Test #103: olfactory-bulb-3d::coreneuron_cpu_online ........................... Passed 129.98 sec | |
| Start 105: olfactory-bulb-3d::compare_results | |
| 103/105 Test #105: olfactory-bulb-3d::compare_results ................................. Passed 1.10 sec | |
| 104/105 Test #24: external_nrntest ................................................... Passed 821.06 sec | |
| Start 92: tqperf::coreneuron | |
| 105/105 Test #92: tqperf::coreneuron ................................................. Passed 21.04 sec | |
| 100% tests passed, 0 tests failed out of 105 | |
| Total Test time (real) = 1074.84 sec | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| section_end:1644838383:step_script [0Ksection_start:1644838383: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=97466 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 7 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153687 responseStatus[0;m=201 Created token[0;m=gD38ohyj | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=97510 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153687 responseStatus[0;m=201 Created token[0;m=gD38ohyj | |
| section_end:1644838385:upload_artifacts_on_success [0Ksection_start:1644838385:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644838386:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644837290:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644837290:resolve_secrets [0Ksection_start:1644837290: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor046170682, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153681 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153681_PROD_P112_CP1_C2 | |
| Job parameters: memory=76G, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=16 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| chown: changing ownership of â/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548/J153660/spack-build/spack-stage-neuron-develop-ccjdz33a47dcm6emvjsbg2kpa4job22w/spack-src/src/nrnoc/intfire4.c.tmpâ: No such file or directory | |
| [31;1mERROR: Preparation failed: exit status 2[0;m | |
| [32;1mWill be retried in 3s ...[0;m | |
| [0KUsing Custom executor with driver BB5 PROD runner v0.0.3...[0;m | |
| BB5 PROD runner running on bbpv1.epfl.ch, version 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor536120484, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153681 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153681_PROD_P112_CP1_C2 | |
| Job parameters: memory=76G, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=16 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274702 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=16 --cpus-per-task=1 --mem=76G --job-name=GL_J153681_PROD_P112_CP1_C2 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=16 --jobid=274702 --cpus-per-task=1 --mem=76G | |
| section_end:1644837340:prepare_executor [0Ksection_start:1644837340:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644837341:prepare_script [0Ksection_start:1644837341: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:1644837342:get_sources [0Ksection_start:1644837342:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:neuron:mod2c:nvhpc:acc (153658)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=68337 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153658 responseStatus[0;m=200 OK token[0;m=dzpyhSZr | |
| section_end:1644837343:download_artifacts [0Ksection_start:1644837343: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n29 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1116 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153658/spack-build/spack-stage-neuron-develop-6y2lcdemkcc3w4hnyzlkfdgcsiwaao3u/spack-build-6y2lcde | |
| Start 48: external_ringtest::coreneuron_cpu_mpi_offline::preparation | |
| Start 53: external_ringtest::coreneuron_gpu_mpi_offline::preparation | |
| Start 60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation | |
| Start 64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation | |
| Start 70: testcorenrn_deriv::coreneuron_gpu_offline::preparation | |
| Start 74: testcorenrn_deriv::coreneuron_cpu_offline::preparation | |
| Start 80: testcorenrn_gf::coreneuron_gpu_offline::preparation | |
| Start 84: testcorenrn_gf::coreneuron_cpu_offline::preparation | |
| Start 89: testcorenrn_patstim::coreneuron_gpu_offline::preparation | |
| Start 92: testcorenrn_patstim::coreneuron_cpu_offline::preparation | |
| Start 128: testcorenrn_conc::coreneuron_gpu_offline::preparation | |
| 1/166 Test #64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation ............ Passed 2.92 sec | |
| Start 132: testcorenrn_conc::coreneuron_cpu_offline::preparation | |
| 2/166 Test #70: testcorenrn_deriv::coreneuron_gpu_offline::preparation ............. Passed 3.05 sec | |
| Start 138: testcorenrn_kin::coreneuron_gpu_offline::preparation | |
| 3/166 Test #74: testcorenrn_deriv::coreneuron_cpu_offline::preparation ............. Passed 3.09 sec | |
| Start 142: testcorenrn_kin::coreneuron_cpu_offline::preparation | |
| 4/166 Test #60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation ............ Passed 3.11 sec | |
| Start 43: external_ringtest::neuron | |
| 5/166 Test #128: testcorenrn_conc::coreneuron_gpu_offline::preparation .............. Passed 3.58 sec | |
| Start 56: testcorenrn_bbcore::neuron | |
| 6/166 Test #89: testcorenrn_patstim::coreneuron_gpu_offline::preparation ........... Passed 3.87 sec | |
| Start 57: testcorenrn_bbcore::coreneuron_gpu_online | |
| 7/166 Test #80: testcorenrn_gf::coreneuron_gpu_offline::preparation ................ Passed 4.18 sec | |
| Start 98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation | |
| 8/166 Test #92: testcorenrn_patstim::coreneuron_cpu_offline::preparation ........... Passed 4.25 sec | |
| Start 102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation | |
| 9/166 Test #43: external_ringtest::neuron .......................................... Passed 1.42 sec | |
| Start 58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate | |
| 10/166 Test #142: testcorenrn_kin::coreneuron_cpu_offline::preparation ............... Passed 1.86 sec | |
| Start 59: testcorenrn_bbcore::coreneuron_gpu_offline | |
| 11/166 Test #132: testcorenrn_conc::coreneuron_cpu_offline::preparation .............. Passed 2.93 sec | |
| Start 61: testcorenrn_bbcore::coreneuron_cpu_online | |
| 12/166 Test #61: testcorenrn_bbcore::coreneuron_cpu_online .......................... Passed 18.46 sec | |
| Start 62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate | |
| 13/166 Test #53: external_ringtest::coreneuron_gpu_mpi_offline::preparation ......... Passed 25.86 sec | |
| Start 118: testcorenrn_watch::coreneuron_gpu_offline::preparation | |
| 14/166 Test #58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate ......... Passed 22.08 sec | |
| Start 63: testcorenrn_bbcore::coreneuron_cpu_offline | |
| 15/166 Test #62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate ......... Passed 4.17 sec | |
| Start 66: testcorenrn_deriv::neuron | |
| 16/166 Test #118: testcorenrn_watch::coreneuron_gpu_offline::preparation ............. Passed 2.82 sec | |
| Start 122: testcorenrn_watch::coreneuron_cpu_offline::preparation | |
| 17/166 Test #63: testcorenrn_bbcore::coreneuron_cpu_offline ......................... Passed 2.27 sec | |
| Start 67: testcorenrn_deriv::coreneuron_gpu_online | |
| 18/166 Test #66: testcorenrn_deriv::neuron .......................................... Passed 1.86 sec | |
| Start 68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate | |
| 19/166 Test #122: testcorenrn_watch::coreneuron_cpu_offline::preparation ............. Passed 2.84 sec | |
| Start 44: external_ringtest::neuron_mpi | |
| 20/166 Test #67: testcorenrn_deriv::coreneuron_gpu_online ........................... Passed 7.91 sec | |
| Start 69: testcorenrn_deriv::coreneuron_gpu_offline | |
| 21/166 Test #68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate .......... Passed 7.12 sec | |
| Start 71: testcorenrn_deriv::coreneuron_cpu_online | |
| 22/166 Test #44: external_ringtest::neuron_mpi ...................................... Passed 9.18 sec | |
| Start 45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore | |
| 23/166 Test #69: testcorenrn_deriv::coreneuron_gpu_offline .......................... Passed 4.92 sec | |
| Start 72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate | |
| 24/166 Test #72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate .......... Passed 3.59 sec | |
| Start 73: testcorenrn_deriv::coreneuron_cpu_offline | |
| 25/166 Test #138: testcorenrn_kin::coreneuron_gpu_offline::preparation ............... Passed 53.04 sec | |
| Start 87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore | |
| 26/166 Test #73: testcorenrn_deriv::coreneuron_cpu_offline .......................... Passed 16.65 sec | |
| Start 88: testcorenrn_patstim::coreneuron_gpu_offline | |
| 27/166 Test #57: testcorenrn_bbcore::coreneuron_gpu_online .......................... Passed 61.38 sec | |
| Start 124: testcorenrn_conc::neuron | |
| 28/166 Test #88: testcorenrn_patstim::coreneuron_gpu_offline ........................ Passed 4.19 sec | |
| Start 125: testcorenrn_conc::coreneuron_gpu_online | |
| 29/166 Test #124: testcorenrn_conc::neuron ........................................... Passed 2.22 sec | |
| Start 126: testcorenrn_conc::coreneuron_gpu_online_psolve_alternate | |
| 30/166 Test #125: testcorenrn_conc::coreneuron_gpu_online ............................ Passed 7.52 sec | |
| Start 127: testcorenrn_conc::coreneuron_gpu_offline | |
| 31/166 Test #126: testcorenrn_conc::coreneuron_gpu_online_psolve_alternate ........... Passed 6.80 sec | |
| Start 129: testcorenrn_conc::coreneuron_cpu_online | |
| 32/166 Test #127: testcorenrn_conc::coreneuron_gpu_offline ........................... Passed 10.47 sec | |
| Start 130: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate | |
| 33/166 Test #102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation ........... Passed 86.51 sec | |
| Start 46: external_ringtest::coreneuron_cpu_mpi | |
| 34/166 Test #98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation ........... Passed 87.27 sec | |
| Start 50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore | |
| 35/166 Test #129: testcorenrn_conc::coreneuron_cpu_online ............................ Passed 18.48 sec | |
| Start 131: testcorenrn_conc::coreneuron_cpu_offline | |
| 36/166 Test #56: testcorenrn_bbcore::neuron ......................................... Passed 89.44 sec | |
| Start 134: testcorenrn_kin::neuron | |
| 37/166 Test #71: testcorenrn_deriv::coreneuron_cpu_online ........................... Passed 62.34 sec | |
| Start 135: testcorenrn_kin::coreneuron_gpu_online | |
| 38/166 Test #134: testcorenrn_kin::neuron ............................................ Passed 21.06 sec | |
| Start 136: testcorenrn_kin::coreneuron_gpu_online_psolve_alternate | |
| 39/166 Test #131: testcorenrn_conc::coreneuron_cpu_offline ........................... Passed 32.65 sec | |
| Start 137: testcorenrn_kin::coreneuron_gpu_offline | |
| 40/166 Test #84: testcorenrn_gf::coreneuron_cpu_offline::preparation ................ Passed 126.03 sec | |
| Start 51: external_ringtest::coreneuron_gpu_mpi | |
| 41/166 Test #46: external_ringtest::coreneuron_cpu_mpi .............................. Passed 35.44 sec | |
| Start 52: external_ringtest::coreneuron_gpu_mpi_offline | |
| 42/166 Test #130: testcorenrn_conc::coreneuron_cpu_online_psolve_alternate ........... Passed 57.75 sec | |
| Start 139: testcorenrn_kin::coreneuron_cpu_online | |
| 43/166 Test #87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore ............ Passed 86.27 sec | |
| Start 140: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate | |
| 44/166 Test #135: testcorenrn_kin::coreneuron_gpu_online ............................. Passed 42.62 sec | |
| Start 141: testcorenrn_kin::coreneuron_cpu_offline | |
| 45/166 Test #48: external_ringtest::coreneuron_cpu_mpi_offline::preparation ......... Passed 148.78 sec | |
| Start 47: external_ringtest::coreneuron_cpu_mpi_offline | |
| 46/166 Test #59: testcorenrn_bbcore::coreneuron_gpu_offline ......................... Passed 144.57 sec | |
| Start 148: channel_benchmark_hippo::neuron | |
| 47/166 Test #137: testcorenrn_kin::coreneuron_gpu_offline ............................ Passed 24.56 sec | |
| Start 149: channel_benchmark_hippo::coreneuron_gpu_online | |
| 48/166 Test #52: external_ringtest::coreneuron_gpu_mpi_offline ...................... Passed 30.12 sec | |
| Start 76: testcorenrn_gf::neuron | |
| 49/166 Test #76: testcorenrn_gf::neuron ............................................. Passed 3.87 sec | |
| Start 77: testcorenrn_gf::coreneuron_gpu_online | |
| 50/166 Test #51: external_ringtest::coreneuron_gpu_mpi .............................. Passed 34.74 sec | |
| Start 78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate | |
| 51/166 Test #136: testcorenrn_kin::coreneuron_gpu_online_psolve_alternate ............ Passed 49.93 sec | |
| Start 150: channel_benchmark_hippo::coreneuron_gpu_filemode | |
| 52/166 Test #141: testcorenrn_kin::coreneuron_cpu_offline ............................ Passed 24.54 sec | |
| Start 151: channel_benchmark_hippo::coreneuron_cpu_online | |
| 53/166 Test #139: testcorenrn_kin::coreneuron_cpu_online ............................. Passed 25.46 sec | |
| Start 152: channel_benchmark_hippo::coreneuron_cpu_filemode | |
| 54/166 Test #140: testcorenrn_kin::coreneuron_cpu_online_psolve_alternate ............ Passed 25.27 sec | |
| Start 154: channel_benchmark_sscx::neuron | |
| 55/166 Test #47: external_ringtest::coreneuron_cpu_mpi_offline ...................... Passed 28.81 sec | |
| Start 79: testcorenrn_gf::coreneuron_gpu_offline | |
| 56/166 Test #77: testcorenrn_gf::coreneuron_gpu_online .............................. Passed 42.51 sec | |
| Start 81: testcorenrn_gf::coreneuron_cpu_online | |
| 57/166 Test #45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore .......... Passed 163.86 sec | |
| Start 82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate | |
| 58/166 Test #50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore .......... Passed 126.55 sec | |
| Start 83: testcorenrn_gf::coreneuron_cpu_offline | |
| 59/166 Test #79: testcorenrn_gf::coreneuron_gpu_offline ............................. Passed 44.69 sec | |
| Start 86: testcorenrn_patstim::neuron | |
| 60/166 Test #86: testcorenrn_patstim::neuron ........................................ Passed 3.43 sec | |
| Start 90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore | |
| 61/166 Test #78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate ............. Passed 68.93 sec | |
| Start 91: testcorenrn_patstim::coreneuron_cpu_offline | |
| 62/166 Test #81: testcorenrn_gf::coreneuron_cpu_online .............................. Passed 35.19 sec | |
| Start 94: testcorenrn_vecplay::neuron | |
| 63/166 Test #83: testcorenrn_gf::coreneuron_cpu_offline ............................. Passed 37.39 sec | |
| Start 95: testcorenrn_vecplay::coreneuron_gpu_online | |
| 64/166 Test #91: testcorenrn_patstim::coreneuron_cpu_offline ........................ Passed 29.78 sec | |
| Start 96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate | |
| 65/166 Test #82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate ............. Passed 65.29 sec | |
| Start 97: testcorenrn_vecplay::coreneuron_gpu_offline | |
| 66/166 Test #149: channel_benchmark_hippo::coreneuron_gpu_online ..................... Passed 120.99 sec | |
| Start 155: channel_benchmark_sscx::coreneuron_gpu_online | |
| 67/166 Test #148: channel_benchmark_hippo::neuron .................................... Passed 121.92 sec | |
| Start 156: channel_benchmark_sscx::coreneuron_gpu_filemode | |
| 68/166 Test #94: testcorenrn_vecplay::neuron ........................................ Passed 38.09 sec | |
| Start 99: testcorenrn_vecplay::coreneuron_cpu_online | |
| 69/166 Test #90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore ............ Passed 57.01 sec | |
| Start 100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate | |
| 70/166 Test #154: channel_benchmark_sscx::neuron ..................................... Passed 129.54 sec | |
| Start 157: channel_benchmark_sscx::coreneuron_cpu_online | |
| 71/166 Test #95: testcorenrn_vecplay::coreneuron_gpu_online ......................... Passed 43.52 sec | |
| Start 101: testcorenrn_vecplay::coreneuron_cpu_offline | |
| 72/166 Test #97: testcorenrn_vecplay::coreneuron_gpu_offline ........................ Passed 40.50 sec | |
| Start 114: testcorenrn_watch::neuron | |
| 73/166 Test #99: testcorenrn_vecplay::coreneuron_cpu_online ......................... Passed 36.65 sec | |
| Start 115: testcorenrn_watch::coreneuron_gpu_online | |
| 74/166 Test #114: testcorenrn_watch::neuron .......................................... Passed 4.00 sec | |
| Start 116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate | |
| 75/166 Test #150: channel_benchmark_hippo::coreneuron_gpu_filemode ................... Passed 151.46 sec | |
| Start 158: channel_benchmark_sscx::coreneuron_cpu_filemode | |
| 76/166 Test #100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate ........ Passed 40.84 sec | |
| Start 117: testcorenrn_watch::coreneuron_gpu_offline | |
| 77/166 Test #101: testcorenrn_vecplay::coreneuron_cpu_offline ........................ Passed 26.08 sec | |
| Start 119: testcorenrn_watch::coreneuron_cpu_online | |
| 78/166 Test #96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate ........ Passed 66.08 sec | |
| Start 120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate | |
| 79/166 Test #151: channel_benchmark_hippo::coreneuron_cpu_online ..................... Passed 165.16 sec | |
| Start 1: testneuron | |
| 80/166 Test #1: testneuron ......................................................... Passed 0.05 sec | |
| Start 2: ringtest | |
| 81/166 Test #152: channel_benchmark_hippo::coreneuron_cpu_filemode ................... Passed 164.81 sec | |
| Start 3: connect_dend | |
| 82/166 Test #2: ringtest ........................................................... Passed 0.23 sec | |
| Start 4: pynrn_tests::basic_tests | |
| 83/166 Test #3: connect_dend ....................................................... Passed 0.18 sec | |
| Start 5: parallel_tests | |
| 84/166 Test #115: testcorenrn_watch::coreneuron_gpu_online ........................... Passed 29.81 sec | |
| Start 121: testcorenrn_watch::coreneuron_cpu_offline | |
| 85/166 Test #5: parallel_tests ..................................................... Passed 10.66 sec | |
| Start 6: parallel_partrans | |
| 86/166 Test #4: pynrn_tests::basic_tests ........................................... Passed 10.78 sec | |
| Start 7: parallel_netpar | |
| 87/166 Test #7: parallel_netpar .................................................... Passed 4.78 sec | |
| Start 8: parallel_bas | |
| 88/166 Test #6: parallel_partrans .................................................. Passed 5.08 sec | |
| Start 9: coreneuron_modtests::fornetcon_py_cpu | |
| 89/166 Test #8: parallel_bas ....................................................... Passed 16.52 sec | |
| Start 10: coreneuron_modtests::direct_py_cpu | |
| 90/166 Test #119: testcorenrn_watch::coreneuron_cpu_online ........................... Passed 40.24 sec | |
| Start 144: testcorenrn_netstimdirect::direct_netstimdirect | |
| 91/166 Test #117: testcorenrn_watch::coreneuron_gpu_offline .......................... Passed 42.54 sec | |
| Start 145: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate | |
| 92/166 Test #120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate .......... Passed 42.54 sec | |
| Start 11: coreneuron_modtests::direct_hoc_cpu | |
| Start 12: coreneuron_modtests::spikes_py_cpu | |
| 93/166 Test #9: coreneuron_modtests::fornetcon_py_cpu .............................. Passed 25.27 sec | |
| Start 13: coreneuron_modtests::spikes_file_mode_py_cpu | |
| 94/166 Test #121: testcorenrn_watch::coreneuron_cpu_offline .......................... Passed 32.92 sec | |
| Start 14: coreneuron_modtests::fast_imem_py_cpu | |
| Start 15: coreneuron_modtests::datareturn_py_cpu | |
| 95/166 Test #14: coreneuron_modtests::fast_imem_py_cpu .............................. Passed 2.82 sec | |
| Start 16: coreneuron_modtests::test_units_py_cpu | |
| 96/166 Test #116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate .......... Passed 68.24 sec | |
| Start 17: coreneuron_modtests::test_netmove_py_cpu | |
| Start 18: coreneuron_modtests::test_watchrange_py_cpu | |
| 97/166 Test #155: channel_benchmark_sscx::coreneuron_gpu_online ...................... Passed 111.67 sec | |
| Start 19: coreneuron_modtests::test_psolve_py_cpu | |
| 98/166 Test #156: channel_benchmark_sscx::coreneuron_gpu_filemode .................... Passed 113.39 sec | |
| Start 20: coreneuron_modtests::test_natrans_py_cpu | |
| 99/166 Test #10: coreneuron_modtests::direct_py_cpu ................................. Passed 21.13 sec | |
| Start 24: coreneuron_modtests::direct_py_gpu | |
| 100/166 Test #12: coreneuron_modtests::spikes_py_cpu ................................. Passed 19.52 sec | |
| Start 25: coreneuron_modtests::direct_hoc_gpu | |
| 101/166 Test #11: coreneuron_modtests::direct_hoc_cpu ................................ Passed 20.45 sec | |
| Start 26: coreneuron_modtests::spikes_py_gpu | |
| 102/166 Test #15: coreneuron_modtests::datareturn_py_cpu ............................. Passed 13.70 sec | |
| Start 27: coreneuron_modtests::spikes_file_mode_py_gpu | |
| 103/166 Test #13: coreneuron_modtests::spikes_file_mode_py_cpu ....................... Passed 17.09 sec | |
| Start 28: coreneuron_modtests::fast_imem_py_gpu | |
| 104/166 Test #144: testcorenrn_netstimdirect::direct_netstimdirect .................... Passed 25.56 sec | |
| Start 21: coreneuron_modtests::spikes_mpi_py_cpu | |
| 105/166 Test #16: coreneuron_modtests::test_units_py_cpu ............................. Passed 12.79 sec | |
| Start 29: coreneuron_modtests::datareturn_py_gpu | |
| 106/166 Test #145: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate ... Passed 25.28 sec | |
| Start 22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu | |
| 107/166 Test #28: coreneuron_modtests::fast_imem_py_gpu .............................. Passed 1.61 sec | |
| Start 30: coreneuron_modtests::test_units_py_gpu | |
| 108/166 Test #157: channel_benchmark_sscx::coreneuron_cpu_online ...................... Passed 96.15 sec | |
| Start 31: coreneuron_modtests::test_netmove_py_gpu | |
| 109/166 Test #18: coreneuron_modtests::test_watchrange_py_cpu ........................ Passed 11.43 sec | |
| Start 32: coreneuron_modtests::test_watchrange_py_gpu | |
| 110/166 Test #17: coreneuron_modtests::test_netmove_py_cpu ........................... Passed 11.87 sec | |
| Start 33: coreneuron_modtests::test_psolve_py_gpu | |
| 111/166 Test #19: coreneuron_modtests::test_psolve_py_cpu ............................ Passed 13.86 sec | |
| Start 34: coreneuron_modtests::test_natrans_py_gpu | |
| 112/166 Test #20: coreneuron_modtests::test_natrans_py_cpu ........................... Passed 12.19 sec | |
| Start 38: external_nrntest | |
| 113/166 Test #158: channel_benchmark_sscx::coreneuron_cpu_filemode .................... Passed 82.70 sec | |
| Start 65: testcorenrn_bbcore::compare_results | |
| 114/166 Test #65: testcorenrn_bbcore::compare_results ................................ Passed 0.10 sec | |
| Start 75: testcorenrn_deriv::compare_results | |
| 115/166 Test #75: testcorenrn_deriv::compare_results ................................. Passed 0.15 sec | |
| Start 85: testcorenrn_gf::compare_results | |
| 116/166 Test #24: coreneuron_modtests::direct_py_gpu ................................. Passed 13.20 sec | |
| Start 93: testcorenrn_patstim::compare_results | |
| 117/166 Test #85: testcorenrn_gf::compare_results .................................... Passed 0.31 sec | |
| Start 103: testcorenrn_vecplay::compare_results | |
| 118/166 Test #93: testcorenrn_patstim::compare_results ............................... Passed 0.26 sec | |
| Start 123: testcorenrn_watch::compare_results | |
| 119/166 Test #103: testcorenrn_vecplay::compare_results ............................... Passed 0.24 sec | |
| Start 133: testcorenrn_conc::compare_results | |
| 120/166 Test #25: coreneuron_modtests::direct_hoc_gpu ................................ Passed 11.61 sec | |
| Start 143: testcorenrn_kin::compare_results | |
| 121/166 Test #27: coreneuron_modtests::spikes_file_mode_py_gpu ....................... Passed 10.33 sec | |
| Start 146: testcorenrn_netstimdirect::compare_results | |
| 122/166 Test #26: coreneuron_modtests::spikes_py_gpu ................................. Passed 10.90 sec | |
| Start 153: channel_benchmark_hippo::compare_results | |
| 123/166 Test #133: testcorenrn_conc::compare_results .................................. Passed 0.43 sec | |
| Start 159: channel_benchmark_sscx::compare_results | |
| 124/166 Test #123: testcorenrn_watch::compare_results ................................. Passed 0.52 sec | |
| 125/166 Test #153: channel_benchmark_hippo::compare_results ........................... Passed 0.20 sec | |
| Start 23: coreneuron_modtests::inputpresyn_py_cpu | |
| 126/166 Test #143: testcorenrn_kin::compare_results ................................... Passed 0.49 sec | |
| 127/166 Test #159: channel_benchmark_sscx::compare_results ............................ Passed 0.51 sec | |
| Start 35: coreneuron_modtests::spikes_mpi_py_gpu | |
| 128/166 Test #146: testcorenrn_netstimdirect::compare_results ......................... Passed 0.67 sec | |
| 129/166 Test #30: coreneuron_modtests::test_units_py_gpu ............................. Passed 8.92 sec | |
| Start 36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu | |
| 130/166 Test #32: coreneuron_modtests::test_watchrange_py_gpu ........................ Passed 7.23 sec | |
| 131/166 Test #34: coreneuron_modtests::test_natrans_py_gpu ........................... Passed 4.90 sec | |
| Start 37: coreneuron_modtests::inputpresyn_py_gpu | |
| 132/166 Test #21: coreneuron_modtests::spikes_mpi_py_cpu ............................. Passed 10.78 sec | |
| 133/166 Test #22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu ................... Passed 10.28 sec | |
| Start 108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation | |
| 134/166 Test #33: coreneuron_modtests::test_psolve_py_gpu ............................ Passed 7.23 sec | |
| 135/166 Test #29: coreneuron_modtests::datareturn_py_gpu ............................. Passed 11.73 sec | |
| 136/166 Test #31: coreneuron_modtests::test_netmove_py_gpu ........................... Passed 10.74 sec | |
| 137/166 Test #108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation .......... Passed 5.84 sec | |
| Start 112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation | |
| 138/166 Test #112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation .......... Passed 2.37 sec | |
| Start 161: olfactory-bulb-3d::neuron::preparation | |
| 139/166 Test #161: olfactory-bulb-3d::neuron::preparation ............................. Passed 0.05 sec | |
| Start 163: olfactory-bulb-3d::coreneuron_gpu_online::preparation | |
| 140/166 Test #163: olfactory-bulb-3d::coreneuron_gpu_online::preparation .............. Passed 0.08 sec | |
| Start 165: olfactory-bulb-3d::coreneuron_cpu_online::preparation | |
| 141/166 Test #165: olfactory-bulb-3d::coreneuron_cpu_online::preparation .............. Passed 0.03 sec | |
| Start 39: reduced_dentate::neuron | |
| 142/166 Test #23: coreneuron_modtests::inputpresyn_py_cpu ............................ Passed 16.98 sec | |
| Start 40: reduced_dentate::coreneuron_cpu | |
| 143/166 Test #37: coreneuron_modtests::inputpresyn_py_gpu ............................ Passed 15.33 sec | |
| 144/166 Test #36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu ................... Passed 16.66 sec | |
| Start 41: reduced_dentate::coreneuron_gpu | |
| 145/166 Test #35: coreneuron_modtests::spikes_mpi_py_gpu ............................. Passed 19.26 sec | |
| 146/166 Test #39: reduced_dentate::neuron ............................................ Passed 24.60 sec | |
| Start 49: external_ringtest::coreneuron_cpu_mpi_threads | |
| 147/166 Test #49: external_ringtest::coreneuron_cpu_mpi_threads ...................... Passed 16.66 sec | |
| Start 54: external_ringtest::coreneuron_gpu_mpi_threads | |
| 148/166 Test #41: reduced_dentate::coreneuron_gpu .................................... Passed 46.57 sec | |
| Start 104: testcorenrn_vecevent::neuron | |
| 149/166 Test #40: reduced_dentate::coreneuron_cpu .................................... Passed 47.84 sec | |
| Start 105: testcorenrn_vecevent::coreneuron_gpu_online | |
| Start 42: reduced_dentate::compare_results | |
| 150/166 Test #42: reduced_dentate::compare_results ................................... Passed 0.21 sec | |
| 151/166 Test #104: testcorenrn_vecevent::neuron ....................................... Passed 2.32 sec | |
| Start 106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate | |
| 152/166 Test #54: external_ringtest::coreneuron_gpu_mpi_threads ...................... Passed 22.85 sec | |
| Start 107: testcorenrn_vecevent::coreneuron_gpu_offline | |
| Start 55: external_ringtest::compare_results | |
| 153/166 Test #55: external_ringtest::compare_results ................................. Passed 0.07 sec | |
| 154/166 Test #105: testcorenrn_vecevent::coreneuron_gpu_online ........................ Passed 9.73 sec | |
| Start 109: testcorenrn_vecevent::coreneuron_cpu_online | |
| 155/166 Test #106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate ....... Passed 9.43 sec | |
| Start 110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate | |
| 156/166 Test #109: testcorenrn_vecevent::coreneuron_cpu_online ........................ Passed 17.36 sec | |
| Start 111: testcorenrn_vecevent::coreneuron_cpu_offline | |
| 157/166 Test #107: testcorenrn_vecevent::coreneuron_gpu_offline ....................... Passed 18.24 sec | |
| Start 160: olfactory-bulb-3d::neuron | |
| 158/166 Test #110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate ....... Passed 16.64 sec | |
| Start 162: olfactory-bulb-3d::coreneuron_gpu_online | |
| 159/166 Test #38: external_nrntest ................................................... Passed 108.12 sec | |
| Start 164: olfactory-bulb-3d::coreneuron_cpu_online | |
| 160/166 Test #111: testcorenrn_vecevent::coreneuron_cpu_offline ....................... Passed 22.13 sec | |
| Start 113: testcorenrn_vecevent::compare_results | |
| 161/166 Test #113: testcorenrn_vecevent::compare_results .............................. Passed 0.06 sec | |
| 162/166 Test #162: olfactory-bulb-3d::coreneuron_gpu_online ........................... Passed 116.79 sec | |
| 163/166 Test #160: olfactory-bulb-3d::neuron .......................................... Passed 146.22 sec | |
| 164/166 Test #164: olfactory-bulb-3d::coreneuron_cpu_online ........................... Passed 138.40 sec | |
| Start 147: tqperf::coreneuron | |
| 165/166 Test #147: tqperf::coreneuron ................................................. Passed 12.26 sec | |
| Start 166: olfactory-bulb-3d::compare_results | |
| 166/166 Test #166: olfactory-bulb-3d::compare_results ................................. Passed 0.23 sec | |
| 100% tests passed, 0 tests failed out of 166 | |
| Total Test time (real) = 656.10 sec | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| section_end:1644838028:step_script [0Ksection_start:1644838028: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=694 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 7 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153681 responseStatus[0;m=201 Created token[0;m=eFeDNcLD | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=784 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153681 responseStatus[0;m=201 Created token[0;m=eFeDNcLD | |
| section_end:1644838030:upload_artifacts_on_success [0Ksection_start:1644838030:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644838031:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| Log was not fetched because job had status: skipped |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644839963:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644839963:resolve_secrets [0Ksection_start:1644839963: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor149860823, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153685 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153685_PROD_P112_CP0_C0 | |
| Job parameters: memory=76G, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=16 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274930 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=16 --cpus-per-task=1 --mem=76G --job-name=GL_J153685_PROD_P112_CP0_C0 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=16 --jobid=274930 --cpus-per-task=1 --mem=76G | |
| section_end:1644840010:prepare_executor [0Ksection_start:1644840010:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644840011:prepare_script [0Ksection_start:1644840011: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:1644840012:get_sources [0Ksection_start:1644840012:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:neuron:nmodl:nvhpc:acc (153662)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=38801 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153662 responseStatus[0;m=200 OK token[0;m=yz6CrK9t | |
| section_end:1644840013:download_artifacts [0Ksection_start:1644840013: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n21 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1200 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153662/spack-build/spack-stage-neuron-develop-2qm6t5rbh7lbu3qrc6stglq74d6emsen/spack-build-2qm6t5r | |
| Start 48: external_ringtest::coreneuron_cpu_mpi_offline::preparation | |
| Start 53: external_ringtest::coreneuron_gpu_mpi_offline::preparation | |
| Start 60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation | |
| Start 64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation | |
| Start 70: testcorenrn_deriv::coreneuron_gpu_offline::preparation | |
| Start 74: testcorenrn_deriv::coreneuron_cpu_offline::preparation | |
| Start 80: testcorenrn_gf::coreneuron_gpu_offline::preparation | |
| Start 84: testcorenrn_gf::coreneuron_cpu_offline::preparation | |
| Start 89: testcorenrn_patstim::coreneuron_gpu_offline::preparation | |
| Start 92: testcorenrn_patstim::coreneuron_cpu_offline::preparation | |
| Start 43: external_ringtest::neuron | |
| 1/145 Test #64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation ............ Passed 2.04 sec | |
| Start 56: testcorenrn_bbcore::neuron | |
| 2/145 Test #60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation ............ Passed 2.08 sec | |
| Start 57: testcorenrn_bbcore::coreneuron_gpu_online | |
| 3/145 Test #43: external_ringtest::neuron .......................................... Passed 2.83 sec | |
| Start 58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate | |
| 4/145 Test #70: testcorenrn_deriv::coreneuron_gpu_offline::preparation ............. Passed 2.91 sec | |
| Start 59: testcorenrn_bbcore::coreneuron_gpu_offline | |
| 5/145 Test #74: testcorenrn_deriv::coreneuron_cpu_offline::preparation ............. Passed 3.33 sec | |
| Start 61: testcorenrn_bbcore::coreneuron_cpu_online | |
| 6/145 Test #89: testcorenrn_patstim::coreneuron_gpu_offline::preparation ........... Passed 3.38 sec | |
| Start 62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate | |
| 7/145 Test #92: testcorenrn_patstim::coreneuron_cpu_offline::preparation ........... Passed 3.82 sec | |
| Start 98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation | |
| 8/145 Test #80: testcorenrn_gf::coreneuron_gpu_offline::preparation ................ Passed 3.96 sec | |
| Start 102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation | |
| 9/145 Test #84: testcorenrn_gf::coreneuron_cpu_offline::preparation ................ Passed 4.00 sec | |
| Start 118: testcorenrn_watch::coreneuron_gpu_offline::preparation | |
| 10/145 Test #56: testcorenrn_bbcore::neuron ......................................... Passed 3.40 sec | |
| Start 63: testcorenrn_bbcore::coreneuron_cpu_offline | |
| 11/145 Test #102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation ........... Passed 4.68 sec | |
| Start 122: testcorenrn_watch::coreneuron_cpu_offline::preparation | |
| 12/145 Test #98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation ........... Passed 5.01 sec | |
| Start 44: external_ringtest::neuron_mpi | |
| 13/145 Test #118: testcorenrn_watch::coreneuron_gpu_offline::preparation ............. Passed 5.02 sec | |
| Start 45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore | |
| 14/145 Test #122: testcorenrn_watch::coreneuron_cpu_offline::preparation ............. Passed 1.54 sec | |
| Start 46: external_ringtest::coreneuron_cpu_mpi | |
| 15/145 Test #44: external_ringtest::neuron_mpi ...................................... Passed 2.57 sec | |
| Start 50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore | |
| 16/145 Test #48: external_ringtest::coreneuron_cpu_mpi_offline::preparation ......... Passed 66.16 sec | |
| Start 47: external_ringtest::coreneuron_cpu_mpi_offline | |
| 17/145 Test #61: testcorenrn_bbcore::coreneuron_cpu_online .......................... Passed 62.86 sec | |
| Start 66: testcorenrn_deriv::neuron | |
| 18/145 Test #63: testcorenrn_bbcore::coreneuron_cpu_offline ......................... Passed 60.62 sec | |
| Start 67: testcorenrn_deriv::coreneuron_gpu_online | |
| 19/145 Test #62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate ......... Passed 62.85 sec | |
| Start 68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate | |
| 20/145 Test #59: testcorenrn_bbcore::coreneuron_gpu_offline ......................... Passed 63.42 sec | |
| Start 69: testcorenrn_deriv::coreneuron_gpu_offline | |
| 21/145 Test #57: testcorenrn_bbcore::coreneuron_gpu_online .......................... Passed 64.29 sec | |
| Start 71: testcorenrn_deriv::coreneuron_cpu_online | |
| 22/145 Test #66: testcorenrn_deriv::neuron .......................................... Passed 2.14 sec | |
| Start 72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate | |
| 23/145 Test #46: external_ringtest::coreneuron_cpu_mpi .............................. Passed 69.36 sec | |
| Start 51: external_ringtest::coreneuron_gpu_mpi | |
| 24/145 Test #53: external_ringtest::coreneuron_gpu_mpi_offline::preparation ......... Passed 79.74 sec | |
| Start 52: external_ringtest::coreneuron_gpu_mpi_offline | |
| 25/145 Test #58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate ......... Passed 87.13 sec | |
| Start 73: testcorenrn_deriv::coreneuron_cpu_offline | |
| 26/145 Test #71: testcorenrn_deriv::coreneuron_cpu_online ........................... Passed 75.88 sec | |
| Start 87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore | |
| 27/145 Test #72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate .......... Passed 76.60 sec | |
| Start 88: testcorenrn_patstim::coreneuron_gpu_offline | |
| 28/145 Test #47: external_ringtest::coreneuron_cpu_mpi_offline ...................... Passed 79.37 sec | |
| Start 76: testcorenrn_gf::neuron | |
| 29/145 Test #67: testcorenrn_deriv::coreneuron_gpu_online ........................... Passed 80.21 sec | |
| Start 127: channel_benchmark_hippo::neuron | |
| 30/145 Test #69: testcorenrn_deriv::coreneuron_gpu_offline .......................... Passed 80.13 sec | |
| Start 128: channel_benchmark_hippo::coreneuron_gpu_online | |
| 31/145 Test #76: testcorenrn_gf::neuron ............................................. Passed 1.84 sec | |
| Start 77: testcorenrn_gf::coreneuron_gpu_online | |
| 32/145 Test #73: testcorenrn_deriv::coreneuron_cpu_offline .......................... Passed 57.56 sec | |
| Start 129: channel_benchmark_hippo::coreneuron_gpu_filemode | |
| 33/145 Test #52: external_ringtest::coreneuron_gpu_mpi_offline ...................... Passed 68.32 sec | |
| Start 78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate | |
| 34/145 Test #51: external_ringtest::coreneuron_gpu_mpi .............................. Passed 68.51 sec | |
| Start 79: testcorenrn_gf::coreneuron_gpu_offline | |
| 35/145 Test #68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate .......... Passed 114.05 sec | |
| Start 130: channel_benchmark_hippo::coreneuron_cpu_online | |
| 36/145 Test #127: channel_benchmark_hippo::neuron .................................... Passed 82.64 sec | |
| Start 131: channel_benchmark_hippo::coreneuron_cpu_filemode | |
| 37/145 Test #88: testcorenrn_patstim::coreneuron_gpu_offline ........................ Passed 92.27 sec | |
| Start 133: channel_benchmark_sscx::neuron | |
| 38/145 Test #79: testcorenrn_gf::coreneuron_gpu_offline ............................. Passed 90.03 sec | |
| Start 81: testcorenrn_gf::coreneuron_cpu_online | |
| 39/145 Test #77: testcorenrn_gf::coreneuron_gpu_online .............................. Passed 90.91 sec | |
| Start 82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate | |
| 40/145 Test #78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate ............. Passed 91.68 sec | |
| Start 83: testcorenrn_gf::coreneuron_cpu_offline | |
| 41/145 Test #133: channel_benchmark_sscx::neuron ..................................... Passed 39.00 sec | |
| Start 134: channel_benchmark_sscx::coreneuron_gpu_online | |
| 42/145 Test #45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore .......... Passed 279.64 sec | |
| Start 86: testcorenrn_patstim::neuron | |
| 43/145 Test #87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore ............ Passed 147.26 sec | |
| Start 135: channel_benchmark_sscx::coreneuron_gpu_filemode | |
| 44/145 Test #50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore .......... Passed 278.31 sec | |
| Start 90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore | |
| 45/145 Test #86: testcorenrn_patstim::neuron ........................................ Passed 2.37 sec | |
| Start 91: testcorenrn_patstim::coreneuron_cpu_offline | |
| 46/145 Test #128: channel_benchmark_hippo::coreneuron_gpu_online ..................... Passed 144.78 sec | |
| Start 136: channel_benchmark_sscx::coreneuron_cpu_online | |
| 47/145 Test #129: channel_benchmark_hippo::coreneuron_gpu_filemode ................... Passed 150.59 sec | |
| Start 137: channel_benchmark_sscx::coreneuron_cpu_filemode | |
| 48/145 Test #83: testcorenrn_gf::coreneuron_cpu_offline ............................. Passed 66.65 sec | |
| Start 94: testcorenrn_vecplay::neuron | |
| 49/145 Test #94: testcorenrn_vecplay::neuron ........................................ Passed 3.36 sec | |
| Start 95: testcorenrn_vecplay::coreneuron_gpu_online | |
| 50/145 Test #81: testcorenrn_gf::coreneuron_cpu_online .............................. Passed 77.66 sec | |
| Start 96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate | |
| 51/145 Test #130: channel_benchmark_hippo::coreneuron_cpu_online ..................... Passed 141.12 sec | |
| Start 1: testneuron | |
| 52/145 Test #1: testneuron ......................................................... Passed 0.06 sec | |
| Start 2: ringtest | |
| 53/145 Test #2: ringtest ........................................................... Passed 0.25 sec | |
| Start 3: connect_dend | |
| 54/145 Test #3: connect_dend ....................................................... Passed 0.14 sec | |
| Start 4: pynrn_tests::basic_tests | |
| 55/145 Test #82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate ............. Passed 84.67 sec | |
| Start 97: testcorenrn_vecplay::coreneuron_gpu_offline | |
| 56/145 Test #4: pynrn_tests::basic_tests ........................................... Passed 4.12 sec | |
| Start 5: parallel_tests | |
| 57/145 Test #5: parallel_tests ..................................................... Passed 8.43 sec | |
| Start 6: parallel_partrans | |
| 58/145 Test #6: parallel_partrans .................................................. Passed 4.90 sec | |
| Start 7: parallel_netpar | |
| 59/145 Test #7: parallel_netpar .................................................... Passed 5.69 sec | |
| Start 8: parallel_bas | |
| 60/145 Test #91: testcorenrn_patstim::coreneuron_cpu_offline ........................ Passed 55.02 sec | |
| Start 99: testcorenrn_vecplay::coreneuron_cpu_online | |
| 61/145 Test #131: channel_benchmark_hippo::coreneuron_cpu_filemode ................... Passed 117.17 sec | |
| Start 9: coreneuron_modtests::fornetcon_py_cpu | |
| 62/145 Test #8: parallel_bas ....................................................... Passed 14.41 sec | |
| Start 10: coreneuron_modtests::direct_py_cpu | |
| 63/145 Test #95: testcorenrn_vecplay::coreneuron_gpu_online ......................... Passed 66.43 sec | |
| Start 100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate | |
| 64/145 Test #134: channel_benchmark_sscx::coreneuron_gpu_online ...................... Passed 101.99 sec | |
| Start 11: coreneuron_modtests::direct_hoc_cpu | |
| 65/145 Test #97: testcorenrn_vecplay::coreneuron_gpu_offline ........................ Passed 65.32 sec | |
| Start 101: testcorenrn_vecplay::coreneuron_cpu_offline | |
| 66/145 Test #90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore ............ Passed 100.06 sec | |
| Start 114: testcorenrn_watch::neuron | |
| 67/145 Test #9: coreneuron_modtests::fornetcon_py_cpu .............................. Passed 51.24 sec | |
| Start 12: coreneuron_modtests::spikes_py_cpu | |
| 68/145 Test #10: coreneuron_modtests::direct_py_cpu ................................. Passed 38.20 sec | |
| Start 13: coreneuron_modtests::spikes_file_mode_py_cpu | |
| 69/145 Test #114: testcorenrn_watch::neuron .......................................... Passed 8.57 sec | |
| Start 115: testcorenrn_watch::coreneuron_gpu_online | |
| 70/145 Test #99: testcorenrn_vecplay::coreneuron_cpu_online ......................... Passed 52.64 sec | |
| Start 116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate | |
| 71/145 Test #96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate ........ Passed 83.12 sec | |
| Start 117: testcorenrn_watch::coreneuron_gpu_offline | |
| 72/145 Test #137: channel_benchmark_sscx::coreneuron_cpu_filemode .................... Passed 102.05 sec | |
| Start 14: coreneuron_modtests::fast_imem_py_cpu | |
| 73/145 Test #14: coreneuron_modtests::fast_imem_py_cpu .............................. Passed 0.54 sec | |
| Start 15: coreneuron_modtests::datareturn_py_cpu | |
| 74/145 Test #136: channel_benchmark_sscx::coreneuron_cpu_online ...................... Passed 109.52 sec | |
| Start 16: coreneuron_modtests::test_units_py_cpu | |
| 75/145 Test #135: channel_benchmark_sscx::coreneuron_gpu_filemode .................... Passed 111.49 sec | |
| Start 17: coreneuron_modtests::test_netmove_py_cpu | |
| 76/145 Test #11: coreneuron_modtests::direct_hoc_cpu ................................ Passed 30.84 sec | |
| Start 18: coreneuron_modtests::test_watchrange_py_cpu | |
| 77/145 Test #100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate ........ Passed 34.35 sec | |
| Start 119: testcorenrn_watch::coreneuron_cpu_online | |
| 78/145 Test #101: testcorenrn_vecplay::coreneuron_cpu_offline ........................ Passed 24.84 sec | |
| Start 120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate | |
| 79/145 Test #12: coreneuron_modtests::spikes_py_cpu ................................. Passed 15.87 sec | |
| Start 19: coreneuron_modtests::test_psolve_py_cpu | |
| 80/145 Test #13: coreneuron_modtests::spikes_file_mode_py_cpu ....................... Passed 16.33 sec | |
| Start 20: coreneuron_modtests::test_natrans_py_cpu | |
| 81/145 Test #15: coreneuron_modtests::datareturn_py_cpu ............................. Passed 16.27 sec | |
| Start 24: coreneuron_modtests::direct_py_gpu | |
| 82/145 Test #16: coreneuron_modtests::test_units_py_cpu ............................. Passed 21.52 sec | |
| Start 25: coreneuron_modtests::direct_hoc_gpu | |
| 83/145 Test #17: coreneuron_modtests::test_netmove_py_cpu ........................... Passed 21.49 sec | |
| Start 26: coreneuron_modtests::spikes_py_gpu | |
| 84/145 Test #115: testcorenrn_watch::coreneuron_gpu_online ........................... Passed 29.06 sec | |
| Start 121: testcorenrn_watch::coreneuron_cpu_offline | |
| 85/145 Test #117: testcorenrn_watch::coreneuron_gpu_offline .......................... Passed 28.63 sec | |
| Start 124: testcorenrn_netstimdirect::direct_netstimdirect | |
| 86/145 Test #116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate .......... Passed 30.98 sec | |
| Start 125: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate | |
| 87/145 Test #18: coreneuron_modtests::test_watchrange_py_cpu ........................ Passed 20.91 sec | |
| Start 27: coreneuron_modtests::spikes_file_mode_py_gpu | |
| 88/145 Test #20: coreneuron_modtests::test_natrans_py_cpu ........................... Passed 16.05 sec | |
| Start 28: coreneuron_modtests::fast_imem_py_gpu | |
| 89/145 Test #28: coreneuron_modtests::fast_imem_py_gpu .............................. Passed 0.89 sec | |
| Start 29: coreneuron_modtests::datareturn_py_gpu | |
| 90/145 Test #119: testcorenrn_watch::coreneuron_cpu_online ........................... Passed 20.69 sec | |
| Start 21: coreneuron_modtests::spikes_mpi_py_cpu | |
| 91/145 Test #120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate .......... Passed 18.59 sec | |
| Start 22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu | |
| 92/145 Test #24: coreneuron_modtests::direct_py_gpu ................................. Passed 17.21 sec | |
| Start 30: coreneuron_modtests::test_units_py_gpu | |
| 93/145 Test #25: coreneuron_modtests::direct_hoc_gpu ................................ Passed 12.05 sec | |
| Start 31: coreneuron_modtests::test_netmove_py_gpu | |
| 94/145 Test #26: coreneuron_modtests::spikes_py_gpu ................................. Passed 12.79 sec | |
| Start 32: coreneuron_modtests::test_watchrange_py_gpu | |
| 95/145 Test #19: coreneuron_modtests::test_psolve_py_cpu ............................ Passed 33.24 sec | |
| Start 33: coreneuron_modtests::test_psolve_py_gpu | |
| 96/145 Test #121: testcorenrn_watch::coreneuron_cpu_offline .......................... Passed 20.20 sec | |
| Start 23: coreneuron_modtests::inputpresyn_py_cpu | |
| 97/145 Test #124: testcorenrn_netstimdirect::direct_netstimdirect .................... Passed 20.15 sec | |
| Start 34: coreneuron_modtests::test_natrans_py_gpu | |
| Start 38: external_nrntest | |
| 98/145 Test #27: coreneuron_modtests::spikes_file_mode_py_gpu ....................... Passed 23.94 sec | |
| Start 65: testcorenrn_bbcore::compare_results | |
| 99/145 Test #65: testcorenrn_bbcore::compare_results ................................ Passed 1.62 sec | |
| Start 75: testcorenrn_deriv::compare_results | |
| 100/145 Test #75: testcorenrn_deriv::compare_results ................................. Passed 1.01 sec | |
| Start 85: testcorenrn_gf::compare_results | |
| 101/145 Test #85: testcorenrn_gf::compare_results .................................... Passed 0.93 sec | |
| Start 93: testcorenrn_patstim::compare_results | |
| 102/145 Test #93: testcorenrn_patstim::compare_results ............................... Passed 0.47 sec | |
| Start 103: testcorenrn_vecplay::compare_results | |
| 103/145 Test #103: testcorenrn_vecplay::compare_results ............................... Passed 0.16 sec | |
| Start 123: testcorenrn_watch::compare_results | |
| 104/145 Test #123: testcorenrn_watch::compare_results ................................. Passed 0.13 sec | |
| Start 132: channel_benchmark_hippo::compare_results | |
| 105/145 Test #132: channel_benchmark_hippo::compare_results ........................... Passed 0.09 sec | |
| Start 138: channel_benchmark_sscx::compare_results | |
| 106/145 Test #138: channel_benchmark_sscx::compare_results ............................ Passed 0.07 sec | |
| 107/145 Test #30: coreneuron_modtests::test_units_py_gpu ............................. Passed 24.93 sec | |
| Start 35: coreneuron_modtests::spikes_mpi_py_gpu | |
| 108/145 Test #32: coreneuron_modtests::test_watchrange_py_gpu ........................ Passed 24.13 sec | |
| 109/145 Test #31: coreneuron_modtests::test_netmove_py_gpu ........................... Passed 25.52 sec | |
| Start 36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu | |
| 110/145 Test #29: coreneuron_modtests::datareturn_py_gpu ............................. Passed 29.05 sec | |
| 111/145 Test #21: coreneuron_modtests::spikes_mpi_py_cpu ............................. Passed 29.57 sec | |
| Start 37: coreneuron_modtests::inputpresyn_py_gpu | |
| 112/145 Test #22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu ................... Passed 29.11 sec | |
| 113/145 Test #33: coreneuron_modtests::test_psolve_py_gpu ............................ Passed 16.28 sec | |
| Start 108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation | |
| 114/145 Test #34: coreneuron_modtests::test_natrans_py_gpu ........................... Passed 15.49 sec | |
| 115/145 Test #23: coreneuron_modtests::inputpresyn_py_cpu ............................ Passed 16.82 sec | |
| 116/145 Test #125: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate ... Passed 35.80 sec | |
| Start 112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation | |
| Start 126: testcorenrn_netstimdirect::compare_results | |
| 117/145 Test #126: testcorenrn_netstimdirect::compare_results ......................... Passed 0.31 sec | |
| 118/145 Test #108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation .......... Passed 9.17 sec | |
| Start 140: olfactory-bulb-3d::neuron::preparation | |
| 119/145 Test #112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation .......... Passed 6.85 sec | |
| Start 142: olfactory-bulb-3d::coreneuron_gpu_online::preparation | |
| 120/145 Test #142: olfactory-bulb-3d::coreneuron_gpu_online::preparation .............. Passed 0.10 sec | |
| Start 144: olfactory-bulb-3d::coreneuron_cpu_online::preparation | |
| 121/145 Test #140: olfactory-bulb-3d::neuron::preparation ............................. Passed 0.52 sec | |
| Start 39: reduced_dentate::neuron | |
| 122/145 Test #144: olfactory-bulb-3d::coreneuron_cpu_online::preparation .............. Passed 0.12 sec | |
| Start 40: reduced_dentate::coreneuron_cpu | |
| 123/145 Test #35: coreneuron_modtests::spikes_mpi_py_gpu ............................. Passed 18.62 sec | |
| 124/145 Test #37: coreneuron_modtests::inputpresyn_py_gpu ............................ Passed 17.02 sec | |
| Start 41: reduced_dentate::coreneuron_gpu | |
| 125/145 Test #36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu ................... Passed 18.57 sec | |
| 126/145 Test #39: reduced_dentate::neuron ............................................ Passed 29.20 sec | |
| Start 49: external_ringtest::coreneuron_cpu_mpi_threads | |
| 127/145 Test #40: reduced_dentate::coreneuron_cpu .................................... Passed 36.48 sec | |
| Start 104: testcorenrn_vecevent::neuron | |
| 128/145 Test #104: testcorenrn_vecevent::neuron ....................................... Passed 2.87 sec | |
| Start 105: testcorenrn_vecevent::coreneuron_gpu_online | |
| 129/145 Test #41: reduced_dentate::coreneuron_gpu .................................... Passed 37.14 sec | |
| Start 106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate | |
| Start 42: reduced_dentate::compare_results | |
| 130/145 Test #42: reduced_dentate::compare_results ................................... Passed 0.09 sec | |
| 131/145 Test #49: external_ringtest::coreneuron_cpu_mpi_threads ...................... Passed 15.72 sec | |
| Start 54: external_ringtest::coreneuron_gpu_mpi_threads | |
| 132/145 Test #105: testcorenrn_vecevent::coreneuron_gpu_online ........................ Passed 8.14 sec | |
| Start 107: testcorenrn_vecevent::coreneuron_gpu_offline | |
| 133/145 Test #107: testcorenrn_vecevent::coreneuron_gpu_offline ....................... Passed 20.96 sec | |
| Start 109: testcorenrn_vecevent::coreneuron_cpu_online | |
| 134/145 Test #54: external_ringtest::coreneuron_gpu_mpi_threads ...................... Passed 27.16 sec | |
| Start 110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate | |
| Start 55: external_ringtest::compare_results | |
| 135/145 Test #55: external_ringtest::compare_results ................................. Passed 0.44 sec | |
| 136/145 Test #109: testcorenrn_vecevent::coreneuron_cpu_online ........................ Passed 36.48 sec | |
| Start 111: testcorenrn_vecevent::coreneuron_cpu_offline | |
| 137/145 Test #106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate ....... Passed 67.14 sec | |
| Start 139: olfactory-bulb-3d::neuron | |
| 138/145 Test #111: testcorenrn_vecevent::coreneuron_cpu_offline ....................... Passed 13.45 sec | |
| Start 141: olfactory-bulb-3d::coreneuron_gpu_online | |
| 139/145 Test #110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate ....... Passed 65.08 sec | |
| Start 143: olfactory-bulb-3d::coreneuron_cpu_online | |
| Start 113: testcorenrn_vecevent::compare_results | |
| 140/145 Test #113: testcorenrn_vecevent::compare_results .............................. Passed 0.10 sec | |
| 141/145 Test #38: external_nrntest ................................................... Passed 199.66 sec | |
| 142/145 Test #141: olfactory-bulb-3d::coreneuron_gpu_online ........................... Passed 146.98 sec | |
| 143/145 Test #139: olfactory-bulb-3d::neuron .......................................... Passed 172.68 sec | |
| 144/145 Test #143: olfactory-bulb-3d::coreneuron_cpu_online ........................... Passed 148.95 sec | |
| Start 145: olfactory-bulb-3d::compare_results | |
| 145/145 Test #145: olfactory-bulb-3d::compare_results ................................. Passed 0.24 sec | |
| 100% tests passed, 0 tests failed out of 145 | |
| Total Test time (real) = 759.09 sec | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| section_end:1644840801:step_script [0Ksection_start:1644840801: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=58206 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 7 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153685 responseStatus[0;m=201 Created token[0;m=kxVbHGtx | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=58259 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153685 responseStatus[0;m=201 Created token[0;m=kxVbHGtx | |
| section_end:1644840803:upload_artifacts_on_success [0Ksection_start:1644840803:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644840803:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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| [0KRunning with gitlab-runner 14.3.2 (e0218c92)[0;m | |
| [0K on BB5 map runner pnPo3yJy[0;m | |
| section_start:1644838343:resolve_secrets [0K[0K[36;1mResolving secrets[0;m[0;m | |
| section_end:1644838343:resolve_secrets [0Ksection_start:1644838343: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 14.3.2, user | |
| TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor977207482, slurm job id | |
| Runner ID 29, project root hpc, project name coreneuron | |
| Pipeline ID 37548, build ref 3469f1e9e6bf04e5d0f9be59fd494b8f281f457f, job ID 153683 | |
| Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548, optional exclusive flag , optional cpus per task flag --cpus-per-task=1 | |
| A slurm job will be created with name GL_J153683_PROD_P112_CP0_C1 | |
| Job parameters: memory=76G, cpus_per_task=1, duration=1:00:00, constraint=volta ntasks=16 account=proj9998 user=bbpcihpcproj12 partition=prod | |
| sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS | |
| Submitted batch job 274871 | |
| job state: R | |
| sbatch: sbatch -p prod -A proj9998 --ntasks=16 --cpus-per-task=1 --mem=76G --job-name=GL_J153683_PROD_P112_CP0_C1 -C volta --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --time=1:00:00 --wrap="sleep infinity" | |
| srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P37548 --ntasks=16 --jobid=274871 --cpus-per-task=1 --mem=76G | |
| section_end:1644838389:prepare_executor [0Ksection_start:1644838389:prepare_script [0K[0K[36;1mPreparing environment[0;m[0;m | |
| Running on ldir01u05.bbp.epfl.ch via bbpv1.epfl.ch... | |
| section_end:1644838391:prepare_script [0Ksection_start:1644838391: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:1644838392:get_sources [0Ksection_start:1644838392:download_artifacts [0K[0K[36;1mDownloading artifacts[0;m[0;m | |
| [32;1mDownloading artifacts for build:neuron:nmodl:nvhpc:omp (153660)...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=9869 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| Downloading artifacts from coordinator... ok [0;m id[0;m=153660 responseStatus[0;m=200 OK token[0;m=VZPSXxs8 | |
| section_end:1644838393:download_artifacts [0Ksection_start:1644838393: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$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env[0;m | |
| [32;1m$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}[0;m | |
| [32;1m$ . ${SPACK_ROOT}/share/spack/setup-env.sh[0;m | |
| [32;1m$ cd ${SPACK_BUILD_DIR}[0;m | |
| [32;1m$ export BOOST_TEST_COLOR_OUTPUT=no[0;m | |
| [32;1m$ i_am_a_failure=0[0;m | |
| [32;1m$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1[0;m | |
| Site: r1i7n29 | |
| Build name: Linux-nvc++ | |
| Create new tag: 20220214-1133 - Experimental | |
| Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P37548/J153660/spack-build/spack-stage-neuron-develop-ccjdz33a47dcm6emvjsbg2kpa4job22w/spack-build-ccjdz33 | |
| Start 48: external_ringtest::coreneuron_cpu_mpi_offline::preparation | |
| Start 53: external_ringtest::coreneuron_gpu_mpi_offline::preparation | |
| Start 60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation | |
| Start 64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation | |
| Start 70: testcorenrn_deriv::coreneuron_gpu_offline::preparation | |
| Start 74: testcorenrn_deriv::coreneuron_cpu_offline::preparation | |
| Start 80: testcorenrn_gf::coreneuron_gpu_offline::preparation | |
| Start 84: testcorenrn_gf::coreneuron_cpu_offline::preparation | |
| Start 89: testcorenrn_patstim::coreneuron_gpu_offline::preparation | |
| Start 92: testcorenrn_patstim::coreneuron_cpu_offline::preparation | |
| Start 43: external_ringtest::neuron | |
| 1/145 Test #89: testcorenrn_patstim::coreneuron_gpu_offline::preparation ........... Passed 2.75 sec | |
| Start 56: testcorenrn_bbcore::neuron | |
| 2/145 Test #70: testcorenrn_deriv::coreneuron_gpu_offline::preparation ............. Passed 2.87 sec | |
| Start 57: testcorenrn_bbcore::coreneuron_gpu_online | |
| 3/145 Test #60: testcorenrn_bbcore::coreneuron_gpu_offline::preparation ............ Passed 2.99 sec | |
| Start 58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate | |
| 4/145 Test #43: external_ringtest::neuron .......................................... Passed 3.09 sec | |
| Start 59: testcorenrn_bbcore::coreneuron_gpu_offline | |
| 5/145 Test #64: testcorenrn_bbcore::coreneuron_cpu_offline::preparation ............ Passed 3.31 sec | |
| Start 61: testcorenrn_bbcore::coreneuron_cpu_online | |
| 6/145 Test #74: testcorenrn_deriv::coreneuron_cpu_offline::preparation ............. Passed 3.50 sec | |
| Start 62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate | |
| 7/145 Test #80: testcorenrn_gf::coreneuron_gpu_offline::preparation ................ Passed 3.61 sec | |
| Start 98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation | |
| 8/145 Test #92: testcorenrn_patstim::coreneuron_cpu_offline::preparation ........... Passed 3.75 sec | |
| Start 102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation | |
| 9/145 Test #84: testcorenrn_gf::coreneuron_cpu_offline::preparation ................ Passed 4.10 sec | |
| Start 118: testcorenrn_watch::coreneuron_gpu_offline::preparation | |
| 10/145 Test #56: testcorenrn_bbcore::neuron ......................................... Passed 1.53 sec | |
| Start 63: testcorenrn_bbcore::coreneuron_cpu_offline | |
| 11/145 Test #98: testcorenrn_vecplay::coreneuron_gpu_offline::preparation ........... Passed 2.41 sec | |
| Start 122: testcorenrn_watch::coreneuron_cpu_offline::preparation | |
| 12/145 Test #102: testcorenrn_vecplay::coreneuron_cpu_offline::preparation ........... Passed 2.58 sec | |
| Start 44: external_ringtest::neuron_mpi | |
| 13/145 Test #118: testcorenrn_watch::coreneuron_gpu_offline::preparation ............. Passed 2.38 sec | |
| Start 45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore | |
| 14/145 Test #122: testcorenrn_watch::coreneuron_cpu_offline::preparation ............. Passed 1.72 sec | |
| Start 46: external_ringtest::coreneuron_cpu_mpi | |
| 15/145 Test #48: external_ringtest::coreneuron_cpu_mpi_offline::preparation ......... Passed 9.75 sec | |
| Start 47: external_ringtest::coreneuron_cpu_mpi_offline | |
| 16/145 Test #63: testcorenrn_bbcore::coreneuron_cpu_offline ......................... Passed 5.44 sec | |
| Start 66: testcorenrn_deriv::neuron | |
| 17/145 Test #62: testcorenrn_bbcore::coreneuron_cpu_online_psolve_alternate ......... Passed 6.76 sec | |
| Start 67: testcorenrn_deriv::coreneuron_gpu_online | |
| 18/145 Test #61: testcorenrn_bbcore::coreneuron_cpu_online .......................... Passed 7.12 sec | |
| Start 68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate | |
| 19/145 Test #53: external_ringtest::coreneuron_gpu_mpi_offline::preparation ......... Passed 11.21 sec | |
| Start 50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore | |
| 20/145 Test #59: testcorenrn_bbcore::coreneuron_gpu_offline ......................... Passed 8.68 sec | |
| Start 69: testcorenrn_deriv::coreneuron_gpu_offline | |
| 21/145 Test #57: testcorenrn_bbcore::coreneuron_gpu_online .......................... Passed 9.01 sec | |
| Start 71: testcorenrn_deriv::coreneuron_cpu_online | |
| 22/145 Test #58: testcorenrn_bbcore::coreneuron_gpu_online_psolve_alternate ......... Passed 10.09 sec | |
| Start 72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate | |
| 23/145 Test #44: external_ringtest::neuron_mpi ...................................... Passed 11.33 sec | |
| Start 51: external_ringtest::coreneuron_gpu_mpi | |
| 24/145 Test #47: external_ringtest::coreneuron_cpu_mpi_offline ...................... Passed 8.82 sec | |
| Start 52: external_ringtest::coreneuron_gpu_mpi_offline | |
| 25/145 Test #66: testcorenrn_deriv::neuron .......................................... Passed 9.14 sec | |
| Start 73: testcorenrn_deriv::coreneuron_cpu_offline | |
| 26/145 Test #69: testcorenrn_deriv::coreneuron_gpu_offline .......................... Passed 7.51 sec | |
| Start 87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore | |
| 27/145 Test #72: testcorenrn_deriv::coreneuron_cpu_online_psolve_alternate .......... Passed 36.13 sec | |
| Start 88: testcorenrn_patstim::coreneuron_gpu_offline | |
| 28/145 Test #73: testcorenrn_deriv::coreneuron_cpu_offline .......................... Passed 31.83 sec | |
| Start 127: channel_benchmark_hippo::neuron | |
| 29/145 Test #71: testcorenrn_deriv::coreneuron_cpu_online ........................... Passed 39.06 sec | |
| Start 128: channel_benchmark_hippo::coreneuron_gpu_online | |
| 30/145 Test #67: testcorenrn_deriv::coreneuron_gpu_online ........................... Passed 41.06 sec | |
| Start 129: channel_benchmark_hippo::coreneuron_gpu_filemode | |
| 31/145 Test #46: external_ringtest::coreneuron_cpu_mpi .............................. Passed 43.95 sec | |
| Start 76: testcorenrn_gf::neuron | |
| 32/145 Test #76: testcorenrn_gf::neuron ............................................. Passed 6.29 sec | |
| Start 77: testcorenrn_gf::coreneuron_gpu_online | |
| 33/145 Test #51: external_ringtest::coreneuron_gpu_mpi .............................. Passed 50.41 sec | |
| Start 78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate | |
| 34/145 Test #52: external_ringtest::coreneuron_gpu_mpi_offline ...................... Passed 49.82 sec | |
| Start 79: testcorenrn_gf::coreneuron_gpu_offline | |
| 35/145 Test #68: testcorenrn_deriv::coreneuron_gpu_online_psolve_alternate .......... Passed 58.29 sec | |
| Start 130: channel_benchmark_hippo::coreneuron_cpu_online | |
| 36/145 Test #88: testcorenrn_patstim::coreneuron_gpu_offline ........................ Passed 38.63 sec | |
| Start 131: channel_benchmark_hippo::coreneuron_cpu_filemode | |
| 37/145 Test #87: testcorenrn_patstim::coreneuron_gpu_offline_saverestore ............ Passed 76.87 sec | |
| Start 133: channel_benchmark_sscx::neuron | |
| 38/145 Test #77: testcorenrn_gf::coreneuron_gpu_online .............................. Passed 70.12 sec | |
| Start 81: testcorenrn_gf::coreneuron_cpu_online | |
| 39/145 Test #45: external_ringtest::coreneuron_cpu_mpi_offline_saverestore .......... Passed 142.06 sec | |
| Start 82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate | |
| 40/145 Test #79: testcorenrn_gf::coreneuron_gpu_offline ............................. Passed 86.01 sec | |
| Start 83: testcorenrn_gf::coreneuron_cpu_offline | |
| 41/145 Test #81: testcorenrn_gf::coreneuron_cpu_online .............................. Passed 33.16 sec | |
| Start 86: testcorenrn_patstim::neuron | |
| 42/145 Test #127: channel_benchmark_hippo::neuron .................................... Passed 112.24 sec | |
| Start 134: channel_benchmark_sscx::coreneuron_gpu_online | |
| 43/145 Test #86: testcorenrn_patstim::neuron ........................................ Passed 2.83 sec | |
| Start 90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore | |
| 44/145 Test #78: testcorenrn_gf::coreneuron_gpu_online_psolve_alternate ............. Passed 98.06 sec | |
| Start 91: testcorenrn_patstim::coreneuron_cpu_offline | |
| 45/145 Test #50: external_ringtest::coreneuron_gpu_mpi_offline_saverestore .......... Passed 174.48 sec | |
| Start 94: testcorenrn_vecplay::neuron | |
| 46/145 Test #94: testcorenrn_vecplay::neuron ........................................ Passed 2.58 sec | |
| Start 95: testcorenrn_vecplay::coreneuron_gpu_online | |
| 47/145 Test #128: channel_benchmark_hippo::coreneuron_gpu_online ..................... Passed 138.54 sec | |
| Start 135: channel_benchmark_sscx::coreneuron_gpu_filemode | |
| 48/145 Test #129: channel_benchmark_hippo::coreneuron_gpu_filemode ................... Passed 138.83 sec | |
| Start 136: channel_benchmark_sscx::coreneuron_cpu_online | |
| 49/145 Test #83: testcorenrn_gf::coreneuron_cpu_offline ............................. Passed 37.54 sec | |
| Start 96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate | |
| 50/145 Test #82: testcorenrn_gf::coreneuron_cpu_online_psolve_alternate ............. Passed 51.54 sec | |
| Start 97: testcorenrn_vecplay::coreneuron_gpu_offline | |
| 51/145 Test #91: testcorenrn_patstim::coreneuron_cpu_offline ........................ Passed 33.88 sec | |
| Start 99: testcorenrn_vecplay::coreneuron_cpu_online | |
| 52/145 Test #133: channel_benchmark_sscx::neuron ..................................... Passed 115.47 sec | |
| Start 137: channel_benchmark_sscx::coreneuron_cpu_filemode | |
| 53/145 Test #99: testcorenrn_vecplay::coreneuron_cpu_online ......................... Passed 38.92 sec | |
| Start 100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate | |
| 54/145 Test #130: channel_benchmark_hippo::coreneuron_cpu_online ..................... Passed 172.22 sec | |
| Start 1: testneuron | |
| 55/145 Test #1: testneuron ......................................................... Passed 0.06 sec | |
| Start 2: ringtest | |
| 56/145 Test #90: testcorenrn_patstim::coreneuron_cpu_offline_saverestore ............ Passed 76.90 sec | |
| Start 101: testcorenrn_vecplay::coreneuron_cpu_offline | |
| 57/145 Test #2: ringtest ........................................................... Passed 0.28 sec | |
| Start 3: connect_dend | |
| 58/145 Test #3: connect_dend ....................................................... Passed 0.23 sec | |
| Start 4: pynrn_tests::basic_tests | |
| 59/145 Test #4: pynrn_tests::basic_tests ........................................... Passed 4.80 sec | |
| Start 5: parallel_tests | |
| 60/145 Test #131: channel_benchmark_hippo::coreneuron_cpu_filemode ................... Passed 167.72 sec | |
| Start 6: parallel_partrans | |
| 61/145 Test #97: testcorenrn_vecplay::coreneuron_gpu_offline ........................ Passed 63.67 sec | |
| Start 114: testcorenrn_watch::neuron | |
| 62/145 Test #95: testcorenrn_vecplay::coreneuron_gpu_online ......................... Passed 75.54 sec | |
| Start 115: testcorenrn_watch::coreneuron_gpu_online | |
| 63/145 Test #5: parallel_tests ..................................................... Passed 17.94 sec | |
| Start 7: parallel_netpar | |
| 64/145 Test #101: testcorenrn_vecplay::coreneuron_cpu_offline ........................ Passed 23.30 sec | |
| Start 116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate | |
| 65/145 Test #114: testcorenrn_watch::neuron .......................................... Passed 5.21 sec | |
| Start 117: testcorenrn_watch::coreneuron_gpu_offline | |
| 66/145 Test #6: parallel_partrans .................................................. Passed 14.43 sec | |
| Start 8: parallel_bas | |
| 67/145 Test #7: parallel_netpar .................................................... Passed 9.16 sec | |
| Start 9: coreneuron_modtests::fornetcon_py_cpu | |
| 68/145 Test #100: testcorenrn_vecplay::coreneuron_cpu_online_psolve_alternate ........ Passed 36.41 sec | |
| Start 119: testcorenrn_watch::coreneuron_cpu_online | |
| 69/145 Test #134: channel_benchmark_sscx::coreneuron_gpu_online ...................... Passed 117.64 sec | |
| Start 10: coreneuron_modtests::direct_py_cpu | |
| 70/145 Test #8: parallel_bas ....................................................... Passed 13.54 sec | |
| Start 11: coreneuron_modtests::direct_hoc_cpu | |
| 71/145 Test #117: testcorenrn_watch::coreneuron_gpu_offline .......................... Passed 21.68 sec | |
| Start 120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate | |
| 72/145 Test #96: testcorenrn_vecplay::coreneuron_gpu_online_psolve_alternate ........ Passed 98.92 sec | |
| Start 121: testcorenrn_watch::coreneuron_cpu_offline | |
| 73/145 Test #9: coreneuron_modtests::fornetcon_py_cpu .............................. Passed 23.69 sec | |
| Start 12: coreneuron_modtests::spikes_py_cpu | |
| 74/145 Test #115: testcorenrn_watch::coreneuron_gpu_online ........................... Passed 33.66 sec | |
| Start 124: testcorenrn_netstimdirect::direct_netstimdirect | |
| 75/145 Test #10: coreneuron_modtests::direct_py_cpu ................................. Passed 21.34 sec | |
| Start 13: coreneuron_modtests::spikes_file_mode_py_cpu | |
| 76/145 Test #136: channel_benchmark_sscx::coreneuron_cpu_online ...................... Passed 113.17 sec | |
| Start 14: coreneuron_modtests::fast_imem_py_cpu | |
| 77/145 Test #119: testcorenrn_watch::coreneuron_cpu_online ........................... Passed 27.81 sec | |
| Start 125: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate | |
| 78/145 Test #135: channel_benchmark_sscx::coreneuron_gpu_filemode .................... Passed 114.56 sec | |
| Start 15: coreneuron_modtests::datareturn_py_cpu | |
| 79/145 Test #14: coreneuron_modtests::fast_imem_py_cpu .............................. Passed 1.24 sec | |
| Start 16: coreneuron_modtests::test_units_py_cpu | |
| 80/145 Test #116: testcorenrn_watch::coreneuron_gpu_online_psolve_alternate .......... Passed 40.41 sec | |
| Start 17: coreneuron_modtests::test_netmove_py_cpu | |
| Start 18: coreneuron_modtests::test_watchrange_py_cpu | |
| 81/145 Test #11: coreneuron_modtests::direct_hoc_cpu ................................ Passed 22.69 sec | |
| Start 19: coreneuron_modtests::test_psolve_py_cpu | |
| 82/145 Test #121: testcorenrn_watch::coreneuron_cpu_offline .......................... Passed 23.68 sec | |
| Start 20: coreneuron_modtests::test_natrans_py_cpu | |
| Start 24: coreneuron_modtests::direct_py_gpu | |
| 83/145 Test #137: channel_benchmark_sscx::coreneuron_cpu_filemode .................... Passed 104.48 sec | |
| Start 25: coreneuron_modtests::direct_hoc_gpu | |
| 84/145 Test #13: coreneuron_modtests::spikes_file_mode_py_cpu ....................... Passed 16.53 sec | |
| Start 26: coreneuron_modtests::spikes_py_gpu | |
| 85/145 Test #18: coreneuron_modtests::test_watchrange_py_cpu ........................ Passed 15.08 sec | |
| Start 27: coreneuron_modtests::spikes_file_mode_py_gpu | |
| 86/145 Test #16: coreneuron_modtests::test_units_py_cpu ............................. Passed 16.20 sec | |
| Start 28: coreneuron_modtests::fast_imem_py_gpu | |
| 87/145 Test #19: coreneuron_modtests::test_psolve_py_cpu ............................ Passed 14.46 sec | |
| Start 29: coreneuron_modtests::datareturn_py_gpu | |
| 88/145 Test #125: testcorenrn_netstimdirect::direct_netstimdirect_psolve_alternate ... Passed 17.92 sec | |
| Start 21: coreneuron_modtests::spikes_mpi_py_cpu | |
| 89/145 Test #120: testcorenrn_watch::coreneuron_cpu_online_psolve_alternate .......... Passed 31.24 sec | |
| Start 22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu | |
| 90/145 Test #17: coreneuron_modtests::test_netmove_py_cpu ........................... Passed 17.40 sec | |
| Start 30: coreneuron_modtests::test_units_py_gpu | |
| 91/145 Test #15: coreneuron_modtests::datareturn_py_cpu ............................. Passed 18.14 sec | |
| Start 31: coreneuron_modtests::test_netmove_py_gpu | |
| 92/145 Test #28: coreneuron_modtests::fast_imem_py_gpu .............................. Passed 1.47 sec | |
| Start 32: coreneuron_modtests::test_watchrange_py_gpu | |
| 93/145 Test #24: coreneuron_modtests::direct_py_gpu ................................. Passed 10.03 sec | |
| Start 33: coreneuron_modtests::test_psolve_py_gpu | |
| 94/145 Test #20: coreneuron_modtests::test_natrans_py_cpu ........................... Passed 10.06 sec | |
| Start 34: coreneuron_modtests::test_natrans_py_gpu | |
| 95/145 Test #25: coreneuron_modtests::direct_hoc_gpu ................................ Passed 8.70 sec | |
| Start 38: external_nrntest | |
| 96/145 Test #12: coreneuron_modtests::spikes_py_cpu ................................. Passed 31.45 sec | |
| Start 65: testcorenrn_bbcore::compare_results | |
| 97/145 Test #65: testcorenrn_bbcore::compare_results ................................ Passed 0.07 sec | |
| Start 75: testcorenrn_deriv::compare_results | |
| 98/145 Test #75: testcorenrn_deriv::compare_results ................................. Passed 0.06 sec | |
| Start 85: testcorenrn_gf::compare_results | |
| 99/145 Test #85: testcorenrn_gf::compare_results .................................... Passed 0.06 sec | |
| Start 93: testcorenrn_patstim::compare_results | |
| 100/145 Test #93: testcorenrn_patstim::compare_results ............................... Passed 0.06 sec | |
| Start 103: testcorenrn_vecplay::compare_results | |
| 101/145 Test #103: testcorenrn_vecplay::compare_results ............................... Passed 0.06 sec | |
| Start 123: testcorenrn_watch::compare_results | |
| 102/145 Test #123: testcorenrn_watch::compare_results ................................. Passed 0.06 sec | |
| Start 132: channel_benchmark_hippo::compare_results | |
| 103/145 Test #132: channel_benchmark_hippo::compare_results ........................... Passed 0.06 sec | |
| Start 138: channel_benchmark_sscx::compare_results | |
| 104/145 Test #138: channel_benchmark_sscx::compare_results ............................ Passed 0.06 sec | |
| 105/145 Test #27: coreneuron_modtests::spikes_file_mode_py_gpu ....................... Passed 9.44 sec | |
| Start 23: coreneuron_modtests::inputpresyn_py_cpu | |
| 106/145 Test #26: coreneuron_modtests::spikes_py_gpu ................................. Passed 10.99 sec | |
| 107/145 Test #124: testcorenrn_netstimdirect::direct_netstimdirect .................... Passed 32.43 sec | |
| Start 35: coreneuron_modtests::spikes_mpi_py_gpu | |
| Start 126: testcorenrn_netstimdirect::compare_results | |
| 108/145 Test #126: testcorenrn_netstimdirect::compare_results ......................... Passed 0.25 sec | |
| 109/145 Test #30: coreneuron_modtests::test_units_py_gpu ............................. Passed 9.29 sec | |
| Start 36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu | |
| 110/145 Test #32: coreneuron_modtests::test_watchrange_py_gpu ........................ Passed 9.24 sec | |
| 111/145 Test #29: coreneuron_modtests::datareturn_py_gpu ............................. Passed 10.66 sec | |
| Start 37: coreneuron_modtests::inputpresyn_py_gpu | |
| 112/145 Test #31: coreneuron_modtests::test_netmove_py_gpu ........................... Passed 9.42 sec | |
| 113/145 Test #34: coreneuron_modtests::test_natrans_py_gpu ........................... Passed 7.63 sec | |
| 114/145 Test #22: coreneuron_modtests::spikes_mpi_file_mode_py_cpu ................... Passed 10.42 sec | |
| Start 108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation | |
| 115/145 Test #33: coreneuron_modtests::test_psolve_py_gpu ............................ Passed 7.71 sec | |
| 116/145 Test #21: coreneuron_modtests::spikes_mpi_py_cpu ............................. Passed 11.25 sec | |
| 117/145 Test #108: testcorenrn_vecevent::coreneuron_gpu_offline::preparation .......... Passed 2.77 sec | |
| Start 112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation | |
| 118/145 Test #112: testcorenrn_vecevent::coreneuron_cpu_offline::preparation .......... Passed 2.42 sec | |
| Start 140: olfactory-bulb-3d::neuron::preparation | |
| 119/145 Test #140: olfactory-bulb-3d::neuron::preparation ............................. Passed 0.05 sec | |
| Start 142: olfactory-bulb-3d::coreneuron_gpu_online::preparation | |
| 120/145 Test #23: coreneuron_modtests::inputpresyn_py_cpu ............................ Passed 8.31 sec | |
| Start 144: olfactory-bulb-3d::coreneuron_cpu_online::preparation | |
| 121/145 Test #142: olfactory-bulb-3d::coreneuron_gpu_online::preparation .............. Passed 0.08 sec | |
| Start 39: reduced_dentate::neuron | |
| 122/145 Test #144: olfactory-bulb-3d::coreneuron_cpu_online::preparation .............. Passed 0.08 sec | |
| Start 40: reduced_dentate::coreneuron_cpu | |
| 123/145 Test #35: coreneuron_modtests::spikes_mpi_py_gpu ............................. Passed 7.79 sec | |
| 124/145 Test #36: coreneuron_modtests::spikes_mpi_file_mode_py_gpu ................... Passed 7.63 sec | |
| Start 41: reduced_dentate::coreneuron_gpu | |
| 125/145 Test #37: coreneuron_modtests::inputpresyn_py_gpu ............................ Passed 8.13 sec | |
| 126/145 Test #39: reduced_dentate::neuron ............................................ Passed 22.89 sec | |
| Start 49: external_ringtest::coreneuron_cpu_mpi_threads | |
| 127/145 Test #40: reduced_dentate::coreneuron_cpu .................................... Passed 30.99 sec | |
| Start 104: testcorenrn_vecevent::neuron | |
| 128/145 Test #104: testcorenrn_vecevent::neuron ....................................... Passed 3.92 sec | |
| Start 105: testcorenrn_vecevent::coreneuron_gpu_online | |
| 129/145 Test #49: external_ringtest::coreneuron_cpu_mpi_threads ...................... Passed 16.69 sec | |
| Start 54: external_ringtest::coreneuron_gpu_mpi_threads | |
| 130/145 Test #41: reduced_dentate::coreneuron_gpu .................................... Passed 40.67 sec | |
| Start 106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate | |
| Start 42: reduced_dentate::compare_results | |
| 131/145 Test #42: reduced_dentate::compare_results ................................... Passed 0.08 sec | |
| 132/145 Test #105: testcorenrn_vecevent::coreneuron_gpu_online ........................ Passed 8.41 sec | |
| Start 107: testcorenrn_vecevent::coreneuron_gpu_offline | |
| 133/145 Test #107: testcorenrn_vecevent::coreneuron_gpu_offline ....................... Passed 14.17 sec | |
| Start 109: testcorenrn_vecevent::coreneuron_cpu_online | |
| 134/145 Test #54: external_ringtest::coreneuron_gpu_mpi_threads ...................... Passed 23.44 sec | |
| Start 110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate | |
| Start 55: external_ringtest::compare_results | |
| 135/145 Test #55: external_ringtest::compare_results ................................. Passed 0.07 sec | |
| 136/145 Test #106: testcorenrn_vecevent::coreneuron_gpu_online_psolve_alternate ....... Passed 28.07 sec | |
| Start 111: testcorenrn_vecevent::coreneuron_cpu_offline | |
| 137/145 Test #109: testcorenrn_vecevent::coreneuron_cpu_online ........................ Passed 15.75 sec | |
| Start 139: olfactory-bulb-3d::neuron | |
| 138/145 Test #110: testcorenrn_vecevent::coreneuron_cpu_online_psolve_alternate ....... Passed 11.32 sec | |
| Start 141: olfactory-bulb-3d::coreneuron_gpu_online | |
| 139/145 Test #111: testcorenrn_vecevent::coreneuron_cpu_offline ....................... Passed 5.56 sec | |
| Start 143: olfactory-bulb-3d::coreneuron_cpu_online | |
| Start 113: testcorenrn_vecevent::compare_results | |
| 140/145 Test #113: testcorenrn_vecevent::compare_results .............................. Passed 0.77 sec | |
| 141/145 Test #38: external_nrntest ................................................... Passed 142.24 sec | |
| 142/145 Test #139: olfactory-bulb-3d::neuron .......................................... Passed 156.74 sec | |
| 143/145 Test #141: olfactory-bulb-3d::coreneuron_gpu_online ........................... Passed 194.59 sec | |
| 144/145 Test #143: olfactory-bulb-3d::coreneuron_cpu_online ........................... Passed 197.31 sec | |
| Start 145: olfactory-bulb-3d::compare_results | |
| 145/145 Test #145: olfactory-bulb-3d::compare_results ................................. Passed 0.23 sec | |
| 100% tests passed, 0 tests failed out of 145 | |
| Total Test time (real) = 611.02 sec | |
| [32;1m$ cp -r Testing/ ${CI_PROJECT_DIR}/[0;m | |
| [32;1m$ module load unstable unit-test-translator[0;m | |
| Autoloading python/3.9.7 | |
| [32;1m$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml[0;m | |
| [32;1m$ exit ${i_am_a_failure}[0;m | |
| section_end:1644839035:step_script [0Ksection_start:1644839035: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=24072 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| initial_environment.env: found 1 matching files and directories[0;m | |
| Testing/: found 7 matching files and directories [0;m | |
| Uploading artifacts as "archive" to coordinator... ok[0;m id[0;m=153683 responseStatus[0;m=201 Created token[0;m=avv3kATG | |
| [32;1mUploading artifacts...[0;m | |
| Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=24126 revision[0;m=58ba2b95 version[0;m=14.2.0 | |
| ctest.xml: found 1 matching files and directories [0;m | |
| Uploading artifacts as "junit" to coordinator... ok[0;m id[0;m=153683 responseStatus[0;m=201 Created token[0;m=avv3kATG | |
| section_end:1644839036:upload_artifacts_on_success [0Ksection_start:1644839036:cleanup_file_variables [0K[0K[36;1mCleaning up project directory and file based variables[0;m[0;m | |
| section_end:1644839037:cleanup_file_variables [0K[32;1mJob succeeded[0;m |
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