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bbpbuildbot/GitLab logs for bluebrain-nmodl#920 Secret

Created September 1, 2022 15:01
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Logfiles for GitLab pipeline https://bbpgitlab.epfl.ch/hpc/nmodl/-/pipelines/72529 (:no_entry:) running on GitHub PR BlueBrain/nmodl#920.
Raw
build-intel.txt
Running with gitlab-runner 15.1.0 (76984217)
 on BB5 map runner pnPo3yJy
section_start:1662043403:resolve_secrets Resolving secrets
section_end:1662043403:resolve_secrets section_start:1662043403:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1342975714, slurm job id
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 72529, build ref b5f1eaea1e478ac8839d74523aef4a4d95d34f1f, job ID 345798
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag
A slurm job will be created with name GL_J345798_PROD_P30_CP1_C2
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 756587
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J345798_PROD_P30_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --ntasks=1 --jobid=756587 --cpus-per-task=6 --mem=30750M
section_end:1662043404:prepare_executor section_start:1662043404:prepare_script Preparing environment
Running on r1i5n0 via bbpv1.epfl.ch...
section_end:1662043407:prepare_script section_start:1662043407:get_sources Getting source from Git repository
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1662043408:get_sources section_start:1662043408:restore_cache Restoring cache
Checking cache for build:intel-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=158618 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1662043413:restore_cache section_start:1662043413:download_artifacts Downloading artifacts
Downloading artifacts for spack_setup (345797)...
Runtime platform  arch=amd64 os=linux pid=159258 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=345797 responseStatus=200 OK token=yWKxws49
section_end:1662043414:download_artifacts section_start:1662043414:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``).
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # home directory.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # pip installable.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:118 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:123 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:128 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:136 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:145 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:207 terminal_title: False
_builtin debug: False
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529/J345798_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install nmodl%intel ~legacy-unit+python
$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})
$ 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\"])")
$ echo "Determined its hash will be ${SPACK_INSTALLED_HASH}"
Determined its hash will be vq4xwpxhyfyr26mospd577raaeicmn5e
$ SPACK_STAGE_DIR=${SPACK_BUILD}/spack-stage-${SPACK_PACKAGE}-develop-${SPACK_INSTALLED_HASH}
$ SPACK_BUILD_DIR=${SPACK_STAGE_DIR}/spack-build-${SPACK_INSTALLED_HASH:0:7}
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/756587/ccache
Primary config: /nvme/bbpcihpcproj12/756587/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Sep 1 16:44:40 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): 0.44 / 0.51 (85.59 %)
Files: 642
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true
==> Error: No installed spec matches the hash: 'vq4xwpxhyfyr26mospd577raaeicmn5e'
$ spack spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%intel~legacy-unit+python
Concretized
--------------------------------
- vq4xwpx nmodl@develop%intel@2021.4.0~ipo~legacy-unit~llvm~llvm_cuda+python build_type=RelWithDebInfo arch=linux-rhel7-skylake
- dwdch6b ^bison@3.8.2%intel@2021.4.0 arch=linux-rhel7-skylake
[^] lp4aqpl ^catch2@2.13.8%intel@2021.4.0~ipo build_type=RelWithDebInfo 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
[^] y626xhz ^cli11@2.1.1%intel@2021.4.0~ipo build_type=RelWithDebInfo arch=linux-rhel7-skylake
- s4ueg72 ^flex@2.6.3%intel@2021.4.0+lex~nls arch=linux-rhel7-skylake
[^] unnpvpo ^fmt@8.1.1%intel@2021.4.0~ipo+pic~shared build_type=RelWithDebInfo cxxstd=11 arch=linux-rhel7-skylake
- 6ggc5yr ^ninja@1.10.2%intel@2021.4.0 arch=linux-rhel7-skylake
[^] 57wruin ^nlohmann-json@3.10.4%intel@2021.4.0~ipo~multiple_headers build_type=RelWithDebInfo arch=linux-rhel7-skylake
[^] gxfilzu ^py-jinja2@3.0.1%intel@2021.4.0~i18n arch=linux-rhel7-skylake
[^] ybq5oea ^py-markupsafe@2.0.1%intel@2021.4.0 arch=linux-rhel7-skylake
[^] 5flpilw ^py-setuptools@57.4.0%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
[^] 4ia4lse ^py-pybind11@2.9.1%intel@2021.4.0~ipo build_type=RelWithDebInfo 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
[^] xmmo4uc ^py-pyyaml@5.3.1%intel@2021.4.0+libyaml arch=linux-rhel7-skylake
[^] rp5ra62 ^libyaml@0.2.5%intel@2021.4.0 arch=linux-rhel7-skylake
[^] ntq2pe6 ^py-sympy@1.9%intel@2021.4.0 arch=linux-rhel7-skylake
[^] r7rades ^py-mpmath@1.1.0%intel@2021.4.0 arch=linux-rhel7-skylake
[^] kxkrl2g ^spdlog@1.9.2%intel@2021.4.0~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake
$ 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
==> 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)
==> flex@2.6.3 : has external module in ['flex/2.6.3']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/flex-2.6.3-3mtl7j (external flex-2.6.3-s4ueg72j7l6vkdyvfxj2tweo7v7s3otx)
==> ninja@1.10.2 : has external module in ['ninja/1.10.2']
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ninja-1.10.2-eh33rh (external ninja-1.10.2-6ggc5yre7qddwxdjmn7sfptpdoiy4dtp)
==> 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/libyaml-0.2.5-rp5ra6
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/nlohmann-json-3.10.4-57wrui
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/fmt-8.1.1-unnpvp
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/cli11-2.1.1-y626xh
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/catch2-2.13.8-lp4aqp
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-mpmath-1.1.0-r7rade
[+] /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/py-pyyaml-5.3.1-xmmo4u
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/spdlog-1.9.2-kxkrl2
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-sympy-1.9-ntq2pe
[+] /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-pip-21.1.2-jesa65
[+] /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-pyparsing-2.4.7-3a3ral
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_intel-2021.4.0-skylake/py-markupsafe-2.0.1-ybq5oe
[+] /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/py-pybind11-2.9.1-4ia4ls
[+] /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-jinja2-3.0.1-gxfilz
[+] /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-pluggy-0.13.0-rh6zve
[+] /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-pytest-6.2.4-tzmlo5
==> Installing nmodl-develop-vq4xwpxhyfyr26mospd577raaeicmn5e
==> No binary for nmodl-develop-vq4xwpxhyfyr26mospd577raaeicmn5e found: installing from source
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529, but it is owned by 0
==> No patches needed for nmodl
==> nmodl: Executing phase: 'cmake'
==> nmodl: Executing phase: 'build'
==> nmodl: Executing phase: 'install'
==> nmodl: Successfully installed nmodl-develop-vq4xwpxhyfyr26mospd577raaeicmn5e
Fetch: 2m 24.43s. Build: 10m 31.95s. Total: 12m 56.38s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/software/install_intel-2021.4.0-skylake/nmodl-develop-vq4xwp
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/756587/ccache
Primary config: /nvme/bbpcihpcproj12/756587/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Sep 1 16:59:15 2022
Hits: 132 / 141 (93.62 %)
Direct: 23 / 141 (16.31 %)
Preprocessed: 109 / 118 (92.37 %)
Misses: 9
Direct: 118
Preprocessed: 9
Uncacheable: 26
Primary storage:
Hits: 155 / 282 (54.96 %)
Misses: 127
Cache size (GB): 0.44 / 0.51 (85.96 %)
Files: 658
Uncacheable:
Called for linking: 26
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ 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')))")
Autoloading python/3.9.7
Autoloading hpe-mpi/2.25.hmpt
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1662044360:step_script section_start:1662044360:archive_cache Saving cache for successful job
Creating cache build:intel-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=188228 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/30/build%3Aintel-2-non_protected
Created cache
section_end:1662044379:archive_cache section_start:1662044379:upload_artifacts_on_success Uploading artifacts for successful job
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=188550 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=345798 responseStatus=201 Created token=yWKxws49
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=188577 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=345798 responseStatus=201 Created token=yWKxws49
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=188607 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=345798 responseStatus=201 Created token=yWKxws49
section_end:1662044381:upload_artifacts_on_success section_start:1662044381:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1662044382:cleanup_file_variables Job succeeded
Raw
build-nvhpc.txt
Running with gitlab-runner 15.1.0 (76984217)
 on BB5 map runner pnPo3yJy
section_start:1662043403:resolve_secrets Resolving secrets
section_end:1662043403:resolve_secrets section_start:1662043403:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2909344377, slurm job id
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 72529, build ref b5f1eaea1e478ac8839d74523aef4a4d95d34f1f, job ID 345799
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag
A slurm job will be created with name GL_J345799_PROD_P30_CP7_C12
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 756588
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J345799_PROD_P30_CP7_C12 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --ntasks=1 --jobid=756588 --cpus-per-task=6 --mem=30750M
section_end:1662043407:prepare_executor section_start:1662043407:prepare_script Preparing environment
Running on r1i5n0 via bbpv1.epfl.ch...
section_end:1662043412:prepare_script section_start:1662043412:get_sources Getting source from Git repository
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1662043412:get_sources section_start:1662043412:restore_cache Restoring cache
Checking cache for build:nvhpc-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=159190 revision=58ba2b95 version=14.2.0
cache.zip is up to date 
Successfully extracted cache
section_end:1662043418:restore_cache section_start:1662043418:download_artifacts Downloading artifacts
Downloading artifacts for spack_setup (345797)...
Runtime platform  arch=amd64 os=linux pid=159770 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=345797 responseStatus=200 OK token=zZF6MvsF
section_end:1662043419:download_artifacts section_start:1662043419:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
$ SPACK_BUILD="${PWD}/spack-build"
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export SPACK_USER_CONFIG_PATH=${PWD}/spack-config
$ mkdir ${SPACK_USER_CONFIG_PATH}
$ cat > ${SPACK_USER_CONFIG_PATH}/config.yaml << END_SCRIPT # collapsed multi-line command
$ spack config blame config
--- config:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-config/config.yaml:2 build_stage:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-config/config.yaml:3 - /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-build
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-config/config.yaml:4 source_cache: /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-source-cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:18 extensions:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:18 - $spack/bluebrain/spack-scripting
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:37 template_dirs:
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:37 - $spack/share/spack/templates
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Temporary locations Spack can try to use for builds.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Recommended options are given below.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Builds can be faster in temporary directories on some (e.g., HPC) systems.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # Specifying `$tempdir` will ensure use of the default temporary directory
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # (i.e., ``$TMP` or ``$TMPDIR``).
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # to specify `$user_cache_path/stage`, which ensures each user builds in their
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # home directory.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # A more traditional path uses the value of `$spack/var/spack/stage`, which
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # pip installable.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 # users in shared temporary spaces.
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:38 #
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/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/P72529/J345797/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/P72529/J345797/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/P72529/J345797/spack/etc/spack/defaults/config.yaml:73 test_stage: $user_cache_path/test
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:82 misc_cache: $user_cache_path/cache
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:94 connect_timeout: 10
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:99 verify_ssl: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:107 suppress_gpg_warnings: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:113 install_missing_compilers: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:118 checksum: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:123 deprecated: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:128 dirty: False
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:136 build_language: C
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:145 locks: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:150 url_fetch_method: urllib
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:176 concretizer: clingo
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:183 db_lock_timeout: 300
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:191 package_lock_timeout: null
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:197 shared_linking: rpath
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:202 allow_sgid: True
/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797/spack/etc/spack/defaults/config.yaml:207 terminal_title: False
_builtin debug: False
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529/J345799_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
$ SPACK_FULL_SPEC="${SPACK_PACKAGE}${SPACK_PACKAGE_COMPILER:+%}${SPACK_PACKAGE_COMPILER} ${SPACK_PACKAGE_SPEC} ${SPACK_PACKAGE_DEPENDENCIES} ${SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB}"
$ echo "Preparing to install ${SPACK_FULL_SPEC}"
Preparing to install nmodl%nvhpc ~legacy-unit+python ^bison%gcc^flex%gcc^py-jinja2%gcc^py-sympy%gcc^py-pyyaml%gcc
$ JSON_SPEC=$(spack spec --json ${SPACK_FULL_SPEC})
$ 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\"])")
$ echo "Determined its hash will be ${SPACK_INSTALLED_HASH}"
Determined its hash will be g52x552rjhzjp4ejxmlvdrdx2y6oagay
$ SPACK_STAGE_DIR=${SPACK_BUILD}/spack-stage-${SPACK_PACKAGE}-develop-${SPACK_INSTALLED_HASH}
$ SPACK_BUILD_DIR=${SPACK_STAGE_DIR}/spack-build-${SPACK_INSTALLED_HASH:0:7}
$ SPACK_SOURCE_DIR=${SPACK_STAGE_DIR}/spack-src
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ module load unstable ccache
$ export CCACHE_BASEDIR=$(realpath -P ${CI_BUILDS_DIR})
$ echo CCACHE_BASEDIR=${CCACHE_BASEDIR}
CCACHE_BASEDIR=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529
$ export CCACHE_MAXSIZE=512M
$ export CCACHE_DIR="${TMPDIR}/ccache"
$ mkdir -p ${CCACHE_DIR}
$ if [ -f ${CI_PROJECT_DIR}/ccache.tar ]; then
$ tar -C "${CCACHE_DIR}" -xf "${CI_PROJECT_DIR}/ccache.tar"
$ fi
$ ccache --zero-stats
Statistics zeroed
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/756588/ccache
Primary config: /nvme/bbpcihpcproj12/756588/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Sep 1 16:44:39 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): 0.45 / 0.51 (87.87 %)
Files: 2017
$ fi
$ module load unstable git ${SPACK_EXTRA_MODULES}
$ spack uninstall -y --dependents /${SPACK_INSTALLED_HASH} || true
==> Error: No installed spec matches the hash: 'g52x552rjhzjp4ejxmlvdrdx2y6oagay'
$ spack spec -Il ${SPACK_FULL_SPEC}
Input spec
--------------------------------
- nmodl%nvhpc~legacy-unit+python
- ^bison%gcc
- ^flex%gcc
- ^py-jinja2%gcc
- ^py-pyyaml%gcc
- ^py-sympy%gcc
Concretized
--------------------------------
- g52x552 nmodl@develop%nvhpc@22.3~ipo~legacy-unit~llvm~llvm_cuda+python build_type=RelWithDebInfo arch=linux-rhel7-skylake
- cppb7al ^bison@3.8.2%gcc@11.2.0 arch=linux-rhel7-skylake
[^] w4s57h3 ^catch2@2.13.8%nvhpc@22.3~ipo build_type=RelWithDebInfo arch=linux-rhel7-skylake
- ucwiakr ^cmake@3.21.4%nvhpc@22.3~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-rhel7-skylake
[^] 634uzvi ^cli11@2.1.1%nvhpc@22.3~ipo build_type=RelWithDebInfo arch=linux-rhel7-skylake
- 4bt76dp ^flex@2.6.3%gcc@11.2.0+lex~nls arch=linux-rhel7-skylake
[^] jeloytj ^fmt@8.1.1%nvhpc@22.3~ipo+pic~shared build_type=RelWithDebInfo cxxstd=11 arch=linux-rhel7-skylake
- cp3ofsp ^ninja@1.10.2%nvhpc@22.3 arch=linux-rhel7-skylake
[^] gyarivi ^nlohmann-json@3.10.4%nvhpc@22.3~ipo~multiple_headers 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
[^] v4z3s5e ^py-setuptools@57.4.0%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
- nvsks4i ^py-pybind11@2.9.1%nvhpc@22.3~ipo build_type=RelWithDebInfo 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
[^] ciusbmc ^py-setuptools-scm@6.3.2%gcc@11.2.0+toml arch=linux-rhel7-skylake
[^] hmcew6w ^py-tomli@1.2.1%gcc@11.2.0 arch=linux-rhel7-skylake
[^] sxd7srs ^py-pip@21.1.2%gcc@11.2.0 arch=linux-rhel7-skylake
[^] y7rfzdj ^py-py@1.9.0%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
[^] vt2or7v ^py-sympy@1.9%gcc@11.2.0 arch=linux-rhel7-skylake
[^] dzb2mfs ^py-mpmath@1.1.0%gcc@11.2.0 arch=linux-rhel7-skylake
[^] v5zxpfc ^spdlog@1.9.2%nvhpc@22.3~ipo+shared build_type=RelWithDebInfo arch=linux-rhel7-skylake
$ 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
==> 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-cppb7alftvhxbedsuxqv72z2thjuoizw)
==> 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-ucwiakreeghdgbo22kbqqhgnnlwxqtnn)
==> 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-2.6.3-4bt76dpxbix6ep4qtz3mv5i2iddilv53)
==> 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-cp3ofspgkdqaqih5vrhotmdwvkozfswp)
==> 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_nvhpc-22.3-skylake/cli11-2.1.1-634uzv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.3-skylake/nlohmann-json-3.10.4-gyariv
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.3-skylake/fmt-8.1.1-jeloyt
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.3-skylake/catch2-2.13.8-w4s57h
[+] /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-pyyaml-5.3.1-ci5oe5
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_nvhpc-22.3-skylake/spdlog-1.9.2-v5zxpf
[+] /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_applications/install_gcc-11.2.0-skylake/py-sympy-1.9-vt2or7
[+] /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-pip-21.1.2-sxd7sr
==> Installing py-pybind11-2.9.1-nvsks4iskmmrhvnvvf23jxk6wx5xuut6
==> No binary for py-pybind11-2.9.1-nvsks4iskmmrhvnvvf23jxk6wx5xuut6 found: installing from source
==> Warning: Expected user 904556 to own /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529, but it is owned by 0
==> Fetching https://mirror.spack.io/_source-cache/archive/c6/c6160321dc98e6e1184cc791fbeadd2907bb4a0ce0e447f2ea4ff8ab56550913.tar.gz
==> No patches needed for py-pybind11
==> py-pybind11: Executing phase: 'cmake'
==> py-pybind11: Executing phase: 'build'
==> py-pybind11: Executing phase: 'install'
==> py-pybind11: Successfully installed py-pybind11-2.9.1-nvsks4iskmmrhvnvvf23jxk6wx5xuut6
Fetch: 0.34s. Build: 14.19s. Total: 14.53s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/software/install_nvhpc-22.3-skylake/py-pybind11-2.9.1-nvsks4
[+] /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-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-tomli-1.2.1-hmcew6
[+] /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-setuptools-scm-6.3.2-ciusbm
[+] /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-pytest-6.2.4-22arfs
==> Installing nmodl-develop-g52x552rjhzjp4ejxmlvdrdx2y6oagay
==> No binary for nmodl-develop-g52x552rjhzjp4ejxmlvdrdx2y6oagay found: installing from source
==> No patches needed for nmodl
==> nmodl: Executing phase: 'cmake'
==> nmodl: Executing phase: 'build'
==> nmodl: Executing phase: 'install'
==> nmodl: Successfully installed nmodl-develop-g52x552rjhzjp4ejxmlvdrdx2y6oagay
Fetch: 2m 5.49s. Build: 8m 55.39s. Total: 11m 0.88s.
[+] /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/software/install_nvhpc-22.3-skylake/nmodl-develop-g52x55
$ chmod -R g+rX "${SPACK_BUILD}"
$ if [[ ${install_failed} == 1 ]]; then exit 1; fi
$ if [ ${SPACK_USE_CCACHE+x} ]; then
$ ccache --cleanup
$ ccache --show-stats --verbose
Summary:
Cache directory: /nvme/bbpcihpcproj12/756588/ccache
Primary config: /nvme/bbpcihpcproj12/756588/ccache/ccache.conf
Secondary config: /gpfs/bbp.cscs.ch/ssd/apps/bsd/2022-01-10/stage_externals/install_gcc-11.2.0-skylake/ccache-4.4.2-6qbndl/etc/ccache.conf
Stats updated: Thu Sep 1 16:57:41 2022
Hits: 132 / 138 (95.65 %)
Direct: 23 / 138 (16.67 %)
Preprocessed: 109 / 115 (94.78 %)
Misses: 6
Direct: 115
Preprocessed: 6
Uncacheable: 25
Primary storage:
Hits: 155 / 276 (56.16 %)
Misses: 121
Cache size (GB): 0.45 / 0.51 (87.96 %)
Files: 2027
Uncacheable:
Called for linking: 25
$ tar -C "${CCACHE_DIR}" -cf "${CI_PROJECT_DIR}/ccache.tar" .
$ fi
$ touch ${SPACK_STAGE_DIR}/spack-configure-args.txt
$ cp ${SPACK_STAGE_DIR}/spack-{build-env,build-out,configure-args}.txt ${CI_PROJECT_DIR}/
$ echo "SPACK_BUILD_DIR=${SPACK_BUILD_DIR}" > ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_FULL_SPEC=${SPACK_FULL_SPEC}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_SOURCE_DIR=${SPACK_SOURCE_DIR}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ SPACK_PACKAGE_SLUGIFY=$(echo -n ${SPACK_PACKAGE} | tr -c '[:alnum:]' '_' | tr '[:lower:]' '[:upper:]')
$ echo "${SPACK_PACKAGE_SLUGIFY}_INSTALLED_HASH=${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ echo "SPACK_PACKAGE_DEPENDENCY_ON_PREVIOUS_JOB=^/${SPACK_INSTALLED_HASH}" >> ${CI_PROJECT_DIR}/spack_build_info.env
$ 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')))")
Autoloading python/3.9.7
Autoloading hpe-mpi/2.25.hmpt
$ if [[ ${num_failures} > 0 ]]; then exit ${num_failures}; fi
section_end:1662044268:step_script section_start:1662044268:archive_cache Saving cache for successful job
Creating cache build:nvhpc-2-non_protected...
Runtime platform  arch=amd64 os=linux pid=186101 revision=58ba2b95 version=14.2.0
ccache.tar: found 1 matching files and directories
Uploading cache.zip to https://bbpobjectstorage.epfl.ch/gitlab-runners-cache/project/30/build%3Anvhpc-2-non_protected
Created cache
section_end:1662044288:archive_cache section_start:1662044288:upload_artifacts_on_success Uploading artifacts for successful job
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=186640 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
initial_environment.env: found 1 matching files and directories
spack-build-env.txt: found 1 matching files and directories
spack-build-out.txt: found 1 matching files and directories
spack-configure-args.txt: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=345799 responseStatus=201 Created token=zZF6MvsF
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=186716 revision=58ba2b95 version=14.2.0
install.xml: found 1 matching files and directories
Uploading artifacts as "junit" to coordinator... ok id=345799 responseStatus=201 Created token=zZF6MvsF
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=186747 revision=58ba2b95 version=14.2.0
spack_build_info.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=345799 responseStatus=201 Created token=zZF6MvsF
section_end:1662044290:upload_artifacts_on_success section_start:1662044290:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1662044291:cleanup_file_variables Job succeeded
Raw
spack-setup.txt
Running with gitlab-runner 15.1.0 (76984217)
 on BB5 map runner pnPo3yJy
section_start:1662043069:resolve_secrets Resolving secrets
section_end:1662043069:resolve_secrets section_start:1662043069:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2735121717, slurm job id
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 72529, build ref b5f1eaea1e478ac8839d74523aef4a4d95d34f1f, job ID 345797
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag
A slurm job will be created with name GL_J345797_PROD_P30_CP1_C2
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 756577
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M --job-name=GL_J345797_PROD_P30_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --ntasks=1 --jobid=756577 --cpus-per-task=6 --mem=30750M
section_end:1662043071:prepare_executor section_start:1662043071:prepare_script Preparing environment
Running on r1i5n0 via bbpv1.epfl.ch...
section_end:1662043074:prepare_script section_start:1662043074:get_sources Getting source from Git repository
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1662043074:get_sources section_start:1662043074:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
$ if [[ -n "${SPACK_ENV_FILE_URL}" && "${PARSE_GITHUB_PR_DESCRIPTIONS,,}" == "true" ]]; then
$ cat > parse_description.py << END_SCRIPT # collapsed multi-line command
$ cat parse_description.py
import os
import re
import requests
pr_info = requests.get("https://api.github.com/repos/{}/pulls/{}".format(
os.environ['CI_EXTERNAL_PULL_REQUEST_TARGET_REPOSITORY'],
os.environ['CI_EXTERNAL_PULL_REQUEST_IID']),
headers={'Accept': 'application/vnd.github.v3+json'})
pr_body = pr_info.json()["body"]
# match something like NEURON_BRANCH=foo/bar
pat = re.compile('^([A-Z0-9_]+)_([A-Z]+)=([A-Z0-9\-\_\/\+]+)$', re.IGNORECASE)
def parse_term(m):
ref_type = m.group(2).lower()
if ref_type not in {'branch', 'tag', 'ref'}: return
print(m.group(1).upper() + '_' + ref_type.upper() + '=' + m.group(3))
if pr_body is not None:
for pr_body_line in pr_body.splitlines():
if not pr_body_line.startswith('CI_BRANCHES:'): continue
for config_term in pr_body_line[12:].split(','):
pat.sub(parse_term, config_term)
$ (module load unstable python-dev; python parse_description.py) > input_variables.env
Autoloading python/3.9.7
Autoloading hpe-mpi/2.25.hmpt
$ else
$ cat input_variables.env
$ for var_to_unset in $(sed 's/^\(.*\?\)_\(BRANCH\|COMMIT\|TAG\)=.*$/\1_BRANCH\n\1_COMMIT\n\1_TAG/' input_variables.env); do # collapsed multi-line command
$ set -o allexport
$ . input_variables.env
$ set +o allexport
$ unset MODULEPATH
$ . /gpfs/bbp.cscs.ch/ssd/apps/bsd/${SPACK_DEPLOYMENT_SUFFIX}/config/modules.sh
$ echo "MODULEPATH=${MODULEPATH}" > spack_clone_variables.env
$ echo Preparing to clone Spack into ${PWD}
Preparing to clone Spack into /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345797
$ if [[ -z "${SPACK_BRANCH}" && ( -n "${SPACK_COMMIT}" || -n "${SPACK_TAG}" ) ]]; then
$ echo Checking out the ${SPACK_BRANCH} of Spack...
Checking out the develop of Spack...
$ module load unstable git
$ git clone -c feature.manyFiles=true --depth 1 --single-branch --branch ${SPACK_BRANCH} ${SPACK_URL} spack
Cloning into 'spack'...
Updating files: 3% (326/9134) Updating files: 4% (366/9134) Updating files: 5% (457/9134) Updating files: 6% (549/9134) Updating files: 7% (640/9134) Updating files: 7% (709/9134) Updating files: 8% (731/9134) Updating files: 9% (823/9134) Updating files: 10% (914/9134) Updating files: 11% (1005/9134) Updating files: 12% (1097/9134) Updating files: 12% (1149/9134) Updating files: 13% (1188/9134) Updating files: 14% (1279/9134) Updating files: 15% (1371/9134) Updating files: 16% (1462/9134) Updating files: 16% (1477/9134) Updating files: 17% (1553/9134) Updating files: 18% (1645/9134) Updating files: 18% (1685/9134) Updating files: 19% (1736/9134) Updating files: 20% (1827/9134) Updating files: 20% (1890/9134) Updating files: 21% (1919/9134) Updating files: 22% (2010/9134) Updating files: 23% (2101/9134) Updating files: 23% (2131/9134) Updating files: 24% (2193/9134) Updating files: 25% (2284/9134) Updating files: 25% (2356/9134) Updating files: 26% (2375/9134) Updating files: 27% (2467/9134) Updating files: 28% (2558/9134) Updating files: 28% (2581/9134) Updating files: 29% (2649/9134) Updating files: 30% (2741/9134) Updating files: 30% (2796/9134) Updating files: 31% (2832/9134) Updating files: 32% (2923/9134) Updating files: 33% (3015/9134) Updating files: 33% (3041/9134) Updating files: 34% (3106/9134) Updating files: 35% (3197/9134) Updating files: 35% (3262/9134) Updating files: 36% (3289/9134) Updating files: 37% (3380/9134) Updating files: 38% (3471/9134) Updating files: 38% (3498/9134) Updating files: 39% (3563/9134) Updating files: 40% (3654/9134) Updating files: 40% (3710/9134) Updating files: 41% (3745/9134) Updating files: 42% (3837/9134) Updating files: 43% (3928/9134) Updating files: 43% (3948/9134) Updating files: 44% (4019/9134) Updating files: 45% (4111/9134) Updating files: 45% (4180/9134) Updating files: 46% (4202/9134) Updating files: 47% (4293/9134) Updating files: 48% (4385/9134) Updating files: 48% (4428/9134) Updating files: 49% (4476/9134) Updating files: 50% (4567/9134) Updating files: 51% (4659/9134) Updating files: 51% (4670/9134) Updating files: 52% (4750/9134) Updating files: 53% (4842/9134) Updating files: 53% (4879/9134) Updating files: 54% (4933/9134) Updating files: 55% (5024/9134) Updating files: 55% (5071/9134) Updating files: 56% (5116/9134) Updating files: 57% (5207/9134) Updating files: 57% (5286/9134) Updating files: 58% (5298/9134) Updating files: 59% (5390/9134) Updating files: 59% (5472/9134) Updating files: 60% (5481/9134) Updating files: 61% (5572/9134) Updating files: 61% (5662/9134) Updating files: 62% (5664/9134) Updating files: 63% (5755/9134) Updating files: 63% (5831/9134) Updating files: 64% (5846/9134) Updating files: 65% (5938/9134) Updating files: 65% (6014/9134) Updating files: 66% (6029/9134) Updating files: 67% (6120/9134) Updating files: 67% (6200/9134) Updating files: 68% (6212/9134) Updating files: 69% (6303/9134) Updating files: 69% (6380/9134) Updating files: 70% (6394/9134) Updating files: 71% (6486/9134) Updating files: 71% (6562/9134) Updating files: 72% (6577/9134) Updating files: 73% (6668/9134) Updating files: 74% (6760/9134) Updating files: 74% (6764/9134) Updating files: 75% (6851/9134) Updating files: 75% (6925/9134) Updating files: 76% (6942/9134) Updating files: 77% (7034/9134) Updating files: 78% (7125/9134) Updating files: 78% (7132/9134) Updating files: 79% (7216/9134) Updating files: 79% (7307/9134) Updating files: 80% (7308/9134) Updating files: 81% (7399/9134) Updating files: 82% (7490/9134) Updating files: 82% (7491/9134) Updating files: 83% (7582/9134) Updating files: 84% (7673/9134) Updating files: 84% (7675/9134) Updating files: 85% (7764/9134) Updating files: 86% (7856/9134) Updating files: 86% (7870/9134) Updating files: 87% (7947/9134) Updating files: 88% (8038/9134) Updating files: 88% (8077/9134) Updating files: 89% (8130/9134) Updating files: 90% (8221/9134) Updating files: 90% (8306/9134) Updating files: 91% (8312/9134) Updating files: 92% (8404/9134) Updating files: 93% (8495/9134) Updating files: 93% (8513/9134) Updating files: 94% (8586/9134) Updating files: 95% (8678/9134) Updating files: 95% (8765/9134) Updating files: 96% (8769/9134) Updating files: 97% (8860/9134) Updating files: 98% (8952/9134) Updating files: 98% (9010/9134) Updating files: 99% (9043/9134) Updating files: 100% (9134/9134) Updating files: 100% (9134/9134), done.
$ export SPACK_ROOT=${PWD}/spack
$ export SPACK_USER_CACHE_PATH="${CI_BUILDS_DIR}"
$ export SPACK_SYSTEM_CONFIG_PATH="/gpfs/bbp.cscs.ch/ssd/apps/bsd/${SPACK_DEPLOYMENT_SUFFIX}/config"
$ echo "SPACK_ROOT=${SPACK_ROOT}" >> spack_clone_variables.env
$ echo "SPACK_USER_CACHE_PATH=${SPACK_USER_CACHE_PATH}" >> spack_clone_variables.env
$ echo "SPACK_SYSTEM_CONFIG_PATH=${SPACK_SYSTEM_CONFIG_PATH}" >> spack_clone_variables.env
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ export XDG_CONFIG_HOME=${CI_BUILDS_DIR}/J${CI_JOB_ID}_local_config
$ echo "Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (${XDG_CONFIG_HOME})"
Configuring git to use CI_JOB_TOKEN to access git@bbpgitlab.epfl.ch (/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529/J345797_local_config)
$ mkdir -p "${XDG_CONFIG_HOME}/git"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n insteadOf = git@bbpgitlab.epfl.ch:" > "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
insteadOf = git@bbpgitlab.epfl.ch:
$ env -0 | sed -nz '/^CUSTOM_ENV_/d;/^[^=]\+_\(BRANCH\|COMMIT\|TAG\)=.\+/p' | xargs -0t spack configure-pipeline --ignore-packages CI_BUILD CI_COMMIT CI_DEFAULT GITLAB_PIPELINES SPACK ${SPACK_SETUP_IGNORE_PACKAGE_VARIABLES} --write-commit-file=commit-mapping.env
spack configure-pipeline --ignore-packages CI_BUILD CI_COMMIT CI_DEFAULT GITLAB_PIPELINES SPACK CVF --write-commit-file=commit-mapping.env CI_COMMIT_BRANCH=check_thread_sade NMODL_COMMIT=b5f1eaea1e478ac8839d74523aef4a4d95d34f1f SPACK_BRANCH=develop CI_DEFAULT_BRANCH=master CVF_BRANCH=main
==> CI_COMMIT: ignoring CI_COMMIT_BRANCH=check_thread_sade
==> SPACK: ignoring SPACK_BRANCH=develop
==> CI_DEFAULT: ignoring CI_DEFAULT_BRANCH=master
==> CVF: ignoring CVF_BRANCH=main
==> nmodl@develop: remove branch/commit/tag
==> nmodl@develop: use commit="b5f1eaea1e478ac8839d74523aef4a4d95d34f1f"
==> nmodl@develop: add preferred=True
$ (cd "${SPACK_ROOT}" && git diff)
diff --git a/bluebrain/repo-bluebrain/packages/nmodl/package.py b/bluebrain/repo-bluebrain/packages/nmodl/package.py
index a79f28b..8850ae1 100644
--- a/bluebrain/repo-bluebrain/packages/nmodl/package.py
+++ b/bluebrain/repo-bluebrain/packages/nmodl/package.py
@@ -14,7 +14,7 @@ class Nmodl(CMakePackage):
git = "https://github.com/BlueBrain/nmodl.git"
# 0.3.1 > 0.3.0.20220110 > 0.3.0 > 0.3b > 0.3 to Spack
- version("develop", branch="master", submodules=True)
+ version('develop', preferred=True, commit='b5f1eaea1e478ac8839d74523aef4a4d95d34f1f', submodules=True) # old: branch="master"
version("llvm", branch="llvm", submodules=True)
version("0.4.0", tag="0.4")
# This is the merge commit of #875, which allows catch2 etc. to be dependencies
$ cat commit-mapping.env
NMODL_COMMIT=b5f1eaea1e478ac8839d74523aef4a4d95d34f1f
$ echo "SPACK_BRANCH=${SPACK_BRANCH}" >> commit-mapping.env
$ echo "SPACK_DEPLOYMENT_SUFFIX=${SPACK_DEPLOYMENT_SUFFIX}" >> commit-mapping.env
$ cat commit-mapping.env >> spack_clone_variables.env
$ spack spec -IL ninja
Input spec
--------------------------------
- ninja
Concretized
--------------------------------
==> Bootstrapping clingo from pre-built binaries
- utrxbc3aohnru5eynalc3hyv4ca4jqte ninja@1.10.2%gcc@11.2.0 arch=linux-rhel7-skylake
$ echo "SPACK_SETUP_COMMIT_MAPPING_URL=${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/jobs/${CI_JOB_ID}/artifacts/commit-mapping.env" >> spack_clone_variables.env
$ spack config --scope site add "config:ccache:true"
$ echo "SPACK_USE_CCACHE=true" >> spack_clone_variables.env
$ echo "CVF_BRANCH=${CVF_BRANCH}" >> spack_clone_variables.env
section_end:1662043397:step_script section_start:1662043397:upload_artifacts_on_success Uploading artifacts for successful job
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=157995 revision=58ba2b95 version=14.2.0
commit-mapping.env: found 1 matching files and directories
input_variables.env: found 1 matching files and directories
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "archive" to coordinator... ok id=345797 responseStatus=201 Created token=mxBPP1Tx
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=158027 revision=58ba2b95 version=14.2.0
spack_clone_variables.env: found 1 matching files and directories
Uploading artifacts as "dotenv" to coordinator... ok id=345797 responseStatus=201 Created token=mxBPP1Tx
section_end:1662043398:upload_artifacts_on_success section_start:1662043398:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1662043398:cleanup_file_variables Job succeeded
Raw
test-intel.txt
Running with gitlab-runner 15.1.0 (76984217)
 on BB5 map runner pnPo3yJy
section_start:1662044384:resolve_secrets Resolving secrets
section_end:1662044384:resolve_secrets section_start:1662044384:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor1167385320, slurm job id
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 72529, build ref b5f1eaea1e478ac8839d74523aef4a4d95d34f1f, job ID 345800
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529, optional exclusive flag , optional cpus per task flag --cpus-per-task=1, optional qos flag
A slurm job will be created with name GL_J345800_PROD_P30_CP1_C2
Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 756797
job state: PD
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J345800_PROD_P30_CP1_C2 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --ntasks=1 --jobid=756797 --cpus-per-task=1 --mem=30750M
section_end:1662044389:prepare_executor section_start:1662044389:prepare_script Preparing environment
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1662044391:prepare_script section_start:1662044391:get_sources Getting source from Git repository
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1662044392:get_sources section_start:1662044392:download_artifacts Downloading artifacts
Downloading artifacts for build:intel (345798)...
Runtime platform  arch=amd64 os=linux pid=159773 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=345798 responseStatus=200 OK token=FasSXPso
section_end:1662044393:download_artifacts section_start:1662044393:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ cd ${SPACK_BUILD_DIR}
$ export BOOST_TEST_COLOR_OUTPUT=no
$ i_am_a_failure=0
$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1
Site: r1i5n0
Build name: Linux-icpc
Create new tag: 20220901-1500 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345798/spack-build/spack-stage-nmodl-develop-vq4xwpxhyfyr26mospd577raaeicmn5e/spack-build-vq4xwpx
Start 1: testcodegen/Scenario: ISPC codegen
1/91 Test #1: testcodegen/Scenario: ISPC codegen .................................................................. Passed 0.06 sec
Start 2: testcodegen/Scenario: unusual / failing mod files
2/91 Test #2: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.05 sec
Start 3: testcodegen/Scenario: Check global variable setup
3/91 Test #3: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.04 sec
Start 4: testcodegen/Scenario: C codegen utility functions
4/91 Test #4: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.04 sec
Start 5: testcodegen/Scenario: ISPC codegen utility functions
5/91 Test #5: testcodegen/Scenario: ISPC codegen utility functions ................................................ Passed 0.04 sec
Start 6: testcodegen/Scenario: Check instance variable definition order
6/91 Test #6: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.04 sec
Start 7: testcodegen/Scenario: Check parameter constness with VERBATIM block
7/91 Test #7: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.04 sec
Start 8: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
8/91 Test #8: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.04 sec
Start 9: testcodegen/Scenario: Adding a variable for a table inside a function
9/91 Test #9: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.04 sec
Start 10: testmodtoken/NMODL Lexer returning valid ModToken object
10/91 Test #10: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.01 sec
Start 11: testmodtoken/Addition of two ModToken objects
11/91 Test #11: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.01 sec
Start 12: testlexer/NMODL Lexer returning valid token types
12/91 Test #12: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.01 sec
Start 13: testparser/Scenario: NMODL can accept \r as return char for one line comment
13/91 Test #13: testparser/Scenario: NMODL can accept \r as return char for one line comment ........................ Passed 0.02 sec
Start 14: testparser/Scenario: NMODL can define macros using DEFINE keyword
14/91 Test #14: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.02 sec
Start 15: testparser/Scenario: Macros can be used anywhere in the mod file
15/91 Test #15: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.02 sec
Start 16: testparser/Scenario: NMODL parser accepts empty unit specification
16/91 Test #16: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.02 sec
Start 17: testparser/Scenario: NMODL parser running number of valid NMODL constructs
17/91 Test #17: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.05 sec
Start 18: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
18/91 Test #18: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.02 sec
Start 19: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
19/91 Test #19: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.02 sec
Start 20: testparser/Scenario: NEURON block can add CURIE information
20/91 Test #20: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.02 sec
Start 21: testparser/Scenario: Check parents in valid NMODL constructs
21/91 Test #21: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.36 sec
Start 22: testparser/Scenario: Legacy differential equation solver
22/91 Test #22: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.02 sec
Start 23: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
23/91 Test #23: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.02 sec
Start 24: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
24/91 Test #24: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.05 sec
Start 25: testvisitor/Scenario: Perform constant folder on NMODL constructs
25/91 Test #25: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.05 sec
Start 26: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
26/91 Test #26: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.05 sec
Start 27: testvisitor/Scenario: GLOBAL to RANGE variable transformer
27/91 Test #27: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.05 sec
Start 28: testvisitor/Scenario: Check insertion of implicit arguments
28/91 Test #28: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.05 sec
Start 29: testvisitor/Scenario: Inlining of external procedure calls
29/91 Test #29: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.05 sec
Start 30: testvisitor/Scenario: Inlining of function call as argument in external function
30/91 Test #30: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.05 sec
Start 31: testvisitor/Scenario: Inlining of simple, one level procedure call
31/91 Test #31: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.05 sec
Start 32: testvisitor/Scenario: Inlining of nested procedure call
32/91 Test #32: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.05 sec
Start 33: testvisitor/Scenario: Inline function call in procedure
33/91 Test #33: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.05 sec
Start 34: testvisitor/Scenario: Inling function call within conditional statement
34/91 Test #34: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.05 sec
Start 35: testvisitor/Scenario: Inline multiple function calls in same statement
35/91 Test #35: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.05 sec
Start 36: testvisitor/Scenario: Inline nested function calls withing arguments
36/91 Test #36: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.05 sec
Start 37: testvisitor/Scenario: Inline function call in non-binary expression
37/91 Test #37: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.05 sec
Start 38: testvisitor/Scenario: Inline function call as standalone expression
38/91 Test #38: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.05 sec
Start 39: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
39/91 Test #39: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.05 sec
Start 40: testvisitor/Scenario: Inlining pass handles local-global name conflict
40/91 Test #40: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.05 sec
Start 41: testvisitor/Scenario: Rename variables that ISPC parses as double constants
41/91 Test #41: testvisitor/Scenario: Rename variables that ISPC parses as double constants ......................... Passed 0.05 sec
Start 42: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
42/91 Test #42: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.04 sec
Start 43: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
43/91 Test #43: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.06 sec
Start 44: testvisitor/Scenario: Localizer test with single global block
44/91 Test #44: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.04 sec
Start 45: testvisitor/Scenario: Localizer test with use of verbatim block
45/91 Test #45: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.05 sec
Start 46: testvisitor/Scenario: Localizer test with multiple global blocks
46/91 Test #46: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.05 sec
Start 47: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
47/91 Test #47: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.05 sec
Start 48: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
48/91 Test #48: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.05 sec
Start 49: testvisitor/Scenario: Perform loop unrolling of FROM construct
49/91 Test #49: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.05 sec
Start 50: testvisitor/Scenario: Running visitor passes multiple times
50/91 Test #50: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.05 sec
Start 51: testvisitor/Scenario: Sympy specific AST to NMODL conversion
51/91 Test #51: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.04 sec
Start 52: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
52/91 Test #52: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.05 sec
Start 53: testvisitor/Scenario: Convert AST back to NMODL form
53/91 Test #53: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.10 sec
Start 54: testvisitor/Scenario: Symbol table generation with Perf stat visitor
54/91 Test #54: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.05 sec
Start 55: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
55/91 Test #55: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.05 sec
Start 56: testvisitor/Scenario: Renaming with presence of local and global variables in same block
56/91 Test #56: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.05 sec
Start 57: testvisitor/Scenario: Renaming in the absence of global blocks
57/91 Test #57: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.04 sec
Start 58: testvisitor/Scenario: Variable renaming in nested blocks
58/91 Test #58: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.05 sec
Start 59: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
59/91 Test #59: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.04 sec
Start 60: testvisitor/Scenario: TABLE stmt
60/91 Test #60: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.04 sec
Start 61: testvisitor/Scenario: Destructor block
61/91 Test #61: testvisitor/Scenario: Destructor block .............................................................. Passed 0.04 sec
Start 62: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
62/91 Test #62: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.05 sec
Start 63: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
63/91 Test #63: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.05 sec
Start 64: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
64/91 Test #64: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 48.79 sec
Start 65: testvisitor/Scenario: Check compare_blocks in sympy unit tests
65/91 Test #65: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 0.83 sec
Start 66: testvisitor/Scenario: Check local vars name-clash prevention
66/91 Test #66: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 0.95 sec
Start 67: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
67/91 Test #67: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 6.67 sec
Start 68: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
68/91 Test #68: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 2.40 sec
Start 69: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
69/91 Test #69: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 1.97 sec
Start 70: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
70/91 Test #70: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 0.97 sec
Start 71: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
71/91 Test #71: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.05 sec
Start 72: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
72/91 Test #72: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.05 sec
Start 73: testvisitor/Parse VERBATIM block using Verbatim Visitor
73/91 Test #73: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.05 sec
Start 74: testvisitor/Scenario: Get node name with index TestVisitor
74/91 Test #74: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.06 sec
Start 75: testprinter/JSON printer converting object to string form
75/91 Test #75: testprinter/JSON printer converting object to string form ........................................... Passed 0.01 sec
Start 76: testsymtab/Scenario: Symbol properties can be added and converted to string
76/91 Test #76: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.01 sec
Start 77: testsymtab/Scenario: Multiple properties can be added to Symbol
77/91 Test #77: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.01 sec
Start 78: testsymtab/Scenario: Symbol table allows operations like insert, lookup
78/91 Test #78: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.01 sec
Start 79: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
79/91 Test #79: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.01 sec
Start 80: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
80/91 Test #80: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.01 sec
Start 81: testnewton/Scenario: Non-linear system to solve with Newton Solver
81/91 Test #81: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.01 sec
Start 82: testfast_math/Scenario: Check fast_math
82/91 Test #82: testfast_math/Scenario: Check fast_math ............................................................. Passed 0.01 sec
Start 83: testunitlexer/Unit Lexer tests for valid tokens
83/91 Test #83: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.01 sec
Start 84: testunitparser/Scenario: Unit parser accepting valid units definition
84/91 Test #84: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.01 sec
Start 85: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
85/91 Test #85: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.01 sec
Start 86: Ode
86/91 Test #86: Ode ................................................................................................. Passed 1.98 sec
Start 87: Pybind
87/91 Test #87: Pybind .............................................................................................. Passed 0.54 sec
Start 88: cabpump.mod
88/91 Test #88: cabpump.mod ......................................................................................... Passed 0.06 sec
Start 89: ican.mod
89/91 Test #89: ican.mod ............................................................................................ Passed 0.05 sec
Start 90: ispc_rename.mod
90/91 Test #90: ispc_rename.mod ..................................................................................... Passed 0.05 sec
Start 91: watch_test.mod
91/91 Test #91: watch_test.mod ...................................................................................... Passed 0.05 sec
100% tests passed, 0 tests failed out of 91
Total Test time (real) = 68.66 sec
$ cp -r Testing/ ${CI_PROJECT_DIR}/
$ module load unstable unit-test-translator
Autoloading python/3.9.7
$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml
$ exit ${i_am_a_failure}
section_end:1662044483:step_script section_start:1662044483:upload_artifacts_on_success Uploading artifacts for successful job
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=161122 revision=58ba2b95 version=14.2.0
initial_environment.env: found 1 matching files and directories
Testing/: found 7 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok id=345800 responseStatus=201 Created token=FasSXPso
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=161149 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=345800 responseStatus=201 Created token=FasSXPso
section_end:1662044484:upload_artifacts_on_success section_start:1662044484:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1662044485:cleanup_file_variables Job succeeded
Raw
test-nvhpc.txt
Running with gitlab-runner 15.1.0 (76984217)
 on BB5 map runner pnPo3yJy
section_start:1662044294:resolve_secrets Resolving secrets
section_end:1662044294:resolve_secrets section_start:1662044294:prepare_executor Preparing the "custom" executor
Using Custom executor with driver BB5 PROD runner v0.0.3...
BB5 PROD runner running on bbpv1.epfl.ch, version 15.1.0, user
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor2291830079, slurm job id
Runner ID 29, project root hpc, project name nmodl
Pipeline ID 72529, build ref b5f1eaea1e478ac8839d74523aef4a4d95d34f1f, job ID 345801
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529, optional exclusive flag , optional cpus per task flag --cpus-per-task=1, optional qos flag
A slurm job will be created with name GL_J345801_PROD_P30_CP0_C7
Job parameters: memory=30750M, cpus_per_task=1, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos=
Not executing the chown -R
sbatch: INFO: Activating auto partition selection plugin, please report errors to HPC/CS
sbatch: INFO: Job specifies cpu constraint, setting --constraint=[skl|clx]
Submitted batch job 756796
job state: PD
job state: PD
job state: PD
job state: PD
job state: PD
job state: PD
job state: PD
job state: PD
job state: PD
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=1 --mem=30750M --job-name=GL_J345801_PROD_P30_CP0_C7 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P72529 --ntasks=1 --jobid=756796 --cpus-per-task=1 --mem=30750M
section_end:1662044305:prepare_executor section_start:1662044305:prepare_script Preparing environment
Running on r1i7n22 via bbpv1.epfl.ch...
section_end:1662044308:prepare_script section_start:1662044308:get_sources Getting source from Git repository
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1662044309:get_sources section_start:1662044309:download_artifacts Downloading artifacts
Downloading artifacts for build:nvhpc (345799)...
Runtime platform  arch=amd64 os=linux pid=158628 revision=58ba2b95 version=14.2.0
Downloading artifacts from coordinator... ok  id=345799 responseStatus=200 OK token=Uchdt2z8
section_end:1662044309:download_artifacts section_start:1662044309:step_script Executing "step_script" stage of the job script
WARNING: Starting with version 14.0 the 'build_script' stage will be replaced with 'step_script': https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26426
$ env -0 | sort -z | xargs -0 -L 1 echo > initial_environment.env
$ export CTEST_PARALLEL_LEVEL=${SLURM_TASKS_PER_NODE}
$ . ${SPACK_ROOT}/share/spack/setup-env.sh
$ cd ${SPACK_BUILD_DIR}
$ export BOOST_TEST_COLOR_OUTPUT=no
$ i_am_a_failure=0
$ spack build-env ${SPACK_FULL_SPEC} -- ctest --output-on-failure -T Test || i_am_a_failure=1
Site: r1i5n0
Build name: Linux-nvc++
Create new tag: 20220901-1458 - Experimental
Test project /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/bbpcihpcproj12/P72529/J345799/spack-build/spack-stage-nmodl-develop-g52x552rjhzjp4ejxmlvdrdx2y6oagay/spack-build-g52x552
Start 1: testcodegen/Scenario: ISPC codegen
1/91 Test #1: testcodegen/Scenario: ISPC codegen .................................................................. Passed 0.06 sec
Start 2: testcodegen/Scenario: unusual / failing mod files
2/91 Test #2: testcodegen/Scenario: unusual / failing mod files ................................................... Passed 0.05 sec
Start 3: testcodegen/Scenario: Check global variable setup
3/91 Test #3: testcodegen/Scenario: Check global variable setup ................................................... Passed 0.05 sec
Start 4: testcodegen/Scenario: C codegen utility functions
4/91 Test #4: testcodegen/Scenario: C codegen utility functions ................................................... Passed 0.05 sec
Start 5: testcodegen/Scenario: ISPC codegen utility functions
5/91 Test #5: testcodegen/Scenario: ISPC codegen utility functions ................................................ Passed 0.05 sec
Start 6: testcodegen/Scenario: Check instance variable definition order
6/91 Test #6: testcodegen/Scenario: Check instance variable definition order ...................................... Passed 0.05 sec
Start 7: testcodegen/Scenario: Check parameter constness with VERBATIM block
7/91 Test #7: testcodegen/Scenario: Check parameter constness with VERBATIM block ................................. Passed 0.05 sec
Start 8: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand
8/91 Test #8: testcodegen/Scenario: Check NEURON globals are added to the instance struct on demand ............... Passed 0.05 sec
Start 9: testcodegen/Scenario: Adding a variable for a table inside a function
9/91 Test #9: testcodegen/Scenario: Adding a variable for a table inside a function ............................... Passed 0.05 sec
Start 10: testmodtoken/NMODL Lexer returning valid ModToken object
10/91 Test #10: testmodtoken/NMODL Lexer returning valid ModToken object ............................................ Passed 0.01 sec
Start 11: testmodtoken/Addition of two ModToken objects
11/91 Test #11: testmodtoken/Addition of two ModToken objects ....................................................... Passed 0.01 sec
Start 12: testlexer/NMODL Lexer returning valid token types
12/91 Test #12: testlexer/NMODL Lexer returning valid token types ................................................... Passed 0.02 sec
Start 13: testparser/Scenario: NMODL can accept \r as return char for one line comment
13/91 Test #13: testparser/Scenario: NMODL can accept \r as return char for one line comment ........................ Passed 0.02 sec
Start 14: testparser/Scenario: NMODL can define macros using DEFINE keyword
14/91 Test #14: testparser/Scenario: NMODL can define macros using DEFINE keyword ................................... Passed 0.02 sec
Start 15: testparser/Scenario: Macros can be used anywhere in the mod file
15/91 Test #15: testparser/Scenario: Macros can be used anywhere in the mod file .................................... Passed 0.02 sec
Start 16: testparser/Scenario: NMODL parser accepts empty unit specification
16/91 Test #16: testparser/Scenario: NMODL parser accepts empty unit specification .................................. Passed 0.02 sec
Start 17: testparser/Scenario: NMODL parser running number of valid NMODL constructs
17/91 Test #17: testparser/Scenario: NMODL parser running number of valid NMODL constructs .......................... Passed 0.05 sec
Start 18: testparser/Scenario: NMODL parser running number of invalid NMODL constructs
18/91 Test #18: testparser/Scenario: NMODL parser running number of invalid NMODL constructs ........................ Passed 0.02 sec
Start 19: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs
19/91 Test #19: testparser/Scenario: Check that the parser doesn't crash when passing invalid INCLUDE constructs .... Passed 0.02 sec
Start 20: testparser/Scenario: NEURON block can add CURIE information
20/91 Test #20: testparser/Scenario: NEURON block can add CURIE information ......................................... Passed 0.02 sec
Start 21: testparser/Scenario: Check parents in valid NMODL constructs
21/91 Test #21: testparser/Scenario: Check parents in valid NMODL constructs ........................................ Passed 0.38 sec
Start 22: testparser/Scenario: Legacy differential equation solver
22/91 Test #22: testparser/Scenario: Legacy differential equation solver ............................................ Passed 0.02 sec
Start 23: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token
23/91 Test #23: testparser/Scenario: Check if a NEURON block is parsed with correct location info in its token ...... Passed 0.02 sec
Start 24: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp
24/91 Test #24: testvisitor/Scenario: AfterCVodeToCnexpVisitor changes after_cvode solver method to cnexp ........... Passed 0.06 sec
Start 25: testvisitor/Scenario: Perform constant folder on NMODL constructs
25/91 Test #25: testvisitor/Scenario: Perform constant folder on NMODL constructs ................................... Passed 0.05 sec
Start 26: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs
26/91 Test #26: testvisitor/Scenario: Perform DefUse analysis on NMODL constructs ................................... Passed 0.05 sec
Start 27: testvisitor/Scenario: GLOBAL to RANGE variable transformer
27/91 Test #27: testvisitor/Scenario: GLOBAL to RANGE variable transformer .......................................... Passed 0.05 sec
Start 28: testvisitor/Scenario: Check insertion of implicit arguments
28/91 Test #28: testvisitor/Scenario: Check insertion of implicit arguments ......................................... Passed 0.05 sec
Start 29: testvisitor/Scenario: Inlining of external procedure calls
29/91 Test #29: testvisitor/Scenario: Inlining of external procedure calls .......................................... Passed 0.05 sec
Start 30: testvisitor/Scenario: Inlining of function call as argument in external function
30/91 Test #30: testvisitor/Scenario: Inlining of function call as argument in external function .................... Passed 0.05 sec
Start 31: testvisitor/Scenario: Inlining of simple, one level procedure call
31/91 Test #31: testvisitor/Scenario: Inlining of simple, one level procedure call .................................. Passed 0.05 sec
Start 32: testvisitor/Scenario: Inlining of nested procedure call
32/91 Test #32: testvisitor/Scenario: Inlining of nested procedure call ............................................. Passed 0.05 sec
Start 33: testvisitor/Scenario: Inline function call in procedure
33/91 Test #33: testvisitor/Scenario: Inline function call in procedure ............................................. Passed 0.05 sec
Start 34: testvisitor/Scenario: Inling function call within conditional statement
34/91 Test #34: testvisitor/Scenario: Inling function call within conditional statement ............................. Passed 0.05 sec
Start 35: testvisitor/Scenario: Inline multiple function calls in same statement
35/91 Test #35: testvisitor/Scenario: Inline multiple function calls in same statement .............................. Passed 0.05 sec
Start 36: testvisitor/Scenario: Inline nested function calls withing arguments
36/91 Test #36: testvisitor/Scenario: Inline nested function calls withing arguments ................................ Passed 0.05 sec
Start 37: testvisitor/Scenario: Inline function call in non-binary expression
37/91 Test #37: testvisitor/Scenario: Inline function call in non-binary expression ................................. Passed 0.05 sec
Start 38: testvisitor/Scenario: Inline function call as standalone expression
38/91 Test #38: testvisitor/Scenario: Inline function call as standalone expression ................................. Passed 0.05 sec
Start 39: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression
39/91 Test #39: testvisitor/Scenario: Inline procedure call as standalone statement as well as part of expression ... Passed 0.05 sec
Start 40: testvisitor/Scenario: Inlining pass handles local-global name conflict
40/91 Test #40: testvisitor/Scenario: Inlining pass handles local-global name conflict .............................. Passed 0.05 sec
Start 41: testvisitor/Scenario: Rename variables that ISPC parses as double constants
41/91 Test #41: testvisitor/Scenario: Rename variables that ISPC parses as double constants ......................... Passed 0.05 sec
Start 42: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor
42/91 Test #42: testvisitor/Convert NMODL to AST to JSON form using JSONVisitor ..................................... Passed 0.05 sec
Start 43: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor
43/91 Test #43: testvisitor/Scenario: Convert KINETIC to DERIVATIVE using KineticBlock visitor ...................... Passed 0.06 sec
Start 44: testvisitor/Scenario: Localizer test with single global block
44/91 Test #44: testvisitor/Scenario: Localizer test with single global block ....................................... Passed 0.05 sec
Start 45: testvisitor/Scenario: Localizer test with use of verbatim block
45/91 Test #45: testvisitor/Scenario: Localizer test with use of verbatim block ..................................... Passed 0.05 sec
Start 46: testvisitor/Scenario: Localizer test with multiple global blocks
46/91 Test #46: testvisitor/Scenario: Localizer test with multiple global blocks .................................... Passed 0.05 sec
Start 47: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer
47/91 Test #47: testvisitor/Scenario: LOCAL to ASSIGNED variable transformer ........................................ Passed 0.05 sec
Start 48: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor
48/91 Test #48: testvisitor/Scenario: Searching for ast nodes using AstLookupVisitor ................................ Passed 0.05 sec
Start 49: testvisitor/Scenario: Perform loop unrolling of FROM construct
49/91 Test #49: testvisitor/Scenario: Perform loop unrolling of FROM construct ...................................... Passed 0.05 sec
Start 50: testvisitor/Scenario: Running visitor passes multiple times
50/91 Test #50: testvisitor/Scenario: Running visitor passes multiple times ......................................... Passed 0.05 sec
Start 51: testvisitor/Scenario: Sympy specific AST to NMODL conversion
51/91 Test #51: testvisitor/Scenario: Sympy specific AST to NMODL conversion ........................................ Passed 0.05 sec
Start 52: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types
52/91 Test #52: testvisitor/Scenario: NeuronSolveVisitor visitor solves different ODE types ......................... Passed 0.05 sec
Start 53: testvisitor/Scenario: Convert AST back to NMODL form
53/91 Test #53: testvisitor/Scenario: Convert AST back to NMODL form ................................................ Passed 0.11 sec
Start 54: testvisitor/Scenario: Symbol table generation with Perf stat visitor
54/91 Test #54: testvisitor/Scenario: Symbol table generation with Perf stat visitor ................................ Passed 0.05 sec
Start 55: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor
55/91 Test #55: testvisitor/Scenario: Renaming any variable in mod file with RenameVisitor .......................... Passed 0.05 sec
Start 56: testvisitor/Scenario: Renaming with presence of local and global variables in same block
56/91 Test #56: testvisitor/Scenario: Renaming with presence of local and global variables in same block ............ Passed 0.05 sec
Start 57: testvisitor/Scenario: Renaming in the absence of global blocks
57/91 Test #57: testvisitor/Scenario: Renaming in the absence of global blocks ...................................... Passed 0.05 sec
Start 58: testvisitor/Scenario: Variable renaming in nested blocks
58/91 Test #58: testvisitor/Scenario: Variable renaming in nested blocks ............................................ Passed 0.05 sec
Start 59: testvisitor/Scenario: Renaming in presence of local variable in verbatim block
59/91 Test #59: testvisitor/Scenario: Renaming in presence of local variable in verbatim block ...................... Passed 0.05 sec
Start 60: testvisitor/Scenario: TABLE stmt
60/91 Test #60: testvisitor/Scenario: TABLE stmt .................................................................... Passed 0.05 sec
Start 61: testvisitor/Scenario: Destructor block
61/91 Test #61: testvisitor/Scenario: Destructor block .............................................................. Passed 0.05 sec
Start 62: testvisitor/Solve ODEs using legacy NeuronSolveVisitor
62/91 Test #62: testvisitor/Solve ODEs using legacy NeuronSolveVisitor .............................................. Passed 0.05 sec
Start 63: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method
63/91 Test #63: testvisitor/Scenario: Solving ODEs with STEADYSTATE solve method .................................... Passed 0.05 sec
Start 64: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor
64/91 Test #64: testvisitor/Scenario: Addition of CONDUCTANCE using SympyConductance visitor ........................ Passed 49.33 sec
Start 65: testvisitor/Scenario: Check compare_blocks in sympy unit tests
65/91 Test #65: testvisitor/Scenario: Check compare_blocks in sympy unit tests ...................................... Passed 0.83 sec
Start 66: testvisitor/Scenario: Check local vars name-clash prevention
66/91 Test #66: testvisitor/Scenario: Check local vars name-clash prevention ........................................ Passed 0.97 sec
Start 67: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor
67/91 Test #67: testvisitor/Scenario: Solve ODEs with cnexp or euler method using SympySolverVisitor ................ Passed 6.77 sec
Start 68: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor
68/91 Test #68: testvisitor/Scenario: Solve ODEs with derivimplicit method using SympySolverVisitor ................. Passed 2.44 sec
Start 69: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor)
69/91 Test #69: testvisitor/Scenario: LINEAR solve block (SympySolver Visitor) ...................................... Passed 1.97 sec
Start 70: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor
70/91 Test #70: testvisitor/Scenario: Solve NONLINEAR block using SympySolver Visitor ............................... Passed 0.97 sec
Start 71: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor
71/91 Test #71: testvisitor/Scenario: Parse UNITS block of mod files using Units Visitor ............................ Passed 0.05 sec
Start 72: testvisitor/Scenario: Searching for variable name using VarUsageVisitor
72/91 Test #72: testvisitor/Scenario: Searching for variable name using VarUsageVisitor ............................. Passed 0.05 sec
Start 73: testvisitor/Parse VERBATIM block using Verbatim Visitor
73/91 Test #73: testvisitor/Parse VERBATIM block using Verbatim Visitor ............................................. Passed 0.05 sec
Start 74: testvisitor/Scenario: Get node name with index TestVisitor
74/91 Test #74: testvisitor/Scenario: Get node name with index TestVisitor .......................................... Passed 0.05 sec
Start 75: testprinter/JSON printer converting object to string form
75/91 Test #75: testprinter/JSON printer converting object to string form ........................................... Passed 0.01 sec
Start 76: testsymtab/Scenario: Symbol properties can be added and converted to string
76/91 Test #76: testsymtab/Scenario: Symbol properties can be added and converted to string ......................... Passed 0.01 sec
Start 77: testsymtab/Scenario: Multiple properties can be added to Symbol
77/91 Test #77: testsymtab/Scenario: Multiple properties can be added to Symbol ..................................... Passed 0.01 sec
Start 78: testsymtab/Scenario: Symbol table allows operations like insert, lookup
78/91 Test #78: testsymtab/Scenario: Symbol table allows operations like insert, lookup ............................. Passed 0.01 sec
Start 79: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations
79/91 Test #79: testsymtab/Scenario: Global symbol table (ModelSymbol) allows scope based operations ................ Passed 0.01 sec
Start 80: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver
80/91 Test #80: testnewton/Scenario: Non-linear system to solve with Newton Numerical Diff Solver ................... Passed 0.02 sec
Start 81: testnewton/Scenario: Non-linear system to solve with Newton Solver
81/91 Test #81: testnewton/Scenario: Non-linear system to solve with Newton Solver .................................. Passed 0.01 sec
Start 82: testfast_math/Scenario: Check fast_math
82/91 Test #82: testfast_math/Scenario: Check fast_math ............................................................. Passed 0.01 sec
Start 83: testunitlexer/Unit Lexer tests for valid tokens
83/91 Test #83: testunitlexer/Unit Lexer tests for valid tokens ..................................................... Passed 0.01 sec
Start 84: testunitparser/Scenario: Unit parser accepting valid units definition
84/91 Test #84: testunitparser/Scenario: Unit parser accepting valid units definition ............................... Passed 0.02 sec
Start 85: testunitparser/Scenario: Unit parser accepting dependent/nested units definition
85/91 Test #85: testunitparser/Scenario: Unit parser accepting dependent/nested units definition .................... Passed 0.01 sec
Start 86: Ode
86/91 Test #86: Ode ................................................................................................. Passed 1.99 sec
Start 87: Pybind
87/91 Test #87: Pybind .............................................................................................. Passed 0.56 sec
Start 88: cabpump.mod
88/91 Test #88: cabpump.mod ......................................................................................... Passed 0.07 sec
Start 89: ican.mod
89/91 Test #89: ican.mod ............................................................................................ Passed 0.06 sec
Start 90: ispc_rename.mod
90/91 Test #90: ispc_rename.mod ..................................................................................... Passed 0.06 sec
Start 91: watch_test.mod
91/91 Test #91: watch_test.mod ...................................................................................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 91
Total Test time (real) = 69.66 sec
$ cp -r Testing/ ${CI_PROJECT_DIR}/
$ module load unstable unit-test-translator
Autoloading python/3.9.7
$ cmake2junit > ${CI_PROJECT_DIR}/ctest.xml
$ exit ${i_am_a_failure}
section_end:1662044409:step_script section_start:1662044409:upload_artifacts_on_success Uploading artifacts for successful job
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=160233 revision=58ba2b95 version=14.2.0
initial_environment.env: found 1 matching files and directories
Testing/: found 7 matching files and directories 
Uploading artifacts as "archive" to coordinator... ok id=345801 responseStatus=201 Created token=Uchdt2z8
Uploading artifacts...
Runtime platform  arch=amd64 os=linux pid=160247 revision=58ba2b95 version=14.2.0
ctest.xml: found 1 matching files and directories 
Uploading artifacts as "junit" to coordinator... ok id=345801 responseStatus=201 Created token=Uchdt2z8
section_end:1662044411:upload_artifacts_on_success section_start:1662044411:cleanup_file_variables Cleaning up project directory and file based variables
section_end:1662044411:cleanup_file_variables Job succeeded
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