Running with gitlab-runner 15.5.0 (0d4137b8)
  on BB5 map runner pnPo3yJy
section_start:1730887411:resolve_secrets
Resolving secrets
section_end:1730887411:resolve_secrets
section_start:1730887411: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 15.5.0, user 
TMPDIR is /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs/tmp/custom-executor3170963399, slurm job id , CUSTOM_ENV_CI_RUNNER_TAGS is ["bb5_map"]
Runner ID 29, project root hpc, project name nrn
Pipeline ID 237857, build ref , job ID 1479314
Build dir /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P237857, optional exclusive flag , optional cpus per task flag --cpus-per-task=6, optional qos flag , optional reservation flag 
A slurm job will be created with name GL_J1479314_PROD_P2160_CP8_C8
Job parameters: memory=30750M, cpus_per_task=6, duration=1:00:00, constraint=cpu ntasks=1 account=proj9998 user=bbpcihpcproj12 partition=prod qos= reservation=
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 2630518
job state: R
sbatch: sbatch -p prod -A proj9998 --ntasks=1 --cpus-per-task=6 --mem=30750M    --job-name=GL_J1479314_PROD_P2160_CP8_C8 -C cpu --no-requeue -D /gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P237857 --time=1:00:00 --wrap="sleep infinity"
srun: srun --mpi=none --chdir=/gpfs/bbp.cscs.ch/ssd/gitlab_map_jobs//bbpcihpcproj12/P237857 --ntasks=1 --jobid=2630518 --cpus-per-task=6 --mem=30750M     
section_end:1730887413:prepare_executor
section_start:1730887413:prepare_script
Preparing environment
Using git from spack modules
Running on r1i6n19 via bbpv1.epfl.ch...
section_end:1730887416:prepare_script
section_start:1730887416:get_sources
Getting source from Git repository
Using git from spack modules
Skipping Git repository setup
Skipping Git checkout
Skipping Git submodules setup
section_end:1730887416:get_sources
section_start:1730887416: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
Using git from spack modules
$ 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
# special case for SPACK_DEPLOYMENT_SUFFIX=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()
  is_deployment_suffix = ref_type == 'suffix' and m.group(1).lower() == 'spack_deployment'
  if ref_type not in {'branch', 'tag', 'ref'} and not is_deployment_suffix: 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
$ 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/P237857/J1479314
$ 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} ${SPACK_URL} spack
Cloning into 'spack'...
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$ export SPACK_ROOT=${PWD}/spack
$ export SPACK_RESOLVED_COMMIT=$(cd "${SPACK_ROOT}" && git rev-parse HEAD)
$ 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_RESOLVED_COMMIT=${SPACK_RESOLVED_COMMIT}" >> 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/P237857/J1479314_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"
$ echo -e "[url \"https://gitlab-ci-token:${CI_JOB_TOKEN}@bbpgitlab.epfl.ch/\"]\n  insteadOf = ssh://git@bbpgitlab.epfl.ch/" >> "${XDG_CONFIG_HOME}/git/config"
$ cat "${XDG_CONFIG_HOME}/git/config"
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = git@bbpgitlab.epfl.ch:
[url "https://gitlab-ci-token:[MASKED]@bbpgitlab.epfl.ch/"]
  insteadOf = ssh://git@bbpgitlab.epfl.ch/
$ env -0 | sed -nz '/^CUSTOM_ENV_/d;/^[^=]\+_\(BRANCH\|COMMIT\|TAG\)=.\+/p' | xargs -0t spack ${SPACK_EXTRA_FLAGS} configure-pipeline --ignore-packages CI_BUILD CI_COMMIT CI_DEFAULT GITLAB_PIPELINES SPACK SPACK_RESOLVED ${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 SPACK_RESOLVED BLUECONFIGS --write-commit-file=commit-mapping.env CI_COMMIT_BRANCH=jelic/skip_tests SPACK_RESOLVED_COMMIT=38753b8b072f3d29f4e8ebe1b92e39957090758f GITLAB_PIPELINES_BRANCH=main NEURON_COMMIT=b930c9cfe3a5fde620cefc7e5852718c7b30dc75 NMODL_BRANCH=master LIBSONATA_REPORT_BRANCH=master SPACK_BRANCH=develop CI_DEFAULT_BRANCH=master BLUECONFIGS_BRANCH=main 
==> CI_COMMIT: ignoring CI_COMMIT_BRANCH=jelic/skip_tests
==> SPACK_RESOLVED: ignoring SPACK_RESOLVED_COMMIT=38753b8b072f3d29f4e8ebe1b92e39957090758f
==> GITLAB_PIPELINES: ignoring GITLAB_PIPELINES_BRANCH=main
==> SPACK: ignoring SPACK_BRANCH=develop
==> CI_DEFAULT: ignoring CI_DEFAULT_BRANCH=master
==> BLUECONFIGS: ignoring BLUECONFIGS_BRANCH=main
==> nmodl: resolved branch master to da2ae9ff7ebf3a419f175e10a3d28e977b6945f3
==> libsonata-report: resolved branch master to b42e72121c5c299188601f914da0c3f3d0f196ca
==> adding config: packages:neuron:require: '@git.b930c9cfe3a5fde620cefc7e5852718c7b30dc75=develop'
==> adding config: packages:nmodl:require: '@git.da2ae9ff7ebf3a419f175e10a3d28e977b6945f3=develop'
==> adding config: packages:libsonata-report:require: '@git.b42e72121c5c299188601f914da0c3f3d0f196ca=develop'
$ (cd "${SPACK_ROOT}" && git diff)
$ cat commit-mapping.env
NEURON_COMMIT=b930c9cfe3a5fde620cefc7e5852718c7b30dc75
NMODL_COMMIT=da2ae9ff7ebf3a419f175e10a3d28e977b6945f3
LIBSONATA_REPORT_COMMIT=b42e72121c5c299188601f914da0c3f3d0f196ca
$ 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 ${SPACK_EXTRA_FLAGS} spec -IL ninja
==> Warning: Expected user 904556 to own /nvme/bbpcihpcproj12, but it is owned by 0
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spec.json
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/patchelf-0.18.0/linux-centos7-x86_64-gcc-10.2.1-patchelf-0.18.0-afv7arjarb7nzmlh7c5slkfxykybuqce.spack
==> Installing "patchelf@=0.18.0%gcc@=10.2.1 ldflags="-static-libstdc++ -static-libgcc"  build_system=autotools arch=linux-centos7-x86_64" from a buildcache
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spec.json
==> Fetching https://mirror.spack.io/bootstrap/github-actions/v0.5/build_cache/linux-centos7-x86_64/gcc-10.2.1/clingo-bootstrap-spack/linux-centos7-x86_64-gcc-10.2.1-clingo-bootstrap-spack-t4yf34cuvquqp5xd66zybmcfyhwbdlsf.spack
==> Installing "clingo-bootstrap@=spack%gcc@=10.2.1~docs+ipo+optimized+python+static_libstdcpp build_system=cmake build_type=Release generator=make patches=bebb819,ec99431 arch=linux-centos7-x86_64" from a buildcache
Input spec
--------------------------------
 -   ninja

Concretized
--------------------------------
[e]  omn6mm4a3zsbpbkptvdwxs6kkrh6yafw  ninja@1.11.1%gcc@12.3.0+re2c build_system=generic 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 ${SPACK_EXTRA_FLAGS} config --scope site add "config:ccache:true"
$ echo "SPACK_USE_CCACHE=true" >> spack_clone_variables.env
$ echo "BLUECONFIGS_BRANCH=${BLUECONFIGS_BRANCH}" >> commit-mapping.env
$ echo "BLUECONFIGS_BRANCH=${BLUECONFIGS_BRANCH}" >> spack_clone_variables.env
section_end:1730887514:step_script
section_start:1730887514:upload_artifacts_on_success
Uploading artifacts for successful job
Using git from spack modules
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=292610 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=1479314 responseStatus=201 Created token=glcbt-64
Uploading artifacts...
Runtime platform                                    arch=amd64 os=linux pid=292632 revision=58ba2b95 version=14.2.0
spack_clone_variables.env: found 1 matching files and directories 
Uploading artifacts as "dotenv" to coordinator... ok  id=1479314 responseStatus=201 Created token=glcbt-64
section_end:1730887515:upload_artifacts_on_success
section_start:1730887515:cleanup_file_variables
Cleaning up project directory and file based variables
Using git from spack modules
section_end:1730887516:cleanup_file_variables
Job succeeded