Running with gitlab-runner 17.5.3 (12030cf4)
  on Synology Docker t3_wks13p, system ID: r_hmHZ1S6oSJ8k
Resolving secrets
section_start:1739450776:prepare_executor
Preparing the "docker" executor
Using Docker executor with image docker:20.10.16 ...
Starting service docker:20.10.16-dind...
Pulling docker image docker:20.10.16-dind ...
Using docker image sha256:7bed3906fb84670066eed54992837895a699b4795576dc651871645cf191ef07 for docker:20.10.16-dind with digest docker@sha256:56ef400f08be1ca817d7e2cfdb43803786ab28d84c8167e8590622d9bab5b415 ...
Waiting for services to be up and running (timeout 30 seconds)...

*** WARNING: Service runner-t3wks13p-project-109103-concurrent-0-9cc9602365ca15cc-docker-0 probably didn't start properly.

Health check error:
service "runner-t3wks13p-project-109103-concurrent-0-9cc9602365ca15cc-docker-0-wait-for-service" timeout

Health check container logs:
2025-02-13T12:46:55.460595518Z waiting for TCP connection to 172.17.0.3 on [2375 2376]...
2025-02-13T12:46:55.475334599Z dialing 172.17.0.3:2375...
2025-02-13T12:46:55.475547528Z dialing 172.17.0.3:2376...
2025-02-13T12:46:56.476557509Z dialing 172.17.0.3:2376...
2025-02-13T12:46:56.477508894Z dialing 172.17.0.3:2375...
2025-02-13T12:46:57.477530119Z dialing 172.17.0.3:2376...
2025-02-13T12:46:57.478931585Z dialing 172.17.0.3:2375...
2025-02-13T12:46:58.478305021Z dialing 172.17.0.3:2376...
2025-02-13T12:46:58.479685599Z dialing 172.17.0.3:2375...
2025-02-13T12:46:59.479360633Z dialing 172.17.0.3:2376...
2025-02-13T12:46:59.480421834Z dialing 172.17.0.3:2375...
2025-02-13T12:47:00.479760604Z dialing 172.17.0.3:2376...
2025-02-13T12:47:00.481232701Z dialing 172.17.0.3:2375...
2025-02-13T12:47:01.480327429Z dialing 172.17.0.3:2376...
2025-02-13T12:47:01.481752007Z dialing 172.17.0.3:2375...
2025-02-13T12:47:02.483006288Z dialing 172.17.0.3:2376...
2025-02-13T12:47:02.483273811Z dialing 172.17.0.3:2375...
2025-02-13T12:47:03.483034253Z dialing 172.17.0.3:2376...
2025-02-13T12:47:03.483181219Z dialing 172.17.0.3:2375...
2025-02-13T12:47:04.483251888Z dialing 172.17.0.3:2376...
2025-02-13T12:47:04.483581708Z dialing 172.17.0.3:2375...
2025-02-13T12:47:05.485011473Z dialing 172.17.0.3:2376...
2025-02-13T12:47:05.485110475Z dialing 172.17.0.3:2375...
2025-02-13T12:47:06.485262516Z dialing 172.17.0.3:2375...
2025-02-13T12:47:06.485505335Z dialing 172.17.0.3:2376...
2025-02-13T12:47:07.486006641Z dialing 172.17.0.3:2375...
2025-02-13T12:47:07.486147051Z dialing 172.17.0.3:2376...
2025-02-13T12:47:08.493589872Z dialing 172.17.0.3:2375...
2025-02-13T12:47:08.493686911Z dialing 172.17.0.3:2376...

Service container logs:
2025-02-13T12:46:48.550075303Z Generating RSA private key, 4096 bit long modulus (2 primes)
2025-02-13T12:46:49.279733396Z .............................++++
2025-02-13T12:46:51.041749623Z ..........................................................................++++
2025-02-13T12:46:51.043676949Z e is 65537 (0x010001)
2025-02-13T12:46:51.115847554Z Generating RSA private key, 4096 bit long modulus (2 primes)
2025-02-13T12:46:54.397807983Z ............................................................................................................................................++++
2025-02-13T12:46:56.134396223Z .........................................................................++++
2025-02-13T12:46:56.136164435Z e is 65537 (0x010001)
2025-02-13T12:46:56.254508239Z Signature ok
2025-02-13T12:46:56.254595389Z subject=CN = docker:dind server
2025-02-13T12:46:56.255135768Z Getting CA Private Key
2025-02-13T12:46:56.323036639Z /certs/server/cert.pem: OK
2025-02-13T12:46:56.332563824Z Generating RSA private key, 4096 bit long modulus (2 primes)
2025-02-13T12:46:56.511308309Z .....++++
2025-02-13T12:47:06.214165299Z ......................................................................................................................................................................................................................................................................................................................................................................................................................................++++
2025-02-13T12:47:06.216006809Z e is 65537 (0x010001)
2025-02-13T12:47:06.323433369Z Signature ok
2025-02-13T12:47:06.323521630Z subject=CN = docker:dind client
2025-02-13T12:47:06.324040527Z Getting CA Private Key
2025-02-13T12:47:06.391547243Z /certs/client/cert.pem: OK
2025-02-13T12:47:06.976355379Z ip: can't find device 'ip_tables'
2025-02-13T12:47:06.978527005Z ip_tables              28672  3 iptable_mangle,iptable_nat,iptable_filter
2025-02-13T12:47:06.979092606Z x_tables               28672 19 xt_ipvs,xt_mark,iptable_mangle,xt_conntrack,xt_addrtype,ip6table_filter,ip6_tables,xt_MASQUERADE,xt_REDIRECT,xt_nat,xt_recent,xt_iprange,xt_limit,xt_state,xt_tcpudp,xt_multiport,xt_LOG,iptable_filter,ip_tables
2025-02-13T12:47:06.980520629Z modprobe: can't change directory to '/lib/modules': No such file or directory
2025-02-13T12:47:07.000058155Z mount: mounting none on /sys/kernel/security failed: Permission denied
2025-02-13T12:47:07.000179527Z Could not mount /sys/kernel/security.
2025-02-13T12:47:07.000199157Z AppArmor detection and --privileged mode might break.
2025-02-13T12:47:07.004360851Z mount: mounting none on /tmp failed: Permission denied

*********

Pulling docker image docker:20.10.16 ...
Using docker image sha256:9da3ec5b5d761f2ab25fbd7dd0c2c6de980878fdc67fd084c34a0150da9a63f7 for docker:20.10.16 with digest docker@sha256:5bc07a93c9b28e57a58d57fbcf437d1551ff80ae33b4274fb60a1ade2d6c9da4 ...
section_end:1739450854:prepare_executor
section_start:1739450854:prepare_script
Preparing environment
Running on runner-t3wks13p-project-109103-concurrent-0 via 1f9c60dcd660...
section_end:1739450862:prepare_script
section_start:1739450862:get_sources
Getting source from Git repository
Fetching changes with git depth set to 20...
Reinitialized existing Git repository in /builds/JanHab/fxdgm-testing/.git/
Checking out 54d15557 as detached HEAD (ref is main)...
Removing public/

Skipping Git submodules setup
section_end:1739450871:get_sources
section_start:1739450871:step_script
Executing "step_script" stage of the job script
Using docker image sha256:9da3ec5b5d761f2ab25fbd7dd0c2c6de980878fdc67fd084c34a0150da9a63f7 for docker:20.10.16 with digest docker@sha256:5bc07a93c9b28e57a58d57fbcf437d1551ff80ae33b4274fb60a1ade2d6c9da4 ...
$ echo "$CI_REGISTRY_PASSWORD" | docker login $CI_REGISTRY -u $CI_REGISTRY_USER --password-stdin
WARNING! Your password will be stored unencrypted in /root/.docker/config.json.
Configure a credential helper to remove this warning. See
https://docs.docker.com/engine/reference/commandline/login/#credentials-store

Login Succeeded
$ docker pull $CI_REGISTRY_IMAGE:latest || true
latest: Pulling from janhab/fxdgm-testing
Digest: sha256:cab3cb2259d8a197184990b793408516279afc3552685fc6d0541b2ec8a201ad
Status: Image is up to date for registry.git.rwth-aachen.de/janhab/fxdgm-testing:latest
registry.git.rwth-aachen.de/janhab/fxdgm-testing:latest
$ docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:latest .
Sending build context to Docker daemon  302.3MB

Step 1/9 : FROM continuumio/miniconda3:latest
 ---> f912e1ee4124
Step 2/9 : ENV CONDA_DEFAULT_ENV=base
 ---> Using cache
 ---> 754dc819b4b6
Step 3/9 : ENV PATH /opt/conda/envs/${CONDA_DEFAULT_ENV}/bin:$PATH
 ---> Using cache
 ---> e37555b69ad9
Step 4/9 : ENV HOME /root
 ---> Using cache
 ---> a8cd518df950
Step 5/9 : RUN conda install -n ${CONDA_DEFAULT_ENV} -c conda-forge fenics-dolfinx=0.8.0 mpich=4.2.1 pyvista=0.43.10 gcc=12.4.0 sphinx=7.3.7 myst-parser=4.0.0 sphinx-copybutton=0.5.2 sphinx-rtd-theme=3.0.1 pytest=8.3.3 pytest-cov=6.0.0 sqlite=3.41.2 -y
 ---> Using cache
 ---> e3f76242dff7
Step 6/9 : WORKDIR /root
 ---> Using cache
 ---> ac4308d2cdfb
Step 7/9 : ADD . /fxdgm
 ---> f9f8a448c8ff
Step 8/9 : RUN pip install --editable /fxdgm/.
 ---> Running in 86942d09d1b6
Obtaining file:///fxdgm
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Checking if build backend supports build_editable: started
  Checking if build backend supports build_editable: finished with status 'done'
  Getting requirements to build editable: started
  Getting requirements to build editable: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing editable metadata (pyproject.toml): started
  Preparing editable metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: pyvista==0.43.10 in /opt/conda/lib/python3.12/site-packages (from fxdgm==1.0) (0.43.10)
Requirement already satisfied: numpy==1.26.4 in /opt/conda/lib/python3.12/site-packages (from fxdgm==1.0) (1.26.4)
Collecting scipy==1.14.0 (from fxdgm==1.0)
  Downloading scipy-1.14.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl.metadata (113 kB)
Requirement already satisfied: matplotlib>=3.0.1 in /opt/conda/lib/python3.12/site-packages (from pyvista==0.43.10->fxdgm==1.0) (3.10.0)
Requirement already satisfied: pillow in /opt/conda/lib/python3.12/site-packages (from pyvista==0.43.10->fxdgm==1.0) (10.3.0)
Requirement already satisfied: pooch in /opt/conda/lib/python3.12/site-packages (from pyvista==0.43.10->fxdgm==1.0) (1.8.2)
Requirement already satisfied: scooby>=0.5.1 in /opt/conda/lib/python3.12/site-packages (from pyvista==0.43.10->fxdgm==1.0) (0.10.0)
Requirement already satisfied: vtk in /opt/conda/lib/python3.12/site-packages (from pyvista==0.43.10->fxdgm==1.0) (9.3.0)
Requirement already satisfied: contourpy>=1.0.1 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (1.3.1)
Requirement already satisfied: cycler>=0.10 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (4.56.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (1.4.8)
Requirement already satisfied: packaging>=20.0 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (24.1)
Requirement already satisfied: pyparsing>=2.3.1 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (3.2.1)
Requirement already satisfied: python-dateutil>=2.7 in /opt/conda/lib/python3.12/site-packages (from matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (2.9.0.post0)
Requirement already satisfied: platformdirs>=2.5.0 in /opt/conda/lib/python3.12/site-packages (from pooch->pyvista==0.43.10->fxdgm==1.0) (3.10.0)
Requirement already satisfied: requests>=2.19.0 in /opt/conda/lib/python3.12/site-packages (from pooch->pyvista==0.43.10->fxdgm==1.0) (2.32.3)
Requirement already satisfied: six>=1.5 in /opt/conda/lib/python3.12/site-packages (from python-dateutil>=2.7->matplotlib>=3.0.1->pyvista==0.43.10->fxdgm==1.0) (1.17.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /opt/conda/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista==0.43.10->fxdgm==1.0) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /opt/conda/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista==0.43.10->fxdgm==1.0) (3.7)
Requirement already satisfied: urllib3<3,>=1.21.1 in /opt/conda/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista==0.43.10->fxdgm==1.0) (2.2.3)
Requirement already satisfied: certifi>=2017.4.17 in /opt/conda/lib/python3.12/site-packages (from requests>=2.19.0->pooch->pyvista==0.43.10->fxdgm==1.0) (2024.12.14)
Downloading scipy-1.14.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl (35.3 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 35.3/35.3 MB 10.5 MB/s eta 0:00:00
Building wheels for collected packages: fxdgm
  Building editable for fxdgm (pyproject.toml): started
  Building editable for fxdgm (pyproject.toml): finished with status 'done'
  Created wheel for fxdgm: filename=fxdgm-1.0-0.editable-py3-none-any.whl size=17592 sha256=749531e76cc1526c1c74ec10801c280852d9fc10fb3147b5b36558b245772f7d
  Stored in directory: /tmp/pip-ephem-wheel-cache-qwvld140/wheels/1d/df/70/1000b4574337ce998416243a7b55d9b78984631178ecca3e34
Successfully built fxdgm
Installing collected packages: scipy, fxdgm
Successfully installed fxdgm-1.0 scipy-1.14.0
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager, possibly rendering your system unusable.It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv. Use the --root-user-action option if you know what you are doing and want to suppress this warning.
Removing intermediate container 86942d09d1b6
 ---> de6c9aad8696
Step 9/9 : CMD ["bash"]
 ---> Running in af56bf08ba23
Removing intermediate container af56bf08ba23
 ---> bc2ecf88115f
Successfully built bc2ecf88115f
Successfully tagged registry.git.rwth-aachen.de/janhab/fxdgm-testing:latest
$ docker push $CI_REGISTRY_IMAGE:latest
The push refers to repository [registry.git.rwth-aachen.de/janhab/fxdgm-testing]
da58cfc64dd8: Preparing
2c49f9809b67: Preparing
20f9b2886f35: Preparing
6cac6c54627c: Preparing
4d6b52d7407b: Preparing
f0f039847c08: Preparing
f0f039847c08: Waiting
20f9b2886f35: Layer already exists
6cac6c54627c: Layer already exists
4d6b52d7407b: Layer already exists
f0f039847c08: Layer already exists
da58cfc64dd8: Pushed
2c49f9809b67: Pushed
latest: digest: sha256:3a264d2c4bb4e72a5cba3c65d8479a49dedaacdd746db47a2a48e23829be64a2 size: 1593
section_end:1739451312:step_script
section_start:1739451313:cleanup_file_variables
Cleaning up project directory and file based variables
section_end:1739451319:cleanup_file_variables
Job succeeded