Errors found trying to deploy Gisola on a Docker container

[WilliamEpenarandaA]

Greetings @nikosT

I'm trying to deploy Gisola on a Docker container but I found some problems. So before describe problem found, first I was wondering if you consider this option availaible?

I build a container for Gisola program and I enter to that container and ran benchmark test and even I test the conection to a Seiscomp database and It works perfectly, the problem that I found is when I try to run Gisola commands from outside of the container. For instance, the program give this error when I run the suggested test in wiki using docker compose exec

# run benchmark 
docker compose exec --workdir /app/Gisola/src/ gisola conda run -n gisola python3 ./gisola.py -c ../test/config.yaml --event-xml ../test/benchmark/event.xml

The program return this error:

2026-03-28 10:07:21,186 INFO Function 'calculateInversions' executed 5.8 seconds
2026-03-28 10:07:21,187 ERROR Fatal Error occurred
Traceback (most recent call last):
  File "/app/Gisola/src/./gisola.py", line 235, in <module>
    isola.gatherResults()
  File "/app/Gisola/src/config.py", line 181, in inner
    func(*args, **kwargs)
  File "/app/Gisola/src/isola.py", line 428, in gatherResults
    with open(os.path.join(workdir,'inversions', inversion,'inv1.dat')) as _:
FileNotFoundError: [Errno 2] No such file or directory: '../test/results/2020/noa2020vipzs/2026-03-28T10:05:08.276913Z/inversions/0.0.0.0.0.0/inv1.dat'
2026-03-28 10:07:21,190 INFO Moving to next event, if any

Note

SYSTEM AND PROGRAM VERSIONS USED
Linux Distribution: Ubuntu 20.04; Gisola: v1.2.3

I hope you can give some suggestions to solve that problem. It will be very valuable

Thanks in advance for your attention

Sincerely

William Eduardo

[nikosT]

Hi @WilliamEpenarandaA,

Thanks for bringing this up! It's great that you're taking the initiative to containerize Gisola.

Since you mentioned that the benchmark works perfectly when you are inside the container, but fails with FileNotFoundError when executing from the outside via docker compose exec, the issue is almost certainly related to how the environment variables or paths or docker volumes are loaded during non-interactive execution.

When the Python script fails to find inv1.dat, most probably means the underlying Fortran inversion binaries silently failed to execute or write their output.

I'm not sure if conda run perfectly replicates the $PATH, $LD_LIBRARY_PATH, or shell context of a fully activated interactive session.

I suggest to wrap the execution in a standard bash command that explicitly sources Conda, activates the environment, and runs the script in one go. Try running this instead:

docker compose exec gisola /bin/bash -c "source /opt/conda/etc/profile.d/conda.sh && conda activate gisola && cd /app/Gisola/src && python3 ./gisola.py -c ../test/config.yaml --event-xml ../test/benchmark/event.xml"

(Note: You may need to adjust the /opt/conda/etc/... path depending on where Miniconda/Anaconda is installed inside your base image).

In case you are using docker Volumes, then if your docker-compose.yml mounts the Gisola directory as a volume to your host machine, docker compose exec might be running as a different user (e.g., root) than the one who owns the mounted directory. This can prevent the underlying binaries from creating the ../test/results/... directories or writing inv1.dat.

Therefore, you can explicitly pass your host user's UID/GID to the execution command:

docker compose exec --user $(id -u):$(id -g) --workdir /app/Gisola/src/ gisola <rest of your command>

Could you try the /bin/bash -c method above and let me know if it successfully generates the outputs? If it still fails, it would be helpful to check if the inversions/0.0.0.0.0.0/ directory is actually being created empty, or if the directory creation itself is failing. Also, please provide me with a reproducible example. Let me know what you find!

[WilliamEpenarandaA]

Hello @nikosT,

First of all, I appreciate your quick answer. Following your recomendations, First of all, I tried /bin/bash -c method to execute Benchmark test. It failed. I checked inversions folder and found that the directories sucessfully created but inside of them there's any .dat files (See following image)

Then I tried to run the same command but explictly passed my host user's UID/GID using the following execution command:

docker compose exec --user $(id -u):$(id -g) --workdir /app/Gisola/src/ gisola /bin/bash -c "source /opt/conda/etc/profile.d/conda.sh && conda activate gisola && cd /app/Gisola/src && python3 ./gisola.py -c ../test/config.yaml --event-xml ../test/benchmark/event.xml"

It returned the following error:

Matplotlib created a temporary config/cache directory at /tmp/matplotlib-hbgdqt10 because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Traceback (most recent call last):
 File "/app/Gisola/src/./gisola.py", line 99, in <module>
   logger = config.setup_logger('gisola_log', args.log)
 File "/app/Gisola/src/config.py", line 33, in setup_logger
   handler = logging.FileHandler(log_file)
 File "/opt/conda/envs/gisola/lib/python3.9/logging/__init__.py", line 1142, in __init__
   StreamHandler.__init__(self, self._open())
 File "/opt/conda/envs/gisola/lib/python3.9/logging/__init__.py", line 1171, in _open
   return open(self.baseFilename, self.mode, encoding=self.encoding,
PermissionError: [Errno 13] Permission denied: '/app/Gisola/src/log'

Finally, I attach you Dockerfile and docker-compose.yml files used to create gisola container here and below I explain in detail steps that I did for deploy the container.

docker-compose.YML
Dockerfile.txt

Tip

Please remove .txt extension from Dockerfile and change extension of docker-compose file to yml, because I had to assign them like this to be able to attach files here.

Note

Steps done to deploy gisola container:

• First, in the path where you have docker files, I clone Gisola repository and made a little change in environment.yml. I remove the limitation for the specific version of Obspy package because I had troubles creating conda environment.
• Second, I enter Gisola's folder and initialize containers for Seiscomp FDSN service and MySQL db with docker-compose up -d command in the same way described in Installation section of the wiki.
• Finally, I create the gisola container using docker files provided using the following command:

docker compose up -d

Versions used: docker = 29.2.1; docker compose = 5.0.2

Thanks in advance for your interest and don't hesitate to ask me for any further information.

[nikosT]

Hi @WilliamEpenarandaA, apologies for the delay.

1. For the environment.yml you can just move the ObsPy from pip to the Dependencies:

diff --git a/environment.yml b/environment.yml
index ae85e4c..390afa5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -64,6 +64,7 @@ dependencies:
   - xz=5.2.5
   - zlib=1.2.11
   - zstd=1.4.8
+  - obspy=1.2.2  # <-- Add it here to use Conda's pre-built binary
   - pip:
     - basemap==1.3.8
     - chardet==4.0.0
@@ -75,7 +76,6 @@ dependencies:
     - idna==2.10
     - lxml==4.6.2
     - numpy==1.25.2
-    - obspy==1.2.2
     - pandas==1.2.2
     - pytz==2021.1
     - pyyaml==5.4.1

I strongly suggest NOT to change the specified ObsPy version, otherwise might brake things.

2. You can also have DnD (Docker in Docker) for the Gisola's dockerized tools. So, you can invoke one container with a Docker engine inside it that runs the Docker tools (anyway).

3. I performed: docker compose exec -it gisola bash
   and from the container's cell: ./gisola.py -c ../test/config.yaml --event-xml ../test/benchmark/event.xml
   and it works fine. I have MT calculations.
   See:

2026-04-09 11:54:37,287 INFO Function 'calculateInversions' executed 152.81 seconds
/opt/conda/envs/gisola/lib/python3.9/site-packages/obspy/io/quakeml/core.py:1109: UserWarning: 'smi:org.gfz-potsdam.de/geofon/RMHP(10)>>ITAPER(30)>>BW_BP(2,3.0,4)>>STALTA(1,30)' is not a valid QuakeML URI. It will be in the final file but note that the file will not be a valid QuakeML file.
  warnings.warn(msg % obj.id)
/opt/conda/envs/gisola/lib/python3.9/site-packages/obspy/io/quakeml/core.py:1109: UserWarning: 'smi:org.gfz-potsdam.de/geofon/RMHP(10)>>ITAPER(10)>>BW(2,3.0,4)>>STALTA(1,30)' is not a valid QuakeML URI. It will be in the final file but note that the file will not be a valid QuakeML file.
  warnings.warn(msg % obj.id)
2026-04-09 11:54:39,441 INFO Function 'gatherResults' executed 2.15 seconds
2026-04-09 11:54:48,091 INFO Function 'allplots' executed 8.65 seconds

Check please if you run docker without sudo i.e. create a docker group, etc. Check for instance: https://docs.docker.com/engine/install/linux-postinstall/