Omamer crash with latest docker image

[ens-sb]

Hello FastOMA team!

We were running FastOMA on a dataset which was processed sucessfully by a previous version. However, with the latest commit and docker image we get an error in the omamer run step:

Traceback (most recent call last):
  File "/app/bin/omamer", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/app/lib/python3.11/site-packages/omamer/main.py", line 33, in main
    from tables import PerformanceWarning
  File "/app/lib/python3.11/site-packages/tables/__init__.py", line 44, in <module>
    from .utilsextension import get_hdf5_version as _get_hdf5_version
  File "tables/utilsextension.pyx", line 1, in init tables.utilsextension
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

It might be related to this issue: https://stackoverflow.com/a/78641304

Best,
Botond

[sinamajidian]

Hi Botond
Thanks for sharing your experience with the newest version. I faced that because of numpy version and documented it in the wiki. Using the suitable version it should be fine. We are working on the FastOMA docker to make it smooth.
Best,
Sina

[ens-sb]

Thanks for the pointers, Sina! I will try running withouth the container.
Best,
Botond

[alpae]

Hi @ens-sb

I think the from version 0.3.1 onwards, this problem should not exist anymore in the docker container. could you maybe check which version you where using exactly. if you used latest, you might need to pull it again.

Cheers Adrian

[ens-sb]

Hi Adrian,
Thanks for the fix!
Botond