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disable HDF5 file locking #2314

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merged 1 commit into from
Dec 8, 2024

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@cat-bro cat-bro commented Dec 3, 2024

There has been an error in gunicorn logs coming from the tool predictions API:

Dec 03 00:01:47 galaxy galaxyctl[2118437]:   File "h5py/h5f.pyx", line 102, in h5py.h5f.open
Dec 03 00:01:47 galaxy galaxyctl[2118437]: OSError: Unable to synchronously open file (file locking flag values don't match)

From a google search I found recommendations to use HDF5_USE_FILE_LOCKING: "FALSE". Checked out EU and Main infrastructure playbooks and found that they are already using this, and they have adopted it recently. (galaxyproject/usegalaxy-playbook@3724a13#diff-68bca5ccf2e9695dcca9925b36cce7bb8e7bd223d9c6531649be01986c661020R31)

I'm not sure if this means instances are individually compensating for something that has gone wrong in Galaxy

@cat-bro cat-bro requested a review from jlqfab December 8, 2024 22:19
@jlqfab jlqfab merged commit 8063d75 into usegalaxy-au:master Dec 8, 2024
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@cat-bro cat-bro deleted the disable_HDF5_file_locking branch December 8, 2024 23:43
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2 participants