Dedalus2 Install error

Peng Deng

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Mar 11, 2026, 4:08:38 AM (5 days ago) Mar 11

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Dear Dedalus users,

Due to the renewal of the HPC facility in my university, I need to re-install Dedalus2 in the new HPC.

I follow the custom conda installation and use the bash file conda_install_dedalus2.sh.

The sub-environment dedalus2 could be installed, but when I use 'python3 -m dedalus test' to verify the installation, errors pop up. Those errors (see the attached screenshot) seem to relate to multi-thread issue.

Should some options in the bash file (conda_install_dedalus2.sh) be modified accordingly to resolve this issue?

Thanks for your help.

Best,

Peng

install_error.PNG

Calum Skene

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Mar 11, 2026, 5:35:05 AM (5 days ago) Mar 11

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Hi Peng,

Can you try running the tests again with less workers. Something like

PYTEST_WORKERS=3 python3 -m dedalus test

You are currently using 256 workers which is maybe the cause of the issue (especially if on a login node).

Best,

Calum

Peng Deng

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Mar 11, 2026, 8:18:44 AM (4 days ago) Mar 11

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Hi Calum,

Thank you very much for your reply.

I tried 'PYTEST_WORKERS=3 python3 -m dedalus test', but the tests are still run with 256 workers, same errors pop up, see the attached screenshot.

Best,

Peng

install_error_2.PNG

Calum Skene

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Mar 11, 2026, 12:32:46 PM (4 days ago) Mar 11

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Hi Peng,

Ah okay, PYTEST_WORKERS must be a d3 thing. Can you try running the tests in a job with 4 cores or something small. Hopefully this runs better.