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kbase / collections

Data collections code including a service and loaders
MIT License
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use dbmen for eggnog #746

Closed Tianhao-Gu closed 3 months ago

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 46.21%. Comparing base (02f0fbe) to head (7e5d658).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #746 +/- ## ======================================== Coverage 46.21% 46.21% ======================================== Files 78 78 Lines 7028 7028 ======================================== Hits 3248 3248 Misses 3780 3780 ```

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MrCreosote commented 3 months ago

do you think this is causing the slow performance on the worker nodes? If so why wouldn't the login nodes be the same?

Tianhao-Gu commented 3 months ago

do you think this is causing the slow performance on the worker nodes? If so why wouldn't the login nodes be the same?

Still testing the performance. I built the image in login node and test run it in an interactive node. The performance was even worse with this option. With this PR, I just want to build it and run via taskfarmer to see if it improves performance. The performance in general is worse in the worker nodes than in the login node. I used to cut the path to test directly with the login node. Moving forward, I probably will test things in an interactive node to get a better estimation.

Tianhao-Gu commented 3 months ago

But I went over issues on eggnog repo. This option is what the eggnog team suggested in one of the issues. https://github.com/eggnogdb/eggnog-mapper/issues/80

MrCreosote commented 3 months ago

ok, sounds like you can test with the pr image so we don't need to merge this, but lmk if I'm wrong

Tianhao-Gu commented 3 months ago

ok, sounds like you can test with the pr image so we don't need to merge this, but lmk if I'm wrong

yea. I can test it with PR image. I will get back to you once I finished testing the image.

Tianhao-Gu commented 3 months ago

ok, sounds like you can test with the pr image so we don't need to merge this, but lmk if I'm wrong

yea. I can test it with PR image. I will get back to you once I finished testing the image.

closing PR. Surpassingly, a single genome takes more than 30 minutes to finish with this option for both 2 nodes and 5 nodes running mode.