Speedup packing #45
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Speedup packing #45
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added 3 commits
July 29, 2024 14:33
The packaging step was very inefficient especially for metagenomes that have a lot of MAGs. This was because the process was serialized and each one has to read through the input files over and over. This changes it so each file is open and read once and the output is multiplexed to the various outputs files. It also parallelizes the tar file generation. For one test case the previous way was taking 6-7 hours and it nows runs in a few minutes.
- Fix KO naming - Cleanup log output a bit
Closed
mbthornton-lbl
requested changes
Jul 31, 2024
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I think all the comments have been addressed. |
mbthornton-lbl
approved these changes
Aug 5, 2024
chienchi
requested changes
Aug 5, 2024
|
I think we need to update the version to 0.6.0 in Dockerfile_vis and rebuild it. In addition, the version of the docker string in the main WDL file, mbin_nmdc.wdl line 25 for this merge. |
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Let's merge this, then we can do as @chienchi suggested to rebuild the image and then update the WDL. |
chienchi
approved these changes
Aug 5, 2024
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These changes are actually from me.
The packaging step was very inefficient especially for metagenomes
that have a lot of MAGs. This was because the process was
serialized and each one has to read through the input files over
and over. This changes it so each file is open and read once
and the output is multiplexed to the various outputs files.
It also parallelizes the tar file generation.
For one test case the previous way was taking 6-7 hours and it nows
runs in a few minutes.