sokrypton / sokrypton/ColabFold
how to parallelize tsv2exprofiledb?
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Description
I'm observing that the tsv2exprofiledb (that is triggering mmseqs tsv2db), seems that it is not using all of the possible resources). The CPU utilization is only 1%.
Machine specs:
100GB+ ram
10GB/s read disk
1-2GB/s write disk
96 cores
current CPU utilization: 1%
this is making the process quite slow (many many hours). Is it possible to parallelize that step in any way?
USER PID %CPU %MEM VSZ RSS TTY STAT START TIME COMMAND
root 1 0.0 0.0 1112 384 ? Ss 10:04 0:00 /sbin/docker-init -- /app/entrypoint.sh
root 13 0.0 0.0 4496 3080 ? S 10:04 0:00 /bin/bash /app/entrypoint.sh
root 23 0.0 0.0 4364 2712 ? S 10:04 0:00 /bin/bash -ex /app/setup_database.sh /workspace/db
root 42 0.0 0.0 2892 1548 ? S 10:58 0:00 /bin/sh -e /workspace/db/uniref30_2302_db.sh uniref30_2302 uniref30_2302_db
root 71 0.0 0.0 4628 3472 pts/0 Ss 11:16 0:00 /bin/bash
root 94 56.8 0.0 226220 39616 ? R 11:31 0:26 mmseqs tsv2db uniref30_2302_h.tsv uniref30_2302_db_seq_h --output-dbtype 12 -v 3
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with tsv2exprofiledb and the uniref30_2302_db.sh entry point, then inspect the mmseqs tsv2db invocation shown in the report. Measure where the step spends time and determine whether parallelization is supported or would require a design change. Done means documenting or implementing a validated way to use the available resources.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100