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

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First steps

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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

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