Multiple mmseqs instances accessing the same database

[prototaxites]

Are there recommendations for running multiple, parallel MMSeqs instances accessing the same database?

I am currently experiencing an issue where running a single instance of an analysis takes about 20 minutes, but if I set e.g. ~5 instances of the analysis going, they seem to struggle to read the input database and a search that would normally take 5 minutes seems to take >1 hour.

Do I need to load the database into memory with --db-load-mode?

[milot-mirdita]

Using an external tool like vmtouch (or very recently mmseqs touchdb --touch-lock) to keep a DB in memory together with --db-load-mode 2 is generally how you would do that. This is how ColabFold works.

[prototaxites]

Thanks, I will give that a try. I don't see a --touch-lock option in the options for touchdb though, is it important?

❱ mmseqs touchdb --touch-lock                                                                                                                                                                                                                                     
usage: mmseqs touchdb <i:DB> [options]
 By Martin Steinegger <martin.steinegger@snu.ac.kr>
options: common:
 --threads INT   Number of CPU-cores used (all by default) [64]
 -v INT          Verbosity level: 0: quiet, 1: +errors, 2: +warnings, 3: +info [3]

references:
 - Steinegger M, Soding J: MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 35(11), 1026-1028 (2017)
Unrecognized parameter "--touch-lock". Did you mean "--threads" (Threads)?

[milot-mirdita]

--touch-lock is available in git mmseqs. It's not yet part of a release yet.

[prototaxites]

I had a try with mmseqs touchdb without --touch-lock as I am not currently able to run the git version of MMSeqs, but it didn't really do anything for run times.

Is there anything else that would be worth trying? Could I just copy the database (it's about 40Gb) to /dev/shm/<process-specific-location>/ and point each MMSeqs instance at that version instead?