sokrypton / sokrypton/ColabFold
local colabfold_search: Ambiguity in README regarding db-load-mode with vmtouch
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Description
The README states "If the index is in memory use to --db-load-mode 3 parameter in colabfold_search to avoid index loading overhead. If they database is already in memory use --db-load-mode 2 option."
Besides some language issues here, this is not clear, right? "if index in memory use 3" and "if database is in memory use 2". Is the database and the index not the same? In the mmseqs manual p21, it uses mode 2 after mentioning the vmtouch command, but it's not clear whether vmtouch is a required step or optional and if the mode then is supposed to change.
Thanks a lot for your help.
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Review the README section describing colabfold_search's --db-load-mode 2/3 and compare it with the linked MMseqs manual and vmtouch guidance. Clarify the distinction between database and index, whether vmtouch is required or optional, and when each mode applies; done when the instructions are unambiguous.
Written by the indexing model from the issue text.
Assessment
- Domain
- cli, documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100