sokrypton / sokrypton/ColabFold
Specifications for local mmseqs server
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Description
More a question than an issue. I'm in the purchasing phase for a local mmseqs server and vendor asks for CPU specs etc. etc.
From the Readme I know:
(2) single query searches require the full index (the .idx files) to be kept in memory. This can be done with e.g. by using vmtouch. Thus, this type of search requires a machine with at least 768GB RAM for the ColabfoldDB
My plan is to use colabfold_batch --host-url myserver and submit the gpu part to our Slurm cluster. "myserver" should be strong enough. Would be 768G as a "minimum" sufficient or should I go higher? How many CPUs/Cores etc. should I order?
Are there any recommendations for CPU, SSD etc.? Which hardware is the public mmseqs server running on?
Should I ask this question in the mmseqs2-App repo?
Thanks for your recommendations in advance!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the README's ColabFoldDB memory guidance and the referenced mmseqs2-App context; no files, tests, or code entry points are named. Done would require a maintainer-provided hardware recommendation or documentation update covering memory, CPU, storage, and the appropriate repository.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 15/100