sokrypton / sokrypton/ColabFold

Unable to see Memory usage on MMSeq Server

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Description

Current Behavior

I have deployed local MMseqs2 Server for ColabFold on a cloud VM with 196G of Memory and 20 Cores CPU. I also indexes in my storage. However I could not see RAM usage beyond 3Gigs for any AA sequence length of 200 to 300. I did not use vmtouch as I did not have sufficient RAM as ~1TB.

Expected Behavior

I expect to see some RAM usage so that processing time can be reduced. Is there any option I am missing. Please guide me in this

Steps to Reproduce (for bugs)

This is the command running on client side:
colabfold_batch --host-url <host_url> --model-type alphafold2_multimer_v3 --templates --amber 230aa_new.fasta output/230_aa_amber

230aa_new.fasta is a fasta file with one sequence of 23AA
I need information to change and configure the options of --prefilter-mode and --db-load-mode from the client side i.e, with colabfold_batch command or start the mmseqs2 server with different values for the options other than the default.

Environment

  • MMSEQS_COMMIT=${1:-4589151554eb83a70ff0c4d04d21b83cabc203e4}
    *BACKEND_COMMIT=${2:-14e087560f309f989a5e1feb54fd1f9c988076d5}

  • VM Specification:
    Standard E20s v5 (20 vcpus, 160 GiB memory) with Storage Type: Premium SSD LRS, Size: 3TB, Max IOPS: 7500, Max Throughput: 2500MBps, Encryption: SSE with PMK

  • Operating system and version:
    Linux (ubuntu 24.04)

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

No source file or test is named. Start with the colabfold_batch invocation and the MMseqs2 server settings for --prefilter-mode and --db-load-mode; determine where these options are configured and whether the client exposes them. Done means the supported configuration path and expected memory behavior are documented and reproducible.

Written by the indexing model from the issue text.

Assessment

Tech stack
linux
Domain
backend, bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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