sokrypton / sokrypton/ColabFold

Running colabfold_search returns "terminate called recursively" and terminates

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Description

Hi,
I have tried running colabfold_search on a gpu device (specifically, 3 A100-80G gpus). I did the setup_databases as instructed: GPU=1 ./setup_databases.sh path/to/db. The setup was successful.

However, when I tried using it, I can't seem to get it to run to completion successfully. I have attached the log file from running it.

colabfold_github_issue.txt

Here is the code I am using:

# start a gpu server to reduce the latency when performing msa searches
mmseqs gpuserver /user/ColabFold-official-GPU/colabfold_envdb_202108_db --max-seqs 10000 --db-load-mode 2 --prefilter-mode 1 &
PID1=$!

mmseqs gpuserver /user/ColabFold-official-GPU/uniref30_2302_db --max-seqs 10000 --db-load-mode 2 --prefilter-mode 1 &
PID2=$!

time colabfold_search --mmseqs mmseqs inputs/ /user/ColabFold-official-GPU outputs/ --gpu 1 --gpu-server 1 --threads ${N_CPUS} --db-load-mode 2

# Stop the server(s) when done:
kill $PID1
kill $PID2
  1. Also, I can't seem to see the kX speedup that the GPU option offers. The log file above took 2 hours for 100s of sequences (all in .fasta format) even though it did not complete. I have tried both db-load-mode 0 and 2.

Kindly advise on how to resolve this.
Thanks

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  3. Fork the repository and make your change on a branch.
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Research direction

Review the attached colabfold_github_issue.txt log alongside the colabfold_search command and the two mmseqs gpuserver invocations. First reproduce the failure after the stated database setup and compare db-load-mode 0 and 2. Done means the search completes without recursive termination and the reported GPU performance issue is explained or resolved.

Written by the indexing model from the issue text.

Assessment

Tech stack
shell
Domain
bioinformatics, cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
30/100

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