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.
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
- 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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First steps
- Read the whole issue, then the project's contributing guide.
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- 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