sokrypton / sokrypton/ColabFold
Timing out when attempting to make a prediction?
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Description
First off - thank you so much for creating this amazing resource!
Expected Behavior
Receive a response from the MSA server.
Current Behavior
Timeouts when trying to query the MSA server for any protein sequence.
Steps to Reproduce (for bugs)
When trying to run colabfold-batch for any sequence, I get the below timeout error(s).
ColabFold Output (for bugs)
2024-08-29 11:03:36,940 Running colabfold 1.5.5
2024-08-29 11:03:37,350 Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: Interpreter CUDA
2024-08-29 11:03:37,351 Unable to initialize backend 'tpu': module 'jaxlib.xla_extension' has no attribute 'get_tpu_client'
2024-08-29 11:03:40,213 Running on GPU
2024-08-29 11:03:40,985 Found 9 citations for tools or databases
2024-08-29 11:03:40,986 Query 1/1: cd6a78b82fede215cdb80a797f228098a41178fdde0753728f3781e6221fb1ee (length 1167)
2024-08-29 11:03:56,000 Timeout while fetching result from MSA server. Retrying...
2024-08-29 11:05:16,019 Error while fetching result from MSA server. Retrying... (1/5)
2024-08-29 11:05:16,023 Error: HTTPSConnectionPool(host='api.colabfold.com', port=443): Read timed out.
Context
curl https://api.colabfold.com/queue returns
{"queued":0}
Your Environment
I am currently running ColabFold locally using the docker container (https://github.com/sokrypton/ColabFold/wiki/Running-ColabFold-in-Docker) on a cluster system running CentOS7, with a Tesla T4 GPU. The cluster does have access to the internet.
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 Docker setup described in the Running-ColabFold-in-Docker wiki and reproduce the colabfold-batch request against api.colabfold.com. Compare the MSA timeout output with the /queue response and the CentOS7 environment. Done would require identifying whether the failure is in the container, network path, or MSA service and documenting an actionable resolution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- centos, docker
- Domain
- api, bioinformatics, infrastructure
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100