google-deepmind / google-deepmind/alphafold

Memory issue when processing large protein. Is my swap not being leveraged

Open
#665 5 comments 0 reactions 0 assignees View on GitHub
out of memory
Dominant language
Python
Stars
14.9k
Forks
2.9k
PR merge metrics
No merged PRs in 30d

Description

I am running predictions for 2500 residue protein on a system with 80GB RAM, 8TB diskspace, and 1TB swap running Alphafold v2.2 via docker. The process fails with the message "RuntimeError: Resource exhausted: Out of memory while trying to allocate 51935261664 bytes." The ram was upgraded to 128GB, but the job dies with the same error.

docker stats: shows the MEM LIMIT is not including available swap. I am likely mistaken, but I thought it would... Is my swap not being leveraged by the container? How can I modify the docker image, such that when launched the container leverages swap (which I previously thought was available by default)? If I am off target, any advice would be appreciated...

Note: I have another system with 512GB RAM that no problem completing the calculations for the same protein.

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.