Comments (6)
Which commit is this? I did a lot of refactoring today and might have broken something.
However, this does looks more like a foldseek issue and not server issue. What are you searching?
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I think I currently have commit 00f89de checked out?
commit 00f89de8fa191bf3824d07aea24c86c80117f148 (HEAD -> master, origin/master, origin/HEAD)
Author: Milot Mirdita <[email protected]>
Date: Mon Apr 29 17:31:51 2024 +0900
Another try to fix chain names
I'm searching one of my structures (a small protein ~ 50 AA) against the PDB structure database as a test that my setup is functional. I've run this search many times with previous commits without any issues but I saw new updates on the foldseek server so re-cloned the repo to implement them locally
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I tested the same sequence on the public server and this ran without error. Is the public server using your latest commits or a previous commit that I could roll back to?
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Did you rebuilt the docker containers or are you using the containers downloaded from GHCR? Can you try to do a docker compose pull
within the docker-compose
directory to make sure you are also on the latest GHCR container?
(This is the exact setup that the server is using).
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Apologies, I now think that this is relating to my setup. I'm running this inside a Multipass VM (Ubuntu 22.04) and observing the Segmentation fault (core dumped)
error, however when I replicate in WSL2 the search runs perfectly. I will need to figure out why this happens in the VM but not WSL2... Any thoughts? I have allocated 12 Gb of memory to the VM and there is sufficient disk space
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I have no idea about multipass, but I've seen issues with SIMD support and VMs before. Make sure you are using whatever "host" cpu mode multipass might offer.
It's likely that the VM claims to support AVX2 in the /proc/cpuinfo, however then doesn't correctly expose the instructions.
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Related Issues (20)
- local colabfold_batch cannot communicate with local mmseq2 web api HOT 19
- Full target/query alignment being truncated in web UI HOT 3
- docker install error: ghcr.io pull error HOT 7
- pairaln mode does not support the binary version of the taxonomy files HOT 5
- mmseqs-server: errors when called from colabfold_batch HOT 2
- App does not work with latest mmseqs version HOT 2
- Pass --max-seqs through GUI or server API?
- Implement three diferent states for visualizing query structure in Structure Viewer
- Possible to add single or multiple sequences to existing database
- Temporary redirect issue HOT 6
- Foldseek all database view rework
- Running it in kubernetes HOT 4
- Historical jobs not loaded: "Job failed. Please try again later."
- jobs stuck in PENDING status with local mmseqs-web API HOT 2
- "docker-compose run db-setup PDB" not working HOT 2
- host not found in upstream "mmseqs-web-api HOT 7
- "405 Not Allowed" returned for the queries HOT 4
- Foldseek jobs are not persistent from GUI HOT 5
- docker-compose run db-setup XXX fails due to no space left on device
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