sokrypton / sokrypton/ColabFold
Required DB's for GPU Server setup
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Description
Main question is -What Is a must to be downloaded to the local disk for gpuserver mode setup ?
regarding Optional GPU server for enhanced performance ->
I'm confused as what being loaded to GPU vRAM compared to local /path/to/db on disk
GPU vRAM is no near close to local SSD size .. what am i missing ?
GPU vRAM is ~15GB for colabfold_envdb_202108_db and uniref30_2302_db
(mmseqs gpuserver ./colabfold_envdb_202108_db ...)
--
local disk size Is around ~800GB for both DB's
(.venv) [ec2-user@ip-10-4-28-230 db]$ du -ch uniref30_2302_db_seq* | grep total$
182G total
(.venv) [ec2-user@ip-10-4-28-230 db]$ du -ch colabfold_envdb_202108_db* | grep total$
597G total
using colabfold_search I'm specifying both local db path and gpu-server option
colabfold_search <input.fasta> <db_path> <results> --gpu 1 --gpu-server 1
I've use setup_databases.sh from ColabFold repo (Link) which download all DB's ?
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 README section on optional GPU server setup and the referenced setup_databases.sh script. Compare the database paths used by colabfold_search with the GPU-server option, then document which files are required on local disk versus GPU VRAM and what a complete setup_databases.sh download provides.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- shell
- Domain
- bioinformatics, databases, documentation
- Issue type
- Documentation
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100