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 ?

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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

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