soedinglab
GPU supported databases
I was just wondering if any databases have been converted to support GPU already? I have converted uniref90 myself following the small section on that here on your github, but if you had already made all/many of the databases available in a GPU version I would much prefer to dl those.
Currently, we haven't started any plans on prebuilt GPU databases (yet). I agree that this would be useful.
Currently, you have to call makepaddedseqdb on the target database after a createdb or databases call.
See https://github.com/soedinglab/MMseqs2/wiki#gpu-accelerated-search
yes that is exactly what I have done so far on uniref90, and it took some time to process that database. I am just unsure which database (or databases) to convert like that, if I want to use it/them for MSA generation for an AF3 pipeline afterwards. any suggestions?
We plan to make MMseqs2-GPU databases available for ColabFold, which we also plan to optimize to AF3 (or to some of the free alternatives) at some point soon.
FWIW, let me know if you're interested in hosting these optimized databases on AWS. We have a program to sponsor high-impact scientific data sets (e.g. https://registry.opendata.aws/openfold/) and this would def count
@brianloyal it would be fantastic to host the database on AWS. I recall applying to AWS in the past, but unfortunately, we were rejected. Do you have any recommendations to improve our chances this time?
