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nf-core / funcscan

(Meta-)genome screening for functional and natural product gene sequences
https://nf-co.re/funcscan
MIT License
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Adapt deepBGC to use GPUs #326

Open Darcy220606 opened 8 months ago

Darcy220606 commented 8 months ago

Description of feature

Adapt deepBGC to use GPU, at the moment it uses CPU and for large input datasets takes ages to run.

jfy133 commented 7 months ago

I don't think we will be able to do this for 1.2, because of having to re-building the container or something along those lines? @Darcy220606 thoughts?

Darcy220606 commented 7 months ago

@jfy133 i was told once that we can assign a single process in the pipeline to use GPUs, in the configuration file somewhere here 

process {
  withLabel:process_low {
    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
    time = { check_max( 6.h * task.attempt, 'time' ) }
  }
jfy133 commented 7 months ago

Hmm. Ok.. but I thought the tool has to be compiled for the particular GPU yo be used? I'm speaking completely naively though... Never had to dealt with it before myself

jfy133 commented 7 months ago

Looking at deepBGC repo maybe I'm talking out of my butt...

I have a feeling though, if you are right it's about specifying this in a config file, that would imply you just send it to a node with a GPU? This would then be specific to particular clusters and thus not generally applicable within the code itself? 🤔

/Stream of consciousness