GPU optimization #1

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1. BeneKenobi commented on Mar 10, 2023

   

   BeneKenobi

   on Mar 10, 2023

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   Why do you use less gpu_runners_per_device in

   guppy_on_slurm/runbatch_gpu_guppy.sh

   Line 42 in d373459

   gpu_params='--compress_fastq --num_callers 4 --gpu_runners_per_device 4 --chunks_per_runner 512 --chunk_size 3000'

   ? Where there problems with more runners?
2. colindaven commented on Mar 10, 2023

   

   colindaven

   on Mar 10, 2023

   Last edited by colindaven

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   I don't think there was a problem with more runners, it was maybe just set for a different GPU. You need to play with the settings to reach the optimal speed for your GPU, and not everyone has a A100 with 40 GB GPU RAM.

   Just monitor the GPU device usage and RAM using nvidia-smi.

   Remember IO has a big impact, so storing fast5 files on SSD or other fast storage can decrease runtime a lot (36h to 24h for a human genome).

   👍React with 👍1Reacted by Benedikt Schnur