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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Megalodon spawns 26 processes despite specifying 16 processes at runtime #314

Open bbyrns opened 2 years ago

bbyrns commented 2 years ago

Hello, I am attempting to run Megalodon in an HPC environment (SLURM scheduler). I am specifying --processes 16 in my megalodon command, but the software is spawning 26 processes causing it to be severely overcommitted in terms of CPU resources. Is it possible to make the software use only the number of processes requested? Thanks!

marcus1487 commented 2 years ago

The --processes argument really specifies the number of "workers" for the compute intensive tasks. A number of other less compute intensive processes are spawned in order to handle data IO among other tasks.Though 26 processes are spawned the --processes argument should specify approximately the usage required.