gatech-genemark / ProtHint

Protein hint generation pipeline for gene finding in eukaryotic genomes
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number of threads #47

Closed EricDeveaud closed 2 years ago

EricDeveaud commented 2 years ago

Hello,

prothint.py uses multiprocessing.cpu_count() to ge the max value of threads. but multiprocessing.cpu_count() is the number of cpu in the machine. But this is not the same as the number of cpu available to the process. For example, you can run in a taskset context or a batch scheduler like slurm.

see:

$ nproc
96
$ taskset -c 1 nproc
1
$ taskset -c 1 python3 -c "import multiprocessing; print(multiprocessing.cpu_count())"
96

I would suggest to use len(os.sched_getaffinity(0)) instead of multiprocessing.cpu_count()

$ python3 -c "import os; print(len(os.sched_getaffinity(0)))"
96
$ taskset -c 1 python3 -c "import os; print(len(os.sched_getaffinity(0)))"
1

regards

Eric

tomasbruna commented 2 years ago

Thanks, Eric, that makes sense. Added.