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default number of CPUs #201
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Hello
fusioncatcher tools, eg
fusioncatcher.py
,blat_parallel.py
,overlap.py
, ... uses multiprocessing.cpu_count() to ge the numebr of available cpusbut 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
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