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.
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