Comments (5)
EduEyras
commented on May 23, 2024
I think you can use multiple threads indicating the number of processes
with -n/--cpu
Pablo can confirm
Thanks
E.
…On Thu, 8 Sept 2022 at 11:24, YuanMei ***@***.***> wrote:
Hi developer,
Have you added multithreading function to your preprocessing program？
I give 40 cores to it, but it only uses one.
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MiphaZ
commented on May 23, 2024
Here's my setting.
python3 /data/workdir/CHEUI/CHEUI-master/scripts/CHEUI_preprocess_m5C.py -i spleen9.eventalign.txt -m /data/workdir/CHEUI/CHEUI-master/kmer_models/model_kmer.csv -o cheui_multest -n 40
But it uses few threads.
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pabloacera
commented on May 23, 2024
We are using multiprocessing module in that script, which will create the number of subprocesses indicated by the variable. My understanding is that several processes can be run in one CPU core, although is strange that they are all running in 1 core. For us it works fine using all the CPUs every in Linux OS computers and HPCs. Sorry I cannot help you further, If you find out the issue let me know or otherwise welcome to make a pull request and contribute to the code. Cheers.
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itslittman
commented on May 23, 2024
I found that -n for specifying cores only works when run in python 3.7
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MiphaZ
commented on May 23, 2024
OK, I will try in 3.7 now
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