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NUStatBioinfo / DegNorm

Normalizing RNA degradation in RNA-seq data
https://nustatbioinfo.github.io/DegNorm/
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CPU usage #23

Closed josruirod closed 5 years ago

josruirod commented 5 years ago

Hi, Thank you for your development. I have tried to use your program in a shared cluster but I'm finding that at some steps it seem to ignore the -p argument and use all the available resources, particularly in the iterations. In my circumstances, this behaviour makes not possible to use it right now. Do you have any comment? Could this be fixed?

Thank you

ffineis commented 5 years ago

Hello, thx for using DegNorm. Sure, I'll look into it and get back to you soon.

ffineis commented 5 years ago

I made the following changes in https://github.com/NUStatBioinfo/DegNorm/pull/24, it updates the default number of threads to 1 (changed from max available resources - 1). Pull updates from master and reinstall?

That said, you will need the ability to run at least 2 concurrent processes because we call the subprocess module and launch subprocesses to do things like check for the availability of certain software, using samtools, and using pandoc.

josruirod commented 5 years ago

Ok great, thanks for your support. Yes, no problem with using 2 or more threads, but I cannot use all of them. I'll test it and let you know if something is not working.

Thanks

ffineis commented 5 years ago

Wondering if this issue is resolved? Can we close out?

josruirod commented 5 years ago

Yes it can be closed. Thanks for the support