How to constrain Scalismo to run on some cores on a HPC

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herve nicolas

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Jun 15, 2022, 12:41:57 PM6/15/22
to scalismo
Dear all,

While running Scalismo on the HPC, with a fixed number of cores it appears that, the job (I assume java) takes all cores on a node causing conflicts with other jobs.

I am wondering if someone has faced this situation before and/or has a solution to constrain the job on some cores.

I have passed the following java commands in my bash script to address the problem (assuming the problem is related to java garbage collectors) without success.
--XX:ParallelGCThreads=1  -XX:ConcGCThreads=1


P.S.  It is not a Scalismo problem, but if someone has an idea to share, it will be appreciated.


Kind regards,
Nicolas

Marcel Luethi

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Jun 16, 2022, 3:01:15 AM6/16/22
to herve nicolas, scalismo
Hi Herve,

Have you tried: -XX:ActiveProcessorCount=2 ?

Best regards

Marcel

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herve nicolas

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Jun 17, 2022, 10:18:22 AM6/17/22
to Marcel Luethi, scalismo
Hi Marcel,

Thank you for the command.

I tried that without success, the program keep taking more cores than the requested.

I insert these commands in my bash script where I manage the Java heap size, but I get the same behavior because more cores are used

Kind regards,
Nicolas

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Best regards,
Hervé Nicolas NBONSOU T.,
PhD candidate in Biomedical Engineering, University of Cape Town, South Africa,
M.Sc in Physics (Materials and Mechanics), M.Sc in Mathematical Sciences (AIMS)
skype: hnbonsou
Twitter: @Nicolas_Nbonsou
Phone number: +27 664 910 500
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