I have a script compute_all_matrices.sh which launches deepTools' computeMatrix for a whole bunch of different files with various option. The user manual for computeMatrix states:

--numberOfProcessors INT, -p INT

Number of processors to use. Type "max/2" to use half the maximum number of processors or "max" to use all available processors. (default: 1)

I'd like to use up to 8 processors for each one, one after the other, and there are other people using these processors so I can't take them all. However, when I check on htop, it looks like the script compute_all_matrices.sh is only using one processor.

Is there any way to allow the "superscript" to use multiple processors for its "subscripts"?


I am usure why, but apparently my superscript was using all of the processors, just not all of the time. I think I must have only checked the state of CPU usage when it was using only 1 processor. Is this possible? If so, I believe that this question can be closed.

  • have you tried -p 2 ? perhaps a snippet of the invocation of computeMatrix would help. – D'Arcy Nader Jan 14 at 15:13
  • @D'ArcyNader I don't see why -p 2 would change anything, there are 24 total available, and right now it's just me using them. What do you mean by a snippet of its invocation? – Whitehot Jan 14 at 16:15
  • 2
    The script would only ever run on a single CPU. What does htop tell you about your computeMatrix job? – Kusalananda Jan 14 at 16:31
  • @Kusalananda This may have been what confused me. I'm pretty sure computeMatrix was running on just one processor when I checked, but it may have been just for one phase of it, or it could have been that I was in fact compute_all_matrices.sh that was running on just the one. – Whitehot Jan 15 at 12:15

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