1
$\begingroup$

I am running dmpfold, "seq2maps.sh" and from a few days the program is at the "PSICOV" stage:

psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln

"ps aux" gives me this:

daniel     26693  490  2.5 2546588 2514320 ?     Rl   سبت20 25116:58 psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln

Any idea on what could be the matter? Yes, I am runinng "rosetta" too on my 32 CPUs, so all my CPUs are covered to max 100%; howver, RAM is 93Gb and only 32 GB has been used. Thanks

$\endgroup$

1 Answer 1

0
$\begingroup$

In summary just be patient. psicov doesn't parrallelise so a tenfold increase in CPU will not hurry it along.

Also psicov is not RAM intensive given the machine you are describing, so you haven't hit a RAM bottleneck.

I don't know the ps output format you are using I'm use to seeing %CPU and %MEM from ps -aux on Susie and OSX. You should also try,

top -c -u username

or for OSX top -u

You should see the psicov happily chuntering away consuming ~100% of a single process. There is a UNIX/Linux guru specialist on BioSE who could almost certainly provide better diagnostics.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.