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

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

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

<pre><code>top -c -u username
</code></pre>

<p>or for OSX <code>top -u</code></p>

<p>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.</p>

CC BY-SA 4.0
2019-09-23T11:50:22.370Z
2019-09-23T11:55:57.763Z
2019-09-23T11:55:57.763Z
M__
<p>I am running dmpfold, "seq2maps.sh" and from a few days the program is at the "PSICOV" stage:</p>

<pre><code>psicov -z 15 -o -d 0.03 tail-fiber-sequence.aln
</code></pre>

<p>"ps aux" gives me this:</p>

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

<p>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</p>

<protein-structure>
A program "PSICOV" "stopped" from a few days on Ubuntu 18.04?
# A program "PSICOV" "stopped" from a few days on Ubuntu 18.04?

(Asked by: username_0 on 2019-09-23)

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

**Tags:** protein-structure

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## 1 answers

### Answer by username_1 on 2019-09-23. Score: 0 | Accepted answer

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.


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