Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-23T11:50:22.370Z
Answers.LastActivityDate: 2019-09-23T11:55:57.763Z
Answers.LastEditDate: 2019-09-23T11:55:57.763Z
Answers.UserDisplayName: M__
Body: <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>
  
Tags: <protein-structure>
Title: A program "PSICOV" "stopped" from a few days on Ubuntu 18.04?
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  