Difference between revisions of "How to process results from a large-scale docking"

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(Created page with "Written by Jiankun Lyu, 20171018 == Check for completion and resubmit failed jobs == In a large calculation such as this one with tens of thousands of separate processes, it...")
 
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Written by Jiankun Lyu, 20171018
 
Written by Jiankun Lyu, 20171018
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This tutorial uses the DOCK3.7.1rc1.
  
 
== Check for completion and resubmit failed jobs ==
 
== Check for completion and resubmit failed jobs ==
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  csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh
 
  csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh
  
This script puts all the directories of failed jobs in a file called dirlist_new. Before resubmiting those jobs, I
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This script puts all the directories of failed jobs in a file called dirlist_new.
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mv dirlist dirlist_ori
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mv dirlist_new dirlist
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Then resubmit them
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$DOCKBASE/docking/submit/submit.csh
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== Combine Results ==
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python $DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt 1000

Revision as of 18:49, 18 October 2017

Written by Jiankun Lyu, 20171018

This tutorial uses the DOCK3.7.1rc1.

Check for completion and resubmit failed jobs

In a large calculation such as this one with tens of thousands of separate processes, it is not unusual for some jobs to fail for some reason. Checking for successful completion, and re-starting failed processes, is a normal part of running such a large job.

Run the script below in your docking directory

csh /nfs/home/tbalius/zzz.github/DOCK/docking/submit/get_not_finished.csh

This script puts all the directories of failed jobs in a file called dirlist_new.

mv dirlist dirlist_ori
mv dirlist_new dirlist

Then resubmit them

$DOCKBASE/docking/submit/submit.csh

Combine Results

python $DOCKBASE/analysis/extract_all_blazing_fast.py dirlist extract_all.txt 1000