How to process results from a large-scale docking: Difference between revisions
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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 | ||
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. | 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 | |||
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