Difference between revisions of "MUD - Michael's Utilities for Docking"

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*Main Workflow
 
*Main Workflow
#Submit a parallel job to the cluser
+
*Submit a parallel job to the cluser
 
  $mud/submit.csh
 
  $mud/submit.csh
<p>Uses 'dirlist' to determine which directories to run. Similar to startdockbksX, but also indicates job submission by touching a submitted file in each directory.
+
Uses 'dirlist' to determine which directories to run. Similar to startdockbksX, but also indicates job submission by touching a submitted file in each directory.
#Check parallel job status
+
*Check parallel job status
 
  $mud/check.py
 
  $mud/check.py
 
Indicates the status of unfinished (or unsubmitted) jobs. Note that it simply returns nothing if everything is finished.
 
Indicates the status of unfinished (or unsubmitted) jobs. Note that it simply returns nothing if everything is finished.
#Restart all failed subjobs
+
*Restart all failed subjobs
 
  $mud/restart.py
 
  $mud/restart.py
 
This works even if some subjobs are still running. Occasionally, however, jobs can fail with no detectable remnants. To force those jobs to restart you can use the -f option, but beware that this will also restart all subjobs that are still running.
 
This works even if some subjobs are still running. Occasionally, however, jobs can fail with no detectable remnants. To force those jobs to restart you can use the -f option, but beware that this will also restart all subjobs that are still running.

Revision as of 08:42, 29 October 2008

What's in MUD?

  • Tools to start, check, and restart dock jobs
  • Tools to combine, enrich, plot, and view docking results

Setting up MUD

  • For convenience, point a shell variable to the base mud directory to save typing
set mud=~mysinger/code/mud/trunk
  • If you use MUD a lot, you can add this to your ~/.login
  • Then simply run commands like this:
$mud/submit.csh
$mud/check.py -h
  • Use -h or --help to get full help information for the .py (python) scripts
  • The .csh scripts will automatically print usage information if mis-used
  • The scripts automatically use their invocation path to find other scripts and libraries they depend on.

Job Control

  • Main Workflow
  • Submit a parallel job to the cluser
$mud/submit.csh

Uses 'dirlist' to determine which directories to run. Similar to startdockbksX, but also indicates job submission by touching a submitted file in each directory.

  • Check parallel job status
$mud/check.py

Indicates the status of unfinished (or unsubmitted) jobs. Note that it simply returns nothing if everything is finished.

  • Restart all failed subjobs
$mud/restart.py

This works even if some subjobs are still running. Occasionally, however, jobs can fail with no detectable remnants. To force those jobs to restart you can use the -f option, but beware that this will also restart all subjobs that are still running.

Other more specialized commands

  • Submit a single directory to the cluster
$mud/subsge_single.csh
  • Submit a single directory to the local machine
$mud/sublocal.csh
  • Remove docking output leaving only input - will even DELETE finished jobs
$mud/clean.py
  • Restart single directory
$mud/restartdir.py

Job Analysis