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

From DISI
Jump to navigation Jump to search
Line 22: Line 22:
 
*Check job status
 
*Check job status
 
  $mud/check.py
 
  $mud/check.py
*Restart failed jobs
+
*Restart failed subjobs
 
  $mud/restart.py
 
  $mud/restart.py
 +
This works even if some subjobs are still running. Occasionally, however, jobs 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 08:20, 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

Job Control

  • Submit a job to the cluser

Similar to startdockbksX, but records job submission

$mud/submit.csh
  • Check job status
$mud/check.py
  • Restart failed subjobs
$mud/restart.py

This works even if some subjobs are still running. Occasionally, however, jobs 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.