MUD - Michael's Utilities for Docking: Difference between revisions

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

Revision as of 08:44, 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.

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 DELETE even completed jobs
$mud/clean.py
  • Restart single directory
$mud/restartdir.py

Job Analysis