MUD - Michael's Utilities for Docking

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

1. 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.

1. 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.

1. 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