MUD - Michael's Utilities for Docking
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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