[Swift-commit] r5899 - SwiftApps/CMTS/dimers

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-08-10 12:22:52 -0500 (Fri, 10 Aug 2012)
New Revision: 5899

Modified:
   SwiftApps/CMTS/dimers/README
Log:
Added readme


Modified: SwiftApps/CMTS/dimers/README
===================================================================
--- SwiftApps/CMTS/dimers/README	2012-08-10 16:44:54 UTC (rev 5898)
+++ SwiftApps/CMTS/dimers/README	2012-08-10 17:22:52 UTC (rev 5899)
@@ -0,0 +1,70 @@
+Dimers Swift Scripts
+====================
+
+Prerequisites
+-------------
+This README will assume that runs will be started from 
+makena.uchicago.edu.
+
+Please ensure that Swift is in your $PATH. 
+
+Add the following line to $HOME/.bashrc to set the PATH:
+-----
+export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/opt/torque/bin:$PATH
+-----
+
+You will need to create a directory called /scratch/<yourusername>:
+-----
+mkdir /scratch/yourusername
+cd /scratch/yourusername
+-----
+
+IMPORTANT: Please note that runs may fail if started from /home due to some 
+potential NFS issues, so please make sure to always use /scratch.
+
+
+Checking out scripts from SVN
+-----------------------------
+From within your scratch directory, run the following command to get the
+dimers scripts:
+ 
+-----
+svn checkout https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/CMTS/dimers
+-----
+
+These scripts can periodically be updated by running an SVN update within
+the dimers directory:
+-----
+svn update
+-----
+
+How to Run
+----------
+The rundimers.sh script is used to start a run. The options you pass to 
+this script will determine how the dimers script runs.
+
+Usage: rundimers.sh [-s sitename] 
+
+The sitename option determines where a run will take place. Currently, the
+only tested options are "makena" and "grotthuss".
+
+Example:
+
+-----
+./rundimers.sh -s makena
+-----
+
+When your job has finished running for the first time, you will see that a directory 
+has been created called run001. A new directory will be created each time you run 
+the rundimers.sh script.
+
+Outputs
+-------
+Within each run<NNN> directory is a subdirectory called output. This directory will
+contain all relevent outputs created during the run. 
+
+Logs
+----
+Within each run<NNN> directory is a subdirectory called logs. This directory contains
+the standard output and standard error logs from each namd task. If you notice a job
+is failing, reference these files for more detail about what went wrong.