[Swift-commit] r5890 - in SwiftApps/CMTS/rmsd: . docs/figures

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-08-03 15:26:46 -0500 (Fri, 03 Aug 2012)
New Revision: 5890

Added:
   SwiftApps/CMTS/rmsd/docs/figures/fig-distrib.png
   SwiftApps/CMTS/rmsd/docs/figures/fig-local.png
   SwiftApps/CMTS/rmsd/docs/figures/fig-multilocal.png
Removed:
   SwiftApps/CMTS/rmsd/docs/figures/fig.distrib.png
   SwiftApps/CMTS/rmsd/docs/figures/fig.local.png
   SwiftApps/CMTS/rmsd/docs/figures/fig.multilocal.png
Modified:
   SwiftApps/CMTS/rmsd/README
Log:
Some updates to README for running across multiple sites
PDF generation was choking on image names in the format of first.second.png - renamed figures


Modified: SwiftApps/CMTS/rmsd/README
===================================================================
--- SwiftApps/CMTS/rmsd/README	2012-08-02 22:49:31 UTC (rev 5889)
+++ SwiftApps/CMTS/rmsd/README	2012-08-03 20:26:46 UTC (rev 5890)
@@ -4,12 +4,11 @@
 Prerequisites
 -------------
 This README will assume that runs will be started from 
-makena.uchicago.edu.
+makena.uchicago.edu or grotthuss.uchicago.edu
 
 Please ensure that namd2, vmd, and Swift are in your $PATH. These
 applications must be available from the Makena worker
-nodes (applications kept in /state do not seem to be
-available by the worker nodes).
+nodes.
 
 Add the following line to $HOME/.bashrc to set the PATH:
 -----
@@ -41,15 +40,20 @@
 svn update
 -----
 
-How to Run
-----------
+Running Single Site Jobs
+------------------------
+For single site jobs, it is assumed that you are connected to the head node
+where you will be doing the run.
+
+image:figures/fig-local.png["Local", height=390, width=664]
+
 The runrmsd.sh script is used to start a run. The options you pass to 
 this script will determine how the rmsd script runs.
 
 Usage: runrmsd.sh [-s sitename] 
 
-The sitename option determines where a run will take place. Currently, the
-only tested option is "makena".
+The sitename option determines where a run will take place. Currently,
+there are valid options here are "makena" and "grotthuss".
 
 Example:
 
@@ -72,3 +76,39 @@
 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.
+
+Running Remote and Multisite Jobs
+---------------------------------
+It is possible to run this script remotely across multiple sites at once. For example, a test 
+configuration exists called "makgroth" which runs jobs on both Makena and Grotthuss at the same time.
+
+Here is an example of what a configuration might look like.
+
+image:figures/fig-distrib.png["Distributed Configuration", width=700]
+
+There are two requirements for this: SSH agent forwarding must be used, and a grid certificate
+must be in place on each of the machines involved.
+
+The easiest way to set up SSH agent forwarding is to use the "-A" option to ssh. In this 
+example, let us assume that we will be running Swift on a machine called 
+bridled.ci.uchicago.edu, and sending work to grotthuss and makena. 
+
+My laptop is the machine that has the my SSH key. When I connect to bridled, I run this command:
+
+-----
+ssh -A bridled.ci.uchicago.edu
+-----
+
+This will enable me to bring my SSH key to the makena and grotthuss head nodes easily. You must also
+have $HOME/.ssh/authorized_keys setup correctly on makena/grotthuss to avoid getting prompted for a 
+password.
+
+The second thing that will be needed is a grid certificate. You have have the environment variables
+X509_CERT_DIR and X509_USER_PROXY set up to point to your certificates directory and proxy.
+
+Once this is all set up, performing the run is very similar to how you run single site jobs.
+
+-----
+./runrmsd.sh -s makgroth
+-----
+

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