[Swift-commit] r5940 - in SwiftApps/CMTS/scaling: . input_files

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-09-20 15:07:35 -0500 (Thu, 20 Sep 2012)
New Revision: 5940

Added:
   SwiftApps/CMTS/scaling/README
Modified:
   SwiftApps/CMTS/scaling/input_files/h0_eq.conf
   SwiftApps/CMTS/scaling/namd_wrapper.sh
Log:
Increase the length of the simulation
Add README


Added: SwiftApps/CMTS/scaling/README
===================================================================
--- SwiftApps/CMTS/scaling/README	                        (rev 0)
+++ SwiftApps/CMTS/scaling/README	2012-09-20 20:07:35 UTC (rev 5940)
@@ -0,0 +1,99 @@
+CMTS namd scaling tests
+=======================
+
+Overview
+--------
+This set of scripts submits jobs over different 
+numbers of CPUs in order to test scaling of a
+NAMD simulations.
+
+The user needs to supply the following files:
+NAMD psf file (h0_solvion.psf)
+NAMD pdb file (h0_solvion.pdb)
+CHARMM parameter files (par_all22_prot.inp)
+NAMD coordinate restart file (h0_eq.0.restart.coor)
+NAMD velocity restart file (h0_eq.0.restart.vel)
+NAMD system restart file (h0_eq.0.restart.xsc)
+
+These files are all located in the input_files directory.
+When the script is run, it creates configuration files
+from the template and then submits an individual job for
+each "number of nodes".
+
+When all of the jobs have run, plot.sh
+will create the data file scale.dat, which will have
+the number of CPUs and days/ns for job. 
+
+Prerequisites
+-------------
+This README will assume that runs will be started from 
+grotthuss.uchicago.edu or midway.rcc.uchicago.edu.
+
+Please ensure that namd2 and Swift are in your $PATH. These
+applications must be available from worker nodes.
+
+Grotthuss
+~~~~~~~~~
+To run on grotthuss, add the following line to $HOME/.bashrc to set the PATH:
+export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/Network/Servers/vothfile.uchicago.edu/home/davidk/namd_2.8-intel-openmpi:/Network/Servers/vothfile.uchicago.edu/home/davidk/vmd:/opt/torque/bin:$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.
+
+Midway
+~~~~~~
+To run the scaling scripts on midway, add the following lines to your .bashrc
+to load the appropriate modules:
+-----
+module load swift/trunk
+module load namd
+-----
+
+Checking out scripts from SVN
+-----------------------------
+From within your scratch directory, run the following command to get a
+rmsd scripts:
+ 
+-----
+svn checkout https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/CMTS/scaling
+-----
+
+These scripts can periodically be updated by running an SVN update within
+the scaling directory:
+-----
+svn update
+-----
+
+Running Scaling tests
+---------------------
+The runscaling.sh script is used to start a run. The options you pass to 
+this script will determine how the scaling script runs.
+
+Usage: runscaling.sh [-s sitename] 
+
+The sitename option determines where a run will take place. Currently,
+there are valid options here are "grotthuss" and "midway".
+
+Example:
+
+-----
+./runscaling.sh -s grotthuss
+-----
+
+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 runscaling.sh script.
+
+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.
+

Modified: SwiftApps/CMTS/scaling/input_files/h0_eq.conf
===================================================================
--- SwiftApps/CMTS/scaling/input_files/h0_eq.conf	2012-09-20 18:32:34 UTC (rev 5939)
+++ SwiftApps/CMTS/scaling/input_files/h0_eq.conf	2012-09-20 20:07:35 UTC (rev 5940)
@@ -104,4 +104,4 @@
 ## EXECUTION SCRIPT                                        ##
 #############################################################
 
-run 500
+run 5000

Modified: SwiftApps/CMTS/scaling/namd_wrapper.sh
===================================================================
--- SwiftApps/CMTS/scaling/namd_wrapper.sh	2012-09-20 18:32:34 UTC (rev 5939)
+++ SwiftApps/CMTS/scaling/namd_wrapper.sh	2012-09-20 20:07:35 UTC (rev 5940)
@@ -5,4 +5,4 @@
 
 echo Arguments are: $@
 sed -e "s/_JOB_/$numNodes/g" h0_eq.conf > $namdConf
-mpiexec -machinefile $PBS_NODEFILE namd2 $namdConf
+mpiexec namd2 $namdConf