[Swift-commit] r8280 - SwiftApps/subjobs

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-10-21 14:53:02 -0500 (Tue, 21 Oct 2014)
New Revision: 8280

Modified:
   SwiftApps/subjobs/README.txt
   SwiftApps/subjobs/cobalt.mira.xml
Log:
doc

Modified: SwiftApps/subjobs/README.txt
===================================================================
--- SwiftApps/subjobs/README.txt	2014-10-21 19:42:41 UTC (rev 8279)
+++ SwiftApps/subjobs/README.txt	2014-10-21 19:53:02 UTC (rev 8280)
@@ -3,20 +3,20 @@
 
 Introduction
 ------------
-This document describes an approach to run relatively smaller jobs over a
-single large block on BlueGene systems. The technique, called sub-block jobs
-lets users submit multiple, independent, smaller jobs within a single larger
-cobalt block. Sub-block jobs is a mode of running jobs on BlueGene systems
-wherein one can allocate a larger block of compute nodes and repeatedly submit
-jobs of smaller sized sub-blocks to this larger allocation.
+This document describes an approach to run multiple jobs over a single large
+block on BlueGene systems. The technique, called sub-block jobs lets users
+submit multiple, independent, varying size jobs within a single larger cobalt
+block. Sub-block jobs is a mode of running jobs on BlueGene systems wherein
+one can allocate a larger block of compute nodes and repeatedly submit jobs of
+smaller sized sub-blocks to this larger allocation.
 
-This package provides tools and scripts to run Swift applications in sub-block
-mode over the BlueGene resources. The benefit of this approach is that the
-user does not have to invoke the sub-block specific routines involving the
-details of the underlying node interconnect hardware. The approach
-transparently allow user to run jobs directly via Swift. Additionally, users
-can run multiple 'waves' of jobs asynchronously and in parallel without
-restarting the outer block.
+This package provides tools, scripts and example use-cases to run Swift
+applications in sub-block mode over the BlueGene resources. The benefit of
+this approach is that the user does not have to invoke the sub-block specific
+routines involving the details of the underlying node interconnect hardware.
+The approach transparently allow user to run jobs directly via Swift.
+Additionally, users can run multiple 'waves' of jobs asynchronously and in
+parallel without restarting the outer block.
 
 Swift sub-block jobs
 ---------------------
@@ -116,13 +116,73 @@
 NAMD
 ~~~~
 
++NAMD+ is a molecular dynamics simulation code developed at
+http://www.ks.uiuc.edu/Research/namd[uiuc]. To run NAMD example:
+
+----
+cd namd #change to the package's namd directory
+./runvesta.sh #run on vesta
+./runmira.sh  #run on mira
+----
+
+To run NAMD with a different input dataset, change the input files in the
++input_files+ directory and reflect the changes in the +namd.swift+ source code,
+especially the data definitions part:
+
+----
+file psf <"input_files/h0_solvion.psf">;
+file pdb <"input_files/h0_solvion.pdb">;
+file coord_restart <"input_files/h0_eq.0.restart.coor">;
+file velocity_restart <"input_files/h0_eq.0.restart.vel">;
+file system_restart <"input_files/h0_eq.0.restart.xsc">;
+file namd_config <"input_files/h0_eq.conf">;
+file charmm_parameters <"input_files/par_all22_prot.inp">;
+----
+
+Similarly, in order to change the scale and size of runs, make changes to the
+parameters in the sites file as described in section 1 above.
+
 Rosetta
-~~~~~~~
+~~~~~~~~
 
-Dock 6
-~~~~~~~
++Rosetta+ is a molecular http://rosie.rosettacommons.org/docking[docking]
+program used by many large-scale HPC science applications. This implementation
+shows how to run FlexPeptide Docking on ALCF systems. To run the example:
 
+----
+cd rosetta
+./runvesta.sh #run on vesta
+./runmira.sh #run on mira
+----
 
+To change scale, size and/or inputs of the run, change the location of input
+files in the Swift source file (rosetta.swift) like so:
+
+----
+file pdb_files[] <filesys_mapper; location="hlac_complex", suffix=".pdb">;
+----
+
+To change the number of generated +structs+, change the struct argument in the
+call to the rosetta app like so:
+
+----
+(scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2); //change 2 to
+desired number
+----
+
+Dock 
+~~~~~
+
+Dock is another molecular
+http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm[docking] program used by
+many applications. To run the Dock example:
+
+----
+cd dock
+./runvesta.sh #run on vesta
+./runmira.sh #run on mira
+----
+
 Sub-block limitations
 ----------------------
 

Modified: SwiftApps/subjobs/cobalt.mira.xml
===================================================================
--- SwiftApps/subjobs/cobalt.mira.xml	2014-10-21 19:42:41 UTC (rev 8279)
+++ SwiftApps/subjobs/cobalt.mira.xml	2014-10-21 19:53:02 UTC (rev 8280)
@@ -4,7 +4,7 @@
 <pool handle="cluster">
 <execution provider="coaster" jobmanager="local:cobalt" />
 
-<profile namespace="globus" key="slots">2</profile>
+<profile namespace="globus" key="slots">1</profile>
 <profile namespace="globus" key="mode">script</profile>
 
 <profile namespace="karajan" key="jobThrottle">2.99</profile>