[Swift-commit] r8286 - SwiftApps/subjobs

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-10-22 11:27:11 -0500 (Wed, 22 Oct 2014)
New Revision: 8286

Modified:
   SwiftApps/subjobs/README.txt
Log:
doc changes

Modified: SwiftApps/subjobs/README.txt
===================================================================
--- SwiftApps/subjobs/README.txt	2014-10-22 16:07:02 UTC (rev 8285)
+++ SwiftApps/subjobs/README.txt	2014-10-22 16:27:11 UTC (rev 8286)
@@ -124,7 +124,9 @@
 ~~~~
 
 +NAMD+ is a molecular dynamics simulation code developed at
-http://www.ks.uiuc.edu/Research/namd[uiuc]. To run NAMD example:
+http://www.ks.uiuc.edu/Research/namd[uiuc]. The Swift source and configuration
+files along with application inputs can be found in the +namd+ directory in the
+subjobs pacjage. To run NAMD example:
 
 ----
 cd namd #change to the package's namd directory
@@ -153,8 +155,10 @@
 ~~~~~~~~
 
 +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:
+toolkit with many related programs used by many large-scale HPC science
+applications. This implementation shows how to run +FlexPeptide Docking+ on
+ALCF systems. The Swift scripts, configuration and application specific inputs
+are found in the +rosetta+ directory. To run the example:
 
 ----
 cd rosetta
@@ -163,26 +167,36 @@
 ----
 
 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:
+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:
+In the above line all +.pdb+ files in the directory +hlac_complex+ will be
+processed in parallel. Change the +location+ from +hlac_complex+ to where you
+have your input files.
 
+To change the number of generated +structs+ by Flexpep Docking program, change
+the struct argument in the call to the rosetta application like so:
+
 ----
-(scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2); //change 2 to
-desired number
+(scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2);
 ----
 
+In the above line, the number +2+ indicates the number of +structs+ to be generated by the docking. Change this value to the desired size to change the desired number of +structs+. To make changes to other parameters, make changes to the commandline as invoked in the +app+ definition in the Swift script like so:
+
+----
+bgsh "/home/ketan/openmp-gnu-july16-mini/build/src/debug/linux/2.6/64/ppc64/xlc/static-mpi/FlexPepDocking.staticmpi.linuxxlcdebug" "-database" "/home/ketan/minirosetta_database" "-pep_refine" "-s" @pdb_file "-ex1" "-ex2aro" "-use_input_sc" "-nstruct" nstruct "-overwrite" "-scorefile" @_scorefile stdout=@out stderr=@err;
+----
+
 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:
+Dock is another molecular docking
+http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm[program] used by many
+applications. The Swift source, configuration and application related inputs
+can be found in the +dock+ directory. To run the Dock example:
 
 ----
 cd dock
@@ -195,11 +209,11 @@
 
 There are currently the following two limitations with sub-block jobs:
 
-. The maximum size of the outer cobalt job must not exceed 512 nodes, ie. half
-rack.
+. The maximum size of the outer Cobalt job must not exceed 512 nodes, ie. half
+of a hardware rack.
 
 . The successive subjobs must be submitted with a gap of at least 3 seconds in
 between. This means for a large number of shorter than 5 seconds jobs, the
-system will not be underutilized. Consequently, subblocks are suitable for
-tasks which are more than a 2 minutes in duration.
+system will be underutilized. Consequently, subblocks are suitable for
+tasks which are more than a couple of minutes in duration.