[Swift-commit] r8267 - in SwiftApps/subjobs: . rosetta

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-10-09 10:18:28 -0500 (Thu, 09 Oct 2014)
New Revision: 8267

Added:
   SwiftApps/subjobs/rosetta/
   SwiftApps/subjobs/rosetta/apps
   SwiftApps/subjobs/rosetta/cf
   SwiftApps/subjobs/rosetta/cobalt.xml
   SwiftApps/subjobs/rosetta/rosetta.swift
   SwiftApps/subjobs/rosetta/runswift.sh
Log:
adding rosetta subjob dir

Added: SwiftApps/subjobs/rosetta/apps
===================================================================
--- SwiftApps/subjobs/rosetta/apps	                        (rev 0)
+++ SwiftApps/subjobs/rosetta/apps	2014-10-09 15:18:28 UTC (rev 8267)
@@ -0,0 +1,3 @@
+localhost cat /bin/cat null null null
+cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
+

Added: SwiftApps/subjobs/rosetta/cf
===================================================================
--- SwiftApps/subjobs/rosetta/cf	                        (rev 0)
+++ SwiftApps/subjobs/rosetta/cf	2014-10-09 15:18:28 UTC (rev 8267)
@@ -0,0 +1,6 @@
+use.provider.staging=false
+wrapperlog.always.transfer=false
+execution.retries=0
+provider.staging.pin.swiftfiles=false
+sitedir.keep=false
+use.wrapper.staging=false

Added: SwiftApps/subjobs/rosetta/cobalt.xml
===================================================================
--- SwiftApps/subjobs/rosetta/cobalt.xml	                        (rev 0)
+++ SwiftApps/subjobs/rosetta/cobalt.xml	2014-10-09 15:18:28 UTC (rev 8267)
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+
+<pool handle="cluster">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<profile namespace="globus" key="slots">2</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">2.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:40:00</profile>
+<profile namespace="globus" key="walltime">2050</profile>
+
+<profile namespace="globus" key="maxnodes">256</profile>
+<profile namespace="globus" key="nodegranularity">256</profile>
+<profile key="SUBBLOCK_SIZE" namespace="env">16</profile>
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
+<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">16</profile>
+
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+</config>

Added: SwiftApps/subjobs/rosetta/rosetta.swift
===================================================================
--- SwiftApps/subjobs/rosetta/rosetta.swift	                        (rev 0)
+++ SwiftApps/subjobs/rosetta/rosetta.swift	2014-10-09 15:18:28 UTC (rev 8267)
@@ -0,0 +1,21 @@
+type file;
+
+// Rosetta
+app (file _scorefile, file out, file err) rosetta (file pdb_file, int nstruct)
+{
+   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; 
+}
+
+// Files
+file pdb_files[] <filesys_mapper; location="hlac_complex", suffix=".pdb">;
+file logs[];
+
+// Run scaling tests
+foreach pdb,i in pdb_files {
+   file rosetta_output <single_file_mapper; file=strcat("logs/h0scale.", i, ".out")>;
+   file rosetta_error <single_file_mapper; file=strcat("logs/h0scale.", i, ".err")>;
+   file scorefile <single_file_mapper; file=strcat("score.",i, ".sc")>;
+   (scorefile, rosetta_output, rosetta_error) = rosetta(pdb, 2);
+   //logs[i] = rosetta_output;
+}
+

Added: SwiftApps/subjobs/rosetta/runswift.sh
===================================================================
--- SwiftApps/subjobs/rosetta/runswift.sh	                        (rev 0)
+++ SwiftApps/subjobs/rosetta/runswift.sh	2014-10-09 15:18:28 UTC (rev 8267)
@@ -0,0 +1,10 @@
+#! /bin/sh
+
+#Old method
+#qsub -A ATPESC2014 -n 512 -t 15 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml "$@"
+export COBALT_PROJ=ExM
+#New method
+/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps rosetta.swift 
+
+#A testblock run
+#qsub -A ATPESC2013 -n 32 -t 5 -q low --mode c16 --mode script testblock.sh # --disable_preboot


Property changes on: SwiftApps/subjobs/rosetta/runswift.sh
___________________________________________________________________
Added: svn:executable
   + *