[Swift-commit] r8326 - in SwiftApps: ematter subjobs

ketan at ci.uchicago.edu ketan at ci.uchicago.edu
Thu Dec 11 10:24:01 CST 2014


Author: ketan
Date: 2014-12-11 10:24:00 -0600 (Thu, 11 Dec 2014)
New Revision: 8326

Modified:
   SwiftApps/ematter/apps
   SwiftApps/ematter/cf
   SwiftApps/ematter/runbgq
   SwiftApps/ematter/sites.cobalt-local.xml
   SwiftApps/ematter/workflow.bgq.swift
   SwiftApps/subjobs/bg.sh
Log:
changes for bgq

Modified: SwiftApps/ematter/apps
===================================================================
--- SwiftApps/ematter/apps	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/ematter/apps	2014-12-11 16:24:00 UTC (rev 8326)
@@ -3,6 +3,7 @@
 localhost bash /bin/bash null null null
 #
 cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
+#cluster strace strace null null null
 cluster2 bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
 #
 blues lammps lmp_blues null null null

Modified: SwiftApps/ematter/cf
===================================================================
--- SwiftApps/ematter/cf	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/ematter/cf	2014-12-11 16:24:00 UTC (rev 8326)
@@ -1,4 +1,4 @@
-use.provider.staging=true
+use.provider.staging=false
 wrapperlog.always.transfer=false
 execution.retries=0
 provider.staging.pin.swiftfiles=false

Modified: SwiftApps/ematter/runbgq
===================================================================
--- SwiftApps/ematter/runbgq	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/ematter/runbgq	2014-12-11 16:24:00 UTC (rev 8326)
@@ -1,4 +1,4 @@
 #! /bin/sh
 
 /home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.cobalt-local.xml -config cf -tc.file apps workflow.bgq.swift
-#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt-local.xml -config cf -tc.file apps workflow.swift
+#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.cobalt-local.xml -config cf -tc.file apps workflow.bgq.swift

Modified: SwiftApps/ematter/sites.cobalt-local.xml
===================================================================
--- SwiftApps/ematter/sites.cobalt-local.xml	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/ematter/sites.cobalt-local.xml	2014-12-11 16:24:00 UTC (rev 8326)
@@ -7,14 +7,15 @@
 <profile namespace="globus" key="slots">1</profile>
 <profile namespace="globus" key="mode">script</profile>
 
-<profile namespace="karajan" key="jobThrottle">0.99</profile>
+<profile namespace="karajan" key="jobThrottle">20.99</profile>
 <profile namespace="karajan" key="initialScore">10000</profile>
 <profile namespace="globus" key="maxwalltime">00:55:00</profile>
 <profile namespace="globus" key="walltime">3500</profile>
 <profile namespace="globus" key="maxTime">3500</profile>
 
-<profile namespace="globus" key="maxnodes">32</profile>
-<profile namespace="globus" key="nodegranularity">32</profile>
+<profile namespace="globus" key="maxnodes">128</profile>
+<profile namespace="globus" key="nodegranularity">128</profile>
+
 <profile key="SUBBLOCK_SIZE" namespace="env">8</profile>
 
 <!--
@@ -23,14 +24,12 @@
 <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="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">16</profile>
 
-<profile namespace="globus" key="jobsPerNode">4</profile>
-
 <workdirectory>/home/ketan/swiftwork</workdirectory>
 <filesystem provider="local"/>
-
 </pool>
 <pool handle="localhost">
 <execution provider="coaster" url="none" jobmanager="local:local" />

Modified: SwiftApps/ematter/workflow.bgq.swift
===================================================================
--- SwiftApps/ematter/workflow.bgq.swift	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/ematter/workflow.bgq.swift	2014-12-11 16:24:00 UTC (rev 8326)
@@ -2,7 +2,7 @@
 
 // Lammps app definition
 app (file _dump) lammps_app (string _lammps_exe, file _in,
-                            file _geo, file _eam)
+                                        file _geo, file _eam)
 {
    bgsh _lammps_exe "-in" @_in; 
 }
@@ -70,7 +70,7 @@
 }
 
 /* == Input files definitions: Make sure these files are available in the current directory == */
-file lammps_in <"in.lammps">;
+file lammps_in <"input.lammps">;
 file lammps_geo <"AuTiO.geo">;
 file lammps_eam <"Au_u3.eam">;
 
@@ -95,6 +95,7 @@
 /* == Output files definitions == */
 file xyz <"forsmeagol.xyz">;
 file lammps_dump <"lammps.dump">;
+file lammps_out <"lammps.stdout">;
 file fdf_proc<"input_proc.fdf">;
 
 file smeagol_lead_out <"smeagol_out/smeagol.lead.out">;
@@ -110,13 +111,11 @@
 
 string Vs[]=["0.1","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9","1.0"];
 
+
 //Invoke lammps
 (lammps_dump) = lammps_app (lammps_exe, lammps_in,
                             lammps_geo, lammps_eam);
 
-//Invoke pizza
-(xyz) = pizza_app(pizza_src, lammps_dump);
-
 //Invoke smeagol lead
 (au3dm, au3hst, 
  bulklft, bulkrgt,
@@ -125,7 +124,10 @@
                                        opsf, osicpsf,
                                        tipsf, tisicpsf);
 
+//Invoke pizza
+(xyz) = pizza_app(pizza_src, lammps_dump);
 
+
 //Invoke smeagol transport V0
 (tio2auhm, tio2audm, 
  smeagol_transport_out) = smeagol_v0_app(smeagol_exe, au3dm,
@@ -139,7 +141,7 @@
 
 foreach v,i in Vs
 {
-/* == generate fdfs for different voltages == */
+// == generate fdfs for different voltages ==
 string fdfname = strcat("input_", v, ".fdf");
 file fdf_proc_vn <single_file_mapper; file=fdfname>;
 
@@ -157,4 +159,3 @@
 
 
 }
-

Modified: SwiftApps/subjobs/bg.sh
===================================================================
--- SwiftApps/subjobs/bg.sh	2014-12-11 03:21:32 UTC (rev 8325)
+++ SwiftApps/subjobs/bg.sh	2014-12-11 16:24:00 UTC (rev 8326)
@@ -1,4 +1,4 @@
-#! /bin/bash
+#!/bin/bash
 
 mname=$(hostname)
 
@@ -56,14 +56,19 @@
     echo "$0": running runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
     
     #without timeout
-    runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+    #strace -o "$HOME/strace.runjob.out" runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+    #runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+    runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np 2 : "$@"
     
     echo "Runjob finished."
 else
     # run w/o subblocks if no subblock size provided
     echo "Running in nonsubblock mode."
     echo "$0": running runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
+    #strace -o "$HOME/strace.runjob.out" runjob --strace none -p 16 --block $COBALT_PARTNAME : "$@"
     runjob -p 16 --block $COBALT_PARTNAME : "$@"
+
     echo "Finished Running in nonsubblock mode."
 fi
 exit 0




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