[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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