[Swift-commit] r8076 - in SwiftTutorials/ATPESC_2014-08-14/subjobs: . app config hello scripts
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Mon Aug 11 17:45:12 CDT 2014
Author: ketan
Date: 2014-08-11 17:45:12 -0500 (Mon, 11 Aug 2014)
New Revision: 8076
Added:
SwiftTutorials/ATPESC_2014-08-14/subjobs/app/flexpep.swift
SwiftTutorials/ATPESC_2014-08-14/subjobs/app/pe.swift
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/apps
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cf
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cfps
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cobalt.xml
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/localcoast.xml
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/pecos.xml
SwiftTutorials/ATPESC_2014-08-14/subjobs/config/vesta.xml
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsn.swift
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsnsleepmpi.swift
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/in.data
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/mpicatnap.c
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/out.data
SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/runsubjob.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/atest.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/getblocks.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/qsub.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/run.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runflexpepswift.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runjob.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runsubjob.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift_script.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runtestblock.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script2.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script3.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script4.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/subswift.sh
SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/testblock.sh
Log:
adding stuff to subjob dir
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/app/flexpep.swift
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/app/flexpep.swift (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/app/flexpep.swift 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,34 @@
+type file;
+
+app (file _scorefile, file sout, file serr) flexpep (file _pdb)
+{
+ runjob "/projects/ExM/ketan/openmp-gnu-july16-mini/bin/FlexPepDocking.staticmpi.linuxxlcdebug"
+ "-database /home/ketan/minirosetta_database"
+ "-pep_refine" "-s" @_pdb "-ex1" "-ex2aro"
+ "-use_input_sc" "-nstruct" "1" "-overwrite"
+ "-scorefile" @_scorefile
+ stdout=@sout stderr=@serr;
+}
+
+file scores[] <simple_mapper; location="outdir", prefix="f.",suffix=".sc">;
+file pdb_inputs[] <filesys_mapper; location="/home/ketan/hlac-97-D", pattern="*complex*">;
+
+foreach pdb, j in pdb_inputs {
+ file sout<single_file_mapper; file=strcat("outdir/f.",j,".stdout")>;
+ file serr<single_file_mapper; file=strcat("outdir/f.",j,".stderr")>;
+ (scores[j], sout, serr) = flexpep(pdb);
+}
+
+/*
+qsub --env BG_SHAREDMEMSIZE=32MB -t 20 -n 2 --proccount 2 \
+ --mode c1 \
+ /projects/ExM/ketan/openmp-gnu-july16-mini/bin/FlexPepDocking.staticmpi.linuxxlcdebug \
+ -database /home/ketan/minirosetta_database/ \
+ -pep_refine \
+ -s /home/ketan/hlac-97-D/hlac-97-D-AAADAAAAL_complex_0001.pdb \
+ -ex1 \
+ -ex2aro \
+ -use_input_sc \
+ -nstruct 1 -overwrite \
+ -scorefile AAADAAAAL_complex_91R.sc
+*/
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/app/pe.swift
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/app/pe.swift (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/app/pe.swift 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) pe ()
+{
+# sh "-c" "printenv" stdout=@o;
+ sh "-c" "/home/wilde/swift/lab/runjob.sh" stdout=@o;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+foreach j in [1:@toint(@arg("n","1"))] {
+ out[j] = pe();
+}
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/apps
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/apps (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/apps 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,12 @@
+localhost truecmd /bin/true null null null
+localhost falsecmd /bin/falsecmd null null null
+localhost echo /bin/echo null null null
+localhost ls /bin/ls null null null
+localhost sh /bin/sh null null null
+localhost cat /bin/cat null null null
+cluster cat /bin/cat null null null
+pbs cat /bin/cat null null null
+mcs cat /bin/cat null null null
+localhost catnap /home/ketan/subjoblab/catnap.sh null null GLOBUS::maxwalltime="00:01:00"
+#localhost runjob /home/ketan/subjoblab/runjob.sh null null GLOBUS::maxwalltime="00:01:00"
+localhost runjob /home/ketan/subjoblab/runsubjob.sh null null GLOBUS::maxwalltime="00:01:00"
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cf
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cf (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cf 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,7 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cfps
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cfps (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cfps 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,8 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=true
+provider.staging.pin.swiftfiles=true
+use.wrapper.staging=false
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cobalt.xml
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cobalt.xml (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/cobalt.xml 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,23 @@
+<config>
+ <pool handle="cluster">
+ <filesystem provider="local" />
+ <execution provider="coaster" jobmanager="local:cobalt"/>
+ <profile namespace="karajan" key="jobthrottle">5.11</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="jobsPerNode">8</profile>
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxNodes">1</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxTime">900</profile> <!-- seconds -->
+ <workdirectory>_WORK_</workdirectory>
+ <!--
+ <profile namespace="swift" key="stagingMethod">local</profile>
+ <profile namespace="globus" key="project">_PROJECT_</profile>
+ <profile namespace="globus" key="queue">_QUEUE_</profile>
+ <profile namespace="globus" key="internalHostname">_HOST_</profile>
+ <profile namespace="globus" key="kernelprofile">zeptoos</profile>
+ <profile namespace="globus" key="alcfbgpnat">true</profile>
+ <profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+ -->
+ </pool>
+</config>
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/localcoast.xml
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/localcoast.xml (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/localcoast.xml 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,17 @@
+ <config>
+
+ <pool handle="localhost">
+ <execution provider="coaster" jobmanager="local:local"/>
+
+ <profile namespace="karajan" key="jobthrottle">4.79</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxNodes">32</profile>
+ <profile namespace="globus" key="nodeGranularity">32</profile>
+ <profile namespace="globus" key="maxWalltime">3300</profile>
+
+ <filesystem provider="local"/>
+ <workdirectory>/home/ketan/swiftwork</workdirectory>
+ </pool>
+
+</config>
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/pecos.xml
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/pecos.xml (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/pecos.xml 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,25 @@
+ <config>
+
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <!-- <filesystem provider="local"/> -->
+ <workdirectory>/tmp/ketan/swiftwork</workdirectory>
+ <profile namespace="swift" key="stagingMethod">local</profile>
+ </pool>
+
+ <pool handle="cluster"> <!-- vesta -->
+ <execution provider="coaster-persistent" url="http://localhost:59900" jobmanager="local:local"/>
+ <!-- <execution provider="coaster" jobmanager="ssh-cl:pbs" url="login4.beagle.ci.uchicago.edu"/> -->
+ <profile namespace="globus" key="jobsPerNode">2</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="maxWalltime">00:05:00</profile>
+ <profile namespace="globus" key="slots">5</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="karajan" key="jobThrottle">4.80</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <workdirectory>/home/ketan/swiftwork</workdirectory>
+ </pool>
+
+</config>
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/config/vesta.xml
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/config/vesta.xml (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/config/vesta.xml 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,23 @@
+<config>
+ <pool handle="cluster">
+ <!-- <filesystem provider="gridftp" URL="gsiftp://miradtn.alcf.anl.gov" /> -->
+ <execution provider="coaster" jobmanager="ssh-cl:local" url="vestalac1.pub.alcf.anl.gov" />
+ <profile namespace="karajan" key="jobthrottle">5.11</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="jobsPerNode">8</profile>
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxNodes">1</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxTime">900</profile> <!-- seconds -->
+ <workdirectory>/gpfs/mira-home/wilde/swiftwork</workdirectory>
+ <!--
+ <profile namespace="swift" key="stagingMethod">local</profile>
+ <profile namespace="globus" key="project">_PROJECT_</profile>
+ <profile namespace="globus" key="queue">_QUEUE_</profile>
+ <profile namespace="globus" key="internalHostname">_HOST_</profile>
+ <profile namespace="globus" key="kernelprofile">zeptoos</profile>
+ <profile namespace="globus" key="alcfbgpnat">true</profile>
+ <profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+ -->
+ </pool>
+</config>
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsn.swift
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsn.swift (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsn.swift 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) cat (file i)
+{
+ cat @i stdout=@o;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+foreach j in [1:@toint(@arg("n","1"))] {
+ file data<"data.txt">;
+ out[j] = cat(data);
+}
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsnsleepmpi.swift
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsnsleepmpi.swift (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/catsnsleepmpi.swift 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,15 @@
+type file;
+
+app (file o, file sout, file serr) cat (file i)
+{
+ runjob "/home/ketan/subjoblab/mpicatnap" @i @o @arg("s","1") stdout=@sout stderr=@serr;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+
+foreach j in [1:toint(arg("n","1"))] {
+ file data<"data.txt">;
+ file sout<single_file_mapper; file=strcat("outdir/f.",j,".stdout")>;
+ file serr<single_file_mapper; file=strcat("outdir/f.",j,".stderr")>;
+ (out[j],sout,serr) = cat(data);
+}
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/in.data
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/in.data (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/in.data 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1 @@
+this is my input
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/mpicatnap.c
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/mpicatnap.c (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/mpicatnap.c 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,45 @@
+#include <stdio.h>
+#include <mpi.h>
+#include <unistd.h>
+#include <fcntl.h>
+
+int main (argc, argv)
+int argc;
+char *argv[];
+{
+ int rank, size;
+
+ MPI_Init (&argc, &argv); /* starts MPI */
+
+ char *ifile = argv[1];
+ char *ofile = argv[2];
+ int sleeptime = atoi(argv[3]);
+
+ MPI_Comm_rank (MPI_COMM_WORLD, &rank); /* get current MPI process id (rank) */
+ MPI_Comm_size (MPI_COMM_WORLD, &size); /* get number of MPI processes */
+
+ if (rank==0) {
+ printf("ifile=%s ofile=%s sleeptime=%d\n", ifile, ofile, sleeptime);
+
+ int ifd = open(ifile,O_RDONLY);
+ int ofd = open(ofile,O_WRONLY|O_CREAT,0664);
+ char buf[1024*1024];
+ for(;;) {
+ int rc = read(ifd, buf, sizeof(buf));
+ if (rc <= 0) {
+ close(ifd);
+ close(ofd);
+ break;
+ }
+ write(ofd, buf, rc);
+ }
+ }
+
+ sleep(sleeptime);
+
+ char host[512];
+ gethostname(host, 512);
+ printf( "Hello from process %d of %d on %s\n", rank, size, host);
+ MPI_Finalize();
+ return 0;
+}
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/out.data
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/out.data (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/out.data 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1 @@
+this is my input
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/runsubjob.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/runsubjob.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/runsubjob.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,16 @@
+#! /bin/bash
+
+BLOCK=$COBALT_PARTNAME
+SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+SUBBLOCK=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
+
+echo $0: running BLOCK=$BLOCK SLOT=$SWIFT_JOB_SLOT SUBBLOCK=$SUBBLOCK
+echo $0: running cmd: $0 args: $*
+
+echo $0: running runjob --block $BLOCK --corner $SUBBLOCK --shape 1x1x1x1x1 : $*
+
+sleep 1
+runjob --strace 0 --block $BLOCK --corner $SUBBLOCK --shape 1x1x1x1x1 --ranks-per-node 1 : $*
+sleep 1
+
+exit 0
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/hello/runsubjob.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/atest.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/atest.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/atest.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,12 @@
+#! /bin/bash
+
+BLOCKS="VST-20040-31371-128
+VST-22040-33371-128
+VST-02040-13371-128
+VST-00040-11371-128"
+
+ba=($BLOCKS)
+
+for i in ${!ba[*]}; do
+ echo ba[$i]=${ba[$i]}
+done
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/atest.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/getblocks.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/getblocks.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/getblocks.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+set -x
+
+qsub -A ATPESC2014 -n 32 -t 5 -q low --mode script --disable_preboot testblock.sh
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/getblocks.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/qsub.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/qsub.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/qsub.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,12 @@
+qsub --env BG_SHAREDMEMSIZE=32MB -t 20 -n 2 --proccount 2 \
+ --mode c1 \
+ /projects/ExM/ketan/openmp-gnu-july16-mini/bin/FlexPepDocking.staticmpi.linuxxlcdebug \
+ -database /home/ketan/minirosetta_database/ \
+ -pep_refine \
+ -s /home/ketan/hlac-97-D/hlac-97-D-AAADAAAAL_complex_0001.pdb \
+ -ex1 \
+ -ex2aro \
+ -use_input_sc \
+ -nstruct 1 -overwrite \
+ -scorefile AAADAAAAL_complex_91R.sc
+
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/run.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/run.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/run.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,5 @@
+#! /bin/sh
+
+set -x
+
+qsub -A ATPESC2014 -n 512 -t 5 -q low --mode script --disable_preboot script3.sh # ADD as params: mpicatnap in.data out.data 3
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/run.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runflexpepswift.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runflexpepswift.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runflexpepswift.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+qsub -A ATPESC2014 -n 64 -t 59 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml flexpep.swift
+
+# --disable_preboot
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runflexpepswift.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runjob.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runjob.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runjob.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,24 @@
+#! /bin/bash
+
+# BLOCKS="VST-20040-31371-128
+# VST-22040-33371-128
+# VST-02040-13371-128
+# VST-00040-11371-128
+# VST-22040-33371-128
+# VST-02040-13371-128
+# VST-00040-11371-128
+# VST-22040-33371-128
+# VST-02040-13371-128
+# VST-00040-11371-128
+# VST-22040-33371-128
+# VST-02040-13371-128
+# VST-00040-11371-128"
+
+ba=($BLOCKS)
+BLOCK=${ba[$SWIFT_JOB_SLOT]}
+
+echo running block $SWIFT_JOB_SLOT BLOCK=$BLOCK
+echo running cmd: $0 args: $*
+
+runjob --strace 0 --block $BLOCK : $*
+# runjob --block $BLOCK : $*
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runjob.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runsubjob.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runsubjob.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runsubjob.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,16 @@
+#! /bin/bash
+
+BLOCK=$COBALT_PARTNAME
+SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+SUBBLOCK=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
+
+echo $0: running BLOCK=$BLOCK SLOT=$SWIFT_JOB_SLOT SUBBLOCK=$SUBBLOCK
+echo $0: running cmd: $0 args: $*
+
+echo $0: running runjob --block $BLOCK --corner $SUBBLOCK --shape 1x1x1x1x1 : $*
+
+sleep 1
+runjob --strace 0 --block $BLOCK --corner $SUBBLOCK --shape 1x1x1x1x1 --ranks-per-node 1 : $*
+sleep 1
+
+exit 0
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runsubjob.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+qsub -A ATPESC2014 -n 32 -t 5 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml catsnsleepmpi.swift -n=8 -s=0
+
+# --disable_preboot
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift_script.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift_script.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift_script.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,39 @@
+#!/bin/bash
+
+genblocks()
+{
+ # PARTITION=VST-22060-33171-32
+ PARTITION=$1
+
+ corner=$(echo $PARTITION | sed -e 's/VST-//' -e 's/-.*//')
+
+ echo 'obase=2; for(i=0;i<32;i++) {print i; print "\n"}' | bc |
+ for corner_coord in $(awk -v corner=$corner '{printf("%05d\n", $1+corner)}' ); do
+ corner_node=$(/soft/cobalt/bgq_hardware_mapper/coord2hardware.py $corner_coord)
+ echo $corner_node
+ done
+}
+
+export SWIFT_SUBBLOCKS=$(genblocks $COBALT_PARTNAME)
+
+echo $0: SWIFT_SUBBLOCKS=$SWIFT_SUBBLOCKS
+
+if [ "_$SWIFT_SUBBLOCKS" = _ ]; then
+ echo ERROR: $0: SWIFT_SUBBLOCKS is null.
+ exit 1
+fi
+
+export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS)
+
+nsb=${#SWIFT_SUBBLOCK_ARRAY[@]}
+for ((sb=0;sb<nsb;sb++))
+do
+ echo $0: SUBBLOCK $sb: ${SWIFT_SUBBLOCK_ARRAY[$sb]}
+done
+
+export PATH=/home/ketan/swift-0.95-RC6/bin:$PATH
+#cd /home/wilde/swift/lab # FIXME
+
+swift $*
+
+# swift -config cf -tc.file apps -sites.file localcoast.xml catsnsleepmpi.swift -n=100 -s=2
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runswift_script.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runtestblock.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runtestblock.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runtestblock.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,4 @@
+#! /bin/sh
+
+qsub -A ATPESC2013 -n 32 -t 5 -q low --mode c16 --mode script testblock.sh # --disable_preboot
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/runtestblock.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+BLOCKS=`get-bootable-blocks --size 128 $COBALT_PARTNAME`
+
+echo BLOCKS="$BLOCKS"
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK &
+done
+wait
+
+for BLOCK in $BLOCKS
+do
+ runjob --block $BLOCK : `pwd`/mpicatnap in.data out.data 3 &
+done
+wait
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK --free &
+done
+wait
+
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script2.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script2.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script2.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+export BLOCKS=$(get-bootable-blocks --size 32 $COBALT_PARTNAME)
+
+export BLOCK_ARRAY=($BLOCKS)
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK &
+done
+wait
+
+#for BLOCK in $BLOCKS
+nb=${#BLOCK_ARRAY[@]}
+for ((b=0;b<nb;b++))
+do
+ export SWIFT_JOB_SLOT=$b
+ $(pwd)/runjob.sh $(pwd)/mpicatnap in.data out.data 3 &
+done
+wait
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK --free &
+done
+wait
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script2.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script3.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script3.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script3.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+set -x
+
+export BLOCKS=$(get-bootable-blocks --size 32 $COBALT_PARTNAME)
+
+echo script3.sh: BLOCKS=$BLOCKS
+
+if [ "_${BLOCKS}" = "_" ]; then
+ echo ERROR: script3.sh: BLOCKS is null.
+ exit 1
+fi
+
+export BLOCK_ARRAY=($BLOCKS)
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK &
+done
+wait
+
+# #for BLOCK in $BLOCKS
+# nb=${#BLOCK_ARRAY[@]}
+# for ((b=0;b<nb;b++))
+# do
+# export SWIFT_JOB_SLOT=$b
+# /home/wilde/swift/lab/runjob.sh `pwd`/mpicatnap in.data out.data 3 &
+# done
+# wait
+
+nb=${#BLOCK_ARRAY[@]}
+for ((b=0;b<nb;b++))
+do
+ echo script3.sh: BLOCK $b: ${ba[$SWIFT_JOB_SLOT]}
+done
+
+export PATH=/home/wilde/swift/rev/swift-0.94.1/bin:$PATH
+cd /home/wilde/swift/lab
+
+swift -config cf -tc.file apps -sites.file localcoast.xml catsnsleepmpi.swift -n=100 -s=2
+
+for BLOCK in $BLOCKS
+do
+ boot-block --block $BLOCK --free &
+done
+wait
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script3.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script4.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script4.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/script4.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -x
+
+genblocks()
+{
+ # PARTITION=VST-22060-33171-32
+ PARTITION=$1
+
+ corner=$(echo $PARTITION | sed -e 's/VST-//' -e 's/-.*//')
+
+ echo 'obase=2; for(i=0;i<32;i++) {print i; print "\n"}' | bc |
+ for corner_coord in $(awk -v corner=$corner '{printf("%05d\n", $1+corner)}' ); do
+ corner_node=$(/soft/cobalt/bgq_hardware_mapper/coord2hardware.py $corner_coord)
+ echo $corner_node
+ done
+}
+
+export corners=$(genblocks $COBALT_PARTNAME)
+
+BLOCK=$COBALT_PARTNAME
+
+for corner in $corners; do
+ echo "$0: BLOCK=$BLOCK corner=$corner"
+ echo "DOING: runjob --block $BLOCK --corner $corner --shape 1x1x1x1x1 : `pwd`/mpicatnap in.data out.data.$corner 3"
+ runjob --block $BLOCK --corner $corner --shape 1x1x1x1x1 --ranks-per-node 4 : `pwd`/mpicatnap in.data out.data.$corner 3 &
+done
+
+wait
+
+exit 0
+
+nsub=${#BLOCK_ARRAY[@]}
+for ((b=0;b<nb;b++))
+do
+ echo script3.sh: BLOCK $b: ${ba[$SWIFT_JOB_SLOT]}
+done
+
+
+export PATH=/home/ketan/swift-0.95-RC6/bin:$PATH
+#cd /home/wilde/swift/lab
+
+swift -config cf -tc.file apps -sites.file localcoast.xml catsnsleepmpi.swift -n=100 -s=2
+
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/subswift.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/subswift.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/subswift.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1 @@
+qsub -A ATPESC2013 -n 4 -t 5 -q low --mode c16 --mode script runswift.sh # --disable_preboot script.sh mpicatnap in.data out.data 3
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/subswift.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/testblock.sh
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/testblock.sh (rev 0)
+++ SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/testblock.sh 2014-08-11 22:45:12 UTC (rev 8076)
@@ -0,0 +1,40 @@
+#!/bin/bash
+
+set -x
+
+genblocks()
+{
+ # PARTITION=VST-22060-33171-32
+ PARTITION=$1
+
+ corner=$(echo $PARTITION | sed -e 's/VST-//' -e 's/-.*//')
+
+ echo 'obase=2; for(i=0;i<32;i++) {print i; print "\n"}' | bc |
+ for corner_coord in $(awk -v corner=$corner '{printf("%05d\n", $1+corner)}' ); do
+ corner_node=$(/soft/cobalt/bgq_hardware_mapper/coord2hardware.py $corner_coord)
+ echo $corner_node
+ done
+}
+
+export SWIFT_SUBBLOCKS=$(genblocks $COBALT_PARTNAME | head -8)
+
+BLOCK=$COBALT_PARTNAME
+
+for ((iter=0;iter<4;iter++)); do
+
+echo $0: starting iter $iter
+echo
+
+for corner in $SWIFT_SUBBLOCKS; do
+ echo $0: BLOCK=$BLOCK corner=$corner
+ echo DOING: runjob --block $BLOCK --corner $corner --shape 1x1x1x1x1 : `pwd`/mpicatnap in.data out.data.$corner 3
+ sleep 1
+ runjob --block $BLOCK --corner $corner --shape 1x1x1x1x1 --ranks-per-node 1 : `pwd`/mpicatnap in.data out.data.$corner 0 &
+ sleep 1
+done
+
+wait
+
+done
+
+exit 0
Property changes on: SwiftTutorials/ATPESC_2014-08-14/subjobs/scripts/testblock.sh
___________________________________________________________________
Added: svn:executable
+ *
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