From hategan at ci.uchicago.edu Mon Sep 8 13:54:41 2014 From: hategan at ci.uchicago.edu (hategan at ci.uchicago.edu) Date: Mon, 8 Sep 2014 13:54:41 -0500 (CDT) Subject: [Swift-commit] r8234 - branches/release-0.95/src/org/griphyn/vdl/karajan Message-ID: <20140908185441.4388D9CD17@svn.ci.uchicago.edu> Author: hategan Date: 2014-09-08 13:54:40 -0500 (Mon, 08 Sep 2014) New Revision: 8234 Modified: branches/release-0.95/src/org/griphyn/vdl/karajan/HangChecker.java branches/release-0.95/src/org/griphyn/vdl/karajan/Loader.java Log: shut down hang checker at the end of run to prevent triggering it during shutdown Modified: branches/release-0.95/src/org/griphyn/vdl/karajan/HangChecker.java =================================================================== --- branches/release-0.95/src/org/griphyn/vdl/karajan/HangChecker.java 2014-08-28 14:37:41 UTC (rev 8233) +++ branches/release-0.95/src/org/griphyn/vdl/karajan/HangChecker.java 2014-09-08 18:54:40 UTC (rev 8234) @@ -69,6 +69,15 @@ timer = new Timer("Hang checker"); timer.scheduleAtFixedRate(this, CHECK_INTERVAL, CHECK_INTERVAL); } + + public void stop() { + try { + timer.cancel(); + } + catch (Exception e) { + logger.info("Failed to stop hang checker", e); + } + } public void run() { try { Modified: branches/release-0.95/src/org/griphyn/vdl/karajan/Loader.java =================================================================== --- branches/release-0.95/src/org/griphyn/vdl/karajan/Loader.java 2014-08-28 14:37:41 UTC (rev 8233) +++ branches/release-0.95/src/org/griphyn/vdl/karajan/Loader.java 2014-09-08 18:54:40 UTC (rev 8234) @@ -104,6 +104,7 @@ boolean runerror = false; String runID = makeRunId(ap); + HangChecker hangChecker = null; try { String project = ap.getStringValue(ArgumentParser.DEFAULT); @@ -172,7 +173,8 @@ } logger.info("RUN_START"); - new HangChecker(context).start(); + hangChecker = new HangChecker(context); + hangChecker.start(); long start = System.currentTimeMillis(); ec.start(context); @@ -193,6 +195,9 @@ else { logger.info("Swift finished with no errors"); } + if (hangChecker != null) { + hangChecker.stop(); + } if (ma != null) { ma.close(); } From ketan at ci.uchicago.edu Tue Sep 9 12:41:24 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 12:41:24 -0500 (CDT) Subject: [Swift-commit] r8235 - in SwiftApps: EPlus/examples swift-galaxy swift-galaxy/swift Message-ID: <20140909174124.EA4C79CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 12:41:24 -0500 (Tue, 09 Sep 2014) New Revision: 8235 Modified: SwiftApps/EPlus/examples/run.sh SwiftApps/swift-galaxy/setup.py SwiftApps/swift-galaxy/swift/swiftforeach.py Log: changes in EPlus and galaxy Modified: SwiftApps/EPlus/examples/run.sh =================================================================== --- SwiftApps/EPlus/examples/run.sh 2014-09-08 18:54:40 UTC (rev 8234) +++ SwiftApps/EPlus/examples/run.sh 2014-09-09 17:41:24 UTC (rev 8235) @@ -1,2 +1,5 @@ #! /bin/sh -runenergyplus CHICAGO-EXAMPLE.imf CHICAGO.epw + +export PATH=~/EPlus/EnergyPlus-8-0-0/bin:$PATH + +runenergyplus ./CHICAGO-EXAMPLE.imf ./CHICAGO.epw Modified: SwiftApps/swift-galaxy/setup.py =================================================================== --- SwiftApps/swift-galaxy/setup.py 2014-09-08 18:54:40 UTC (rev 8234) +++ SwiftApps/swift-galaxy/setup.py 2014-09-09 17:41:24 UTC (rev 8235) @@ -1,25 +1,44 @@ #!/usr/bin/env python -import xml.etree.ElementTree as ET - """ Setup script to install swift-galaxy framework to your Galaxy installation. + +Usage: ./setup.py """ +import xml.etree.ElementTree as ET import subprocess import sys import os import distutils.spawn import traceback import fnmatch +import tarfile +import urllib galaxyloc=sys.argv[1] +#step 0. Download swift-galaxy.tgz and swift-rel.tgz untar and set path +if not os.path.isfile("/tmp/swift-galaxy.tgz"): + urllib.urlretrieve("http://mcs.anl.gov/~ketan/swift-galaxy.tgz", filename="/tmp/swift-galaxy.tgz") + swiftgaltar = tarfile.open("/tmp/swift-galaxy.tgz") + swiftgaltar.extractall(path="/tmp") + swiftgaltar.close() + +if not os.path.isfile("/tmp/swift-0.94.1-RC3.tar.gz"): + urllib.urlretrieve("http://swift-lang.org/packages/swift-0.94.1-RC3.tar.gz", filename="/tmp/swift-0.94.1-RC3.tar.gz") + swiftar = tarfile.open("/tmp/swift-0.94.1-RC3.tar.gz") + swiftar.extractall(path="/tmp") + swiftar.close() + os.environ["PATH"] = os.environ["PATH"] + ":/tmp/swift-0.94.1-RC3/bin" + #step 1. Create symlink to the swift directory from the tools directory of galaxyloc if not already present -#os.symlink (os.getcwd()+"/swift", galaxyloc+"/tools/swift"); +if os.path.lexists(galaxyloc+"/tools/swift"): + os.remove(galaxyloc+"/tools/swift") +os.symlink ("/tmp/swift-galaxy/swift", galaxyloc+"/tools/swift"); + #step 2. update the tool_conf.xml - tree = ET.parse(galaxyloc+"/tool_conf.xml") root = tree.getroot() @@ -28,15 +47,6 @@ tree.write (galaxyloc+"/tool_conf.xml") -#i = lines.index("") -#lines.insert(i, 'Random text to insert') - -#
-# -# -# -#
- #step 3. Print message print "Swift/Galaxy Installed." Modified: SwiftApps/swift-galaxy/swift/swiftforeach.py =================================================================== --- SwiftApps/swift-galaxy/swift/swiftforeach.py 2014-09-08 18:54:40 UTC (rev 8234) +++ SwiftApps/swift-galaxy/swift/swiftforeach.py 2014-09-09 17:41:24 UTC (rev 8235) @@ -23,7 +23,7 @@ yield a def buildcfg(wdir): - f=open(wdir+"/cf", 'w'); + f=open(wdir+"/cf", 'w') f.write("use.provider.staging=true\n") f.write("wrapperlog.always.transfer=true\n") f.write("execution.retries=0\n") From ketan at ci.uchicago.edu Tue Sep 9 12:49:42 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 12:49:42 -0500 (CDT) Subject: [Swift-commit] r8236 - in SwiftApps: . subjobs Message-ID: <20140909174942.0182E9CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 12:49:41 -0500 (Tue, 09 Sep 2014) New Revision: 8236 Added: SwiftApps/subjobs/ SwiftApps/subjobs/apps SwiftApps/subjobs/bg.sh SwiftApps/subjobs/catsnsleepmpi.swift SwiftApps/subjobs/cf SwiftApps/subjobs/cobalt.xml SwiftApps/subjobs/ensemble_jobs_0.pdf SwiftApps/subjobs/flexpep.swift SwiftApps/subjobs/in.data SwiftApps/subjobs/mpicatnap.c SwiftApps/subjobs/notes.txt SwiftApps/subjobs/runbash.sh SwiftApps/subjobs/runswift.sh Log: adding subjob dir Added: SwiftApps/subjobs/apps =================================================================== --- SwiftApps/subjobs/apps (rev 0) +++ SwiftApps/subjobs/apps 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,3 @@ +localhost cat /bin/cat null null null +cluster bgsh /home/ketan/subjoblab/bg.sh null null null + Added: SwiftApps/subjobs/bg.sh =================================================================== --- SwiftApps/subjobs/bg.sh (rev 0) +++ SwiftApps/subjobs/bg.sh 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,54 @@ +#! /bin/bash + +# Note: This path is for Cetus only +#export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH +# Note: This path is for Mira or Vesta +export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH + +case "$SUBBLOCK_SIZE" in +8) SHAPE="1x2x2x2x1" +;; +16) SHAPE="2x2x2x2x1" +;; +32) SHAPE="2x2x2x2x2" +;; +64) SHAPE="2x2x4x2x2" +;; +128) SHAPE="2x4x4x2x2" +;; +256) SHAPE="2x4x4x4x2" +;; +512) SHAPE="4x4x4x4x2" +;; +*) SHAPE="2x2x2x2x2" + REMAINING_ARGS="$@" +;; +esac + +export SWIFT_SUBBLOCKS=$(get-corners.py "$COBALT_PARTNAME" $SHAPE) +export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS) + +echo "$0": SWIFT_SUBBLOCKS="$SWIFT_SUBBLOCKS" + +if [ "_$SWIFT_SUBBLOCKS" = _ ]; then + echo ERROR: "$0": SWIFT_SUBBLOCKS is null. + exit 1 +fi + +nsb=${#SWIFT_SUBBLOCK_ARRAY[@]} +for ((sb=0;sb; + +foreach j in [1:toInt(arg("n","1"))] { + file data<"data.txt">; + file sout; + file serr; + (out[j],sout,serr) = cat(data); +} Added: SwiftApps/subjobs/cf =================================================================== --- SwiftApps/subjobs/cf (rev 0) +++ SwiftApps/subjobs/cf 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,27 @@ +wrapperlog.always.transfer=false +provider.staging.pin.swiftfiles=false +sitedir.keep=false +kickstart.always.transfer=false +replication.limit=3 +throttle.host.submit=2 +clustering.min.time=15 +kickstart.enabled=maybe +execution.retries=10 +pgraph=false +use.provider.staging=false +tracing.enabled=true +foreach.max.threads=1024 +use.wrapper.staging=false +replication.enabled=false +throttle.submit=4 +throttle.score.job.factor=0.2 +lazy.errors=true +clustering.enabled=false +caching.algorithm=LRU +pgraph.node.options=color="seagreen", style="filled" +replication.min.queue.time=60 +clustering.queue.delay=4 +throttle.file.operations=8 +provenance.log=false +throttle.transfers=4 +pgraph.graph.options=splines="compound", rankdir="TB" Added: SwiftApps/subjobs/cobalt.xml =================================================================== --- SwiftApps/subjobs/cobalt.xml (rev 0) +++ SwiftApps/subjobs/cobalt.xml 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,24 @@ + + + + + + +1 +script + +2.99 +10000 +00:40:00 +2050 + +256 +256 +8 +32 + +/home/ketan/swiftwork + + + + Added: SwiftApps/subjobs/ensemble_jobs_0.pdf =================================================================== (Binary files differ) Property changes on: SwiftApps/subjobs/ensemble_jobs_0.pdf ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: SwiftApps/subjobs/flexpep.swift =================================================================== --- SwiftApps/subjobs/flexpep.swift (rev 0) +++ SwiftApps/subjobs/flexpep.swift 2014-09-09 17:49:41 UTC (rev 8236) @@ -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[] ; +file pdb_inputs[] ; + +foreach pdb, j in pdb_inputs { + file sout; + file serr; + (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: SwiftApps/subjobs/in.data =================================================================== --- SwiftApps/subjobs/in.data (rev 0) +++ SwiftApps/subjobs/in.data 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1 @@ +this is my input Added: SwiftApps/subjobs/mpicatnap.c =================================================================== --- SwiftApps/subjobs/mpicatnap.c (rev 0) +++ SwiftApps/subjobs/mpicatnap.c 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,45 @@ +#include +#include +#include +#include + +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: SwiftApps/subjobs/notes.txt =================================================================== --- SwiftApps/subjobs/notes.txt (rev 0) +++ SwiftApps/subjobs/notes.txt 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,42 @@ +== Sub-block jobs == + +== Components == + +Outer block + +Inner blocks + +Parameters +Blockname + +Blockshape + +Corner + +== Open Issues == + +== Possible applications == + +-- xstack mantivo and proxy by Mike Baru from los alamos +-- Bill Gropp Mlife game +-- XMatix Coehmm Justin MPI code +-- Gromacs, NAMD and LAMMPS + +== ToDo == + +robustness testing +multiple cobalt jobs ("slots") +multiple sites each with unique subblock sizes +docs/tutorials +persistent coasters +conversion from 0.95 to trunk +Use the "direct" mode +cray +integ runsubjob into swiftwrap and/or worker.pl (initially, swiftwrap) +(low prio) + +all above, but for swift/t + + +separate: ksub/kstat; same but through sockets? ipython tools? + Added: SwiftApps/subjobs/runbash.sh =================================================================== --- SwiftApps/subjobs/runbash.sh (rev 0) +++ SwiftApps/subjobs/runbash.sh 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,43 @@ +#!/bin/bash + +#To run: +#qsub -n 256 -t 45 --mode script runbash.sh + +# Note: This path is for Cetus only +#export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH +# Note: This path is for Mira or Vesta +export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH + +SHAPE="1x2x2x2x1" +CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) + + +# Set this low for testing. +# Consult with systems if you need it > 128 +MAXRUNJOB=64 + +i=0 +for j in $(seq 1 200) +do + for CORNER in $CORNERS + do + echo "Run $i corner $CORNER" + stime=$(shuf -i 1-10 -n 1) + runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + # Important - give some time for runjob to get initialized + sleep 6 + i=$((i+1)) + if [ $i -ge $MAXRUNJOB ]; then + echo "Reached MAXRUNJOB $MAXRUNJOB" + break; + fi + done + # The runjobs were backgrounded, wait for them to finish + wait + echo "Done $i" + i=0 +done + +# Cobalt job ends when this script exits +exit 0 + Property changes on: SwiftApps/subjobs/runbash.sh ___________________________________________________________________ Added: svn:executable + * Added: SwiftApps/subjobs/runswift.sh =================================================================== --- SwiftApps/subjobs/runswift.sh (rev 0) +++ SwiftApps/subjobs/runswift.sh 2014-09-09 17:49:41 UTC (rev 8236) @@ -0,0 +1,11 @@ +#! /bin/sh + +#Old method +#qsub -A ATPESC2014 -n 512 -t 15 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml "$@" + +#New method +~/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=32 +#~/prebuilt/swift-devel/cog/modules/swift/dist/swift-svn/bin/swift catsnsleepmpi.swift -n=10 + +#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/runswift.sh ___________________________________________________________________ Added: svn:executable + * From ketan at ci.uchicago.edu Tue Sep 9 12:51:57 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 12:51:57 -0500 (CDT) Subject: [Swift-commit] r8237 - SwiftApps/subjobs Message-ID: <20140909175157.6381C9CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 12:51:57 -0500 (Tue, 09 Sep 2014) New Revision: 8237 Modified: SwiftApps/subjobs/runbash.sh SwiftApps/subjobs/runswift.sh Log: add line to build app Modified: SwiftApps/subjobs/runbash.sh =================================================================== --- SwiftApps/subjobs/runbash.sh 2014-09-09 17:49:41 UTC (rev 8236) +++ SwiftApps/subjobs/runbash.sh 2014-09-09 17:51:57 UTC (rev 8237) @@ -8,6 +8,9 @@ # Note: This path is for Mira or Vesta export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH +#build app +mpixlc mpicatnap.c -o mpicatnap + SHAPE="1x2x2x2x1" CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) Modified: SwiftApps/subjobs/runswift.sh =================================================================== --- SwiftApps/subjobs/runswift.sh 2014-09-09 17:49:41 UTC (rev 8236) +++ SwiftApps/subjobs/runswift.sh 2014-09-09 17:51:57 UTC (rev 8237) @@ -3,6 +3,9 @@ #Old method #qsub -A ATPESC2014 -n 512 -t 15 --mode script runswift_script.sh -config cf -tc.file apps -sites.file localcoast.xml "$@" +#build app +mpixlc mpicatnap.c -o mpicatnap + #New method ~/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=32 #~/prebuilt/swift-devel/cog/modules/swift/dist/swift-svn/bin/swift catsnsleepmpi.swift -n=10 From ketan at ci.uchicago.edu Tue Sep 9 12:53:59 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 12:53:59 -0500 (CDT) Subject: [Swift-commit] r8238 - SwiftApps/subjobs Message-ID: <20140909175359.6E2549CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 12:53:59 -0500 (Tue, 09 Sep 2014) New Revision: 8238 Added: SwiftApps/subjobs/subjob.sh Modified: SwiftApps/subjobs/runbash.sh Log: outer script Modified: SwiftApps/subjobs/runbash.sh =================================================================== --- SwiftApps/subjobs/runbash.sh 2014-09-09 17:51:57 UTC (rev 8237) +++ SwiftApps/subjobs/runbash.sh 2014-09-09 17:53:59 UTC (rev 8238) @@ -1,46 +1,5 @@ #!/bin/bash #To run: -#qsub -n 256 -t 45 --mode script runbash.sh +qsub -n 256 -t 45 --mode script subjob.sh -# Note: This path is for Cetus only -#export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH -# Note: This path is for Mira or Vesta -export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH - -#build app -mpixlc mpicatnap.c -o mpicatnap - -SHAPE="1x2x2x2x1" -CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) - - -# Set this low for testing. -# Consult with systems if you need it > 128 -MAXRUNJOB=64 - -i=0 -for j in $(seq 1 200) -do - for CORNER in $CORNERS - do - echo "Run $i corner $CORNER" - stime=$(shuf -i 1-10 -n 1) - runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & - # Important - give some time for runjob to get initialized - sleep 6 - i=$((i+1)) - if [ $i -ge $MAXRUNJOB ]; then - echo "Reached MAXRUNJOB $MAXRUNJOB" - break; - fi - done - # The runjobs were backgrounded, wait for them to finish - wait - echo "Done $i" - i=0 -done - -# Cobalt job ends when this script exits -exit 0 - Added: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh (rev 0) +++ SwiftApps/subjobs/subjob.sh 2014-09-09 17:53:59 UTC (rev 8238) @@ -0,0 +1,46 @@ +#!/bin/bash + +#To run: +#qsub -n 256 -t 45 --mode script runbash.sh + +# Note: This path is for Cetus only +#export PATH=/soft/cobalt/cetus/bgq_hardware_mapper:$PATH +# Note: This path is for Mira or Vesta +export PATH=/soft/cobalt/bgq_hardware_mapper:$PATH + +#build app +mpixlc mpicatnap.c -o mpicatnap + +SHAPE="1x2x2x2x1" +CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) + + +# Set this low for testing. +# Consult with systems if you need it > 128 +MAXRUNJOB=64 + +i=0 +for j in $(seq 1 200) +do + for CORNER in $CORNERS + do + echo "Run $i corner $CORNER" + stime=$(shuf -i 1-10 -n 1) + runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + # Important - give some time for runjob to get initialized + sleep 6 + i=$((i+1)) + if [ $i -ge $MAXRUNJOB ]; then + echo "Reached MAXRUNJOB $MAXRUNJOB" + break; + fi + done + # The runjobs were backgrounded, wait for them to finish + wait + echo "Done $i" + i=0 +done + +# Cobalt job ends when this script exits +exit 0 + Property changes on: SwiftApps/subjobs/subjob.sh ___________________________________________________________________ Added: svn:executable + * From ketan at ci.uchicago.edu Tue Sep 9 12:55:38 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 12:55:38 -0500 (CDT) Subject: [Swift-commit] r8239 - SwiftApps/subjobs Message-ID: <20140909175538.794889CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 12:55:38 -0500 (Tue, 09 Sep 2014) New Revision: 8239 Modified: SwiftApps/subjobs/runswift.sh Log: small change Modified: SwiftApps/subjobs/runswift.sh =================================================================== --- SwiftApps/subjobs/runswift.sh 2014-09-09 17:53:59 UTC (rev 8238) +++ SwiftApps/subjobs/runswift.sh 2014-09-09 17:55:38 UTC (rev 8239) @@ -7,7 +7,7 @@ mpixlc mpicatnap.c -o mpicatnap #New method -~/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=32 +/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=32 #~/prebuilt/swift-devel/cog/modules/swift/dist/swift-svn/bin/swift catsnsleepmpi.swift -n=10 #A testblock run From ketan at ci.uchicago.edu Tue Sep 9 13:01:13 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Tue, 9 Sep 2014 13:01:13 -0500 (CDT) Subject: [Swift-commit] r8240 - SwiftApps/subjobs Message-ID: <20140909180113.F17B49CFF0@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-09 13:01:13 -0500 (Tue, 09 Sep 2014) New Revision: 8240 Modified: SwiftApps/subjobs/bg.sh SwiftApps/subjobs/subjob.sh Log: small comments and timeout call separate Modified: SwiftApps/subjobs/bg.sh =================================================================== --- SwiftApps/subjobs/bg.sh 2014-09-09 17:55:38 UTC (rev 8239) +++ SwiftApps/subjobs/bg.sh 2014-09-09 18:01:13 UTC (rev 8240) @@ -47,8 +47,12 @@ echo "$0": running cmd: "$0" args: "$@" echo "$0": running runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" --ranks-per-node 1 : "$REMAINING_ARGS" -runjob --strace 0 --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 --np "$SUBBLOCK_SIZE" --timeout 100 : "$@" +#with timeout +#runjob --strace 0 --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 --np "$SUBBLOCK_SIZE" --timeout 100 : "$@" +#without timeout +runjob --strace 0 --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 --np "$SUBBLOCK_SIZE" : "$@" + echo "Runjob finished." exit 0 Modified: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh 2014-09-09 17:55:38 UTC (rev 8239) +++ SwiftApps/subjobs/subjob.sh 2014-09-09 18:01:13 UTC (rev 8240) @@ -26,9 +26,15 @@ do echo "Run $i corner $CORNER" stime=$(shuf -i 1-10 -n 1) - runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + #with timeout + #runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + + #without timeout + runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + # Important - give some time for runjob to get initialized - sleep 6 + sleep 3 + i=$((i+1)) if [ $i -ge $MAXRUNJOB ]; then echo "Reached MAXRUNJOB $MAXRUNJOB" From wozniak at ci.uchicago.edu Tue Sep 9 14:11:59 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Tue, 9 Sep 2014 14:11:59 -0500 (CDT) Subject: [Swift-commit] r8241 - in www/papers: . pdfs Message-ID: <20140909191159.E69D49CD17@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-09 14:11:59 -0500 (Tue, 09 Sep 2014) New Revision: 8241 Added: www/papers/pdfs/DFM_2014.pdf Modified: www/papers/index.php Log: New paper Modified: www/papers/index.php =================================================================== --- www/papers/index.php 2014-09-09 18:01:13 UTC (rev 8240) +++ www/papers/index.php 2014-09-09 19:11:59 UTC (rev 8241) @@ -51,9 +51,19 @@ -->
+ Justin M. Wozniak, Michael Wilde, Ian T. Foster + Language features for scalable distributed-memory dataflow computing + Proc Data-flow Execution Models for + Extreme-scale Computing at PACT + 2014. + [ pdf ] +
+ + +
Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, Ian T. Foster Compiler techniques for massively scalable implicit task parallelism - Proc SC + Proc. SC 2014. [ pdf ]
Added: www/papers/pdfs/DFM_2014.pdf =================================================================== (Binary files differ) Property changes on: www/papers/pdfs/DFM_2014.pdf ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From ketan at ci.uchicago.edu Thu Sep 11 09:53:51 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 09:53:51 -0500 (CDT) Subject: [Swift-commit] r8242 - SwiftApps/subjobs Message-ID: <20140911145351.24F31178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 09:53:51 -0500 (Thu, 11 Sep 2014) New Revision: 8242 Added: SwiftApps/subjobs/README.txt SwiftApps/subjobs/setup Modified: SwiftApps/subjobs/apps Log: adding setup and README Added: SwiftApps/subjobs/README.txt =================================================================== --- SwiftApps/subjobs/README.txt (rev 0) +++ SwiftApps/subjobs/README.txt 2014-09-11 14:53:51 UTC (rev 8242) @@ -0,0 +1,12 @@ +Running Sub-block jobs via Swift +================================= + +Introduction +------------ + + +EC2 CLI API +------------ + + + Modified: SwiftApps/subjobs/apps =================================================================== --- SwiftApps/subjobs/apps 2014-09-09 19:11:59 UTC (rev 8241) +++ SwiftApps/subjobs/apps 2014-09-11 14:53:51 UTC (rev 8242) @@ -1,3 +1,3 @@ localhost cat /bin/cat null null null -cluster bgsh /home/ketan/subjoblab/bg.sh null null null +cluster bgsh bg.sh null null null Added: SwiftApps/subjobs/setup =================================================================== --- SwiftApps/subjobs/setup (rev 0) +++ SwiftApps/subjobs/setup 2014-09-11 14:53:51 UTC (rev 8242) @@ -0,0 +1,4 @@ +#!/bin/bash + +export PATH=$PWD:$PATH + Property changes on: SwiftApps/subjobs/setup ___________________________________________________________________ Added: svn:executable + * From ketan at ci.uchicago.edu Thu Sep 11 09:58:03 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 09:58:03 -0500 (CDT) Subject: [Swift-commit] r8243 - SwiftApps/subjobs Message-ID: <20140911145803.068FB178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 09:58:02 -0500 (Thu, 11 Sep 2014) New Revision: 8243 Modified: SwiftApps/subjobs/README.txt Log: README Modified: SwiftApps/subjobs/README.txt =================================================================== --- SwiftApps/subjobs/README.txt 2014-09-11 14:53:51 UTC (rev 8242) +++ SwiftApps/subjobs/README.txt 2014-09-11 14:58:02 UTC (rev 8243) @@ -3,10 +3,25 @@ Introduction ------------ +Sub-block jobs is a mode of running jobs on BlueGene systems wherein one can +allocate a larger block of compute nodes and repeatedly submit jobs of smaller +sized sub-blocks to this larger allocation. +This package provides tools and scripts to run Swift applications in sub-block mode over the BlueGene resources. -EC2 CLI API ------------- +Running subjobs from Swift +-------------------------- +To set up environment: +---- +source setup +---- +To run an example application + +---- +./runswift +---- + + From ketan at ci.uchicago.edu Thu Sep 11 15:35:42 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 15:35:42 -0500 (CDT) Subject: [Swift-commit] r8244 - SwiftApps/subjobs Message-ID: <20140911203542.0D603178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 15:35:40 -0500 (Thu, 11 Sep 2014) New Revision: 8244 Modified: SwiftApps/subjobs/README.txt Log: update to README Modified: SwiftApps/subjobs/README.txt =================================================================== --- SwiftApps/subjobs/README.txt 2014-09-11 14:58:02 UTC (rev 8243) +++ SwiftApps/subjobs/README.txt 2014-09-11 20:35:40 UTC (rev 8244) @@ -9,8 +9,8 @@ This package provides tools and scripts to run Swift applications in sub-block mode over the BlueGene resources. -Running subjobs from Swift --------------------------- +Swift sub-block jobs +--------------------- To set up environment: @@ -24,4 +24,67 @@ ./runswift ---- +sub-block jobs from bash +------------------------- +To run the example application from bash: + +---- +./runbash +---- + +Swift Sub-block jobs: HowTo +---------------------------- + +In order to convert an ordinary Swift app run in sub-block mode, the following changes are required: + +. Add bg.sh as the application invoker in place of sh. For example, if the app definition is as follows: + +---- +sh @exe @i @o arg("s","1") stdout=@sout stderr=@serr; +---- + +Replace the shell invocation with the bg.sh invocations like so: + +---- +bg.sh @exe @i @o arg("s","1") stdout=@sout stderr=@serr; +---- + +. Add the +SUBBLOCK_SIZE+ environment variable to the sites file. For example: + +---- +16 +---- + +NOTE: The value of +SUBBLOCK_SIZE+ variable must be a power of 2 greater than 8 and less than the +maxnodes+ value. + +A complete example sites file for a sub-block job run on ALCF Vesta is shown below: + +---- + + + + + + +1 +script + +2.99 +10000 +00:40:00 +2050 + +256 +256 +8 +32 + +/home/ketan/swiftwork + + + + +---- + + From ketan at ci.uchicago.edu Thu Sep 11 16:25:18 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 16:25:18 -0500 (CDT) Subject: [Swift-commit] r8245 - SwiftApps/subjobs Message-ID: <20140911212518.9836C178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 16:25:18 -0500 (Thu, 11 Sep 2014) New Revision: 8245 Modified: SwiftApps/subjobs/subjob.sh Log: simplify and more logging Modified: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh 2014-09-11 20:35:40 UTC (rev 8244) +++ SwiftApps/subjobs/subjob.sh 2014-09-11 21:25:18 UTC (rev 8245) @@ -30,7 +30,8 @@ #runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & #without timeout - runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & + #(echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 ; echo $?) & + (echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : /bin/sleep $stime >RUNJOB.$j-$i 2>&1 ; echo Exit status: $?) & # Important - give some time for runjob to get initialized sleep 3 From ketan at ci.uchicago.edu Thu Sep 11 16:29:18 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 16:29:18 -0500 (CDT) Subject: [Swift-commit] r8246 - SwiftApps/subjobs Message-ID: <20140911212918.21942178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 16:29:18 -0500 (Thu, 11 Sep 2014) New Revision: 8246 Modified: SwiftApps/subjobs/runbash.sh Log: small change Modified: SwiftApps/subjobs/runbash.sh =================================================================== --- SwiftApps/subjobs/runbash.sh 2014-09-11 21:25:18 UTC (rev 8245) +++ SwiftApps/subjobs/runbash.sh 2014-09-11 21:29:18 UTC (rev 8246) @@ -1,5 +1,5 @@ #!/bin/bash #To run: -qsub -n 256 -t 45 --mode script subjob.sh +qsub -n 256 -t 50 --mode script subjob.sh From ketan at ci.uchicago.edu Thu Sep 11 16:38:47 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Thu, 11 Sep 2014 16:38:47 -0500 (CDT) Subject: [Swift-commit] r8247 - SwiftApps/subjobs Message-ID: <20140911213847.5C407178884@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-11 16:38:47 -0500 (Thu, 11 Sep 2014) New Revision: 8247 Modified: SwiftApps/subjobs/subjob.sh Log: simplify and more logging Modified: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh 2014-09-11 21:29:18 UTC (rev 8246) +++ SwiftApps/subjobs/subjob.sh 2014-09-11 21:38:47 UTC (rev 8247) @@ -31,7 +31,7 @@ #without timeout #(echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 ; echo $?) & - (echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : /bin/sleep $stime >RUNJOB.$j-$i 2>&1 ; echo Exit status: $?) & + (echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : /bin/sleep $stime >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & # Important - give some time for runjob to get initialized sleep 3 From ketan at ci.uchicago.edu Fri Sep 12 09:44:18 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Fri, 12 Sep 2014 09:44:18 -0500 (CDT) Subject: [Swift-commit] r8248 - SwiftApps/subjobs Message-ID: <20140912144418.5B1819D820@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-12 09:44:18 -0500 (Fri, 12 Sep 2014) New Revision: 8248 Modified: SwiftApps/subjobs/subjob.sh Log: fix n and p Modified: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh 2014-09-11 21:38:47 UTC (rev 8247) +++ SwiftApps/subjobs/subjob.sh 2014-09-12 14:44:18 UTC (rev 8248) @@ -11,7 +11,7 @@ #build app mpixlc mpicatnap.c -o mpicatnap -SHAPE="1x2x2x2x1" +SHAPE="2x2x2x2x2" CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) @@ -31,7 +31,7 @@ #without timeout #(echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 ; echo $?) & - (echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : /bin/sleep $stime >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & + (echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 16 -n 512 : ./mysleep >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & # Important - give some time for runjob to get initialized sleep 3 @@ -44,7 +44,7 @@ done # The runjobs were backgrounded, wait for them to finish wait - echo "Done $i" + echo "Done $j" i=0 done From wozniak at ci.uchicago.edu Mon Sep 15 10:12:55 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Mon, 15 Sep 2014 10:12:55 -0500 (CDT) Subject: [Swift-commit] r8249 - usertools/plotter Message-ID: <20140915151255.2EB8B9DFF9@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-15 10:12:54 -0500 (Mon, 15 Sep 2014) New Revision: 8249 Modified: usertools/plotter/README.txt Log: More docs Modified: usertools/plotter/README.txt =================================================================== --- usertools/plotter/README.txt 2014-09-12 14:44:18 UTC (rev 8248) +++ usertools/plotter/README.txt 2014-09-15 15:12:54 UTC (rev 8249) @@ -12,6 +12,8 @@ by using the rich feature set in JFreeChart and providing a simple, scriptable user interface. +It should be easy to extend the plotter to use additional JFreeChart features. + == Installation Just check out from SVN and build with Ant: @@ -58,10 +60,9 @@ (Cf. Java +Double.parseDouble()+.) * True/false may be +true+ or +false+. (Cf. Java +Boolean.parseBoolean()+.) -* Some properties are set on a per-file basis. In this case, part of +* Some properties are set on a per-data-file basis. In this case, part of the key is the file name. - +title+:: Set a plot title. +xlabel,ylabel+:: Set labels for the X and Y axes. +width,height+:: Set the width, height of the output EPS in pixels. @@ -70,7 +71,7 @@ Defaults to an auto-selection made by JFreeChart. +bw+:: If true, use black and white only. Default: +false+. +legend.enabled+:: If true, show a legend. Default: +true+. -+axis.x,axis.y+:: May be +normal+ or +logarithmic+. ++axis.x,axis.y+:: May be +normal+, +logarithmic+, or +date+. For +date+, provide date data as decimal milliseconds since the Unix Epoch. Default: +normal+. Default: +normal+. +label._filename_+:: Set the legend label for the data series from file +_filename_+. @@ -98,6 +99,7 @@ ---- convert my_output.eps my_output.png +convert my_output.eps my_output.pdf ---- == Data @@ -109,10 +111,11 @@ 8 0 # This is a comment -1 7 # This is also a comment +1 7,000,000.1 # This is also a comment ---- As shown, empty lines and +#+ comments are accepted. +Commas are also automatically stripped. == Plotter options From wozniak at ci.uchicago.edu Thu Sep 18 11:54:21 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Thu, 18 Sep 2014 11:54:21 -0500 (CDT) Subject: [Swift-commit] r8250 - in usertools/plotter: . src/plotter Message-ID: <20140918165421.732E59D820@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-18 11:54:20 -0500 (Thu, 18 Sep 2014) New Revision: 8250 Modified: usertools/plotter/README.txt usertools/plotter/src/plotter/Lines.java Log: Support Log and Logarithmic Modified: usertools/plotter/README.txt =================================================================== --- usertools/plotter/README.txt 2014-09-15 15:12:54 UTC (rev 8249) +++ usertools/plotter/README.txt 2014-09-18 16:54:20 UTC (rev 8250) @@ -71,8 +71,10 @@ Defaults to an auto-selection made by JFreeChart. +bw+:: If true, use black and white only. Default: +false+. +legend.enabled+:: If true, show a legend. Default: +true+. -+axis.x,axis.y+:: May be +normal+, +logarithmic+, or +date+. For +date+, provide date data as decimal milliseconds since the Unix Epoch. Default: +normal+. -Default: +normal+. ++axis.x,axis.y+:: May be +normal+, +logarithmic+ (tends to use +scientific notation in labels), +log+, or +date+. For +date+, provide +date data as decimal milliseconds since the Unix Epoch. Default: ++normal+. +label._filename_+:: Set the legend label for the data series from file +_filename_+. +shape._filename_+:: If +none+, use no shape for the data series from Modified: usertools/plotter/src/plotter/Lines.java =================================================================== --- usertools/plotter/src/plotter/Lines.java 2014-09-15 15:12:54 UTC (rev 8249) +++ usertools/plotter/src/plotter/Lines.java 2014-09-18 16:54:20 UTC (rev 8250) @@ -320,9 +320,14 @@ { if (axis_x_type.equals("logarithmic")) { - NumberAxis domainAxis = new LogarithmicAxis(xlabel); + ValueAxis domainAxis = new LogarithmicAxis(xlabel); plot.setDomainAxis(domainAxis); } + else if (axis_x_type.equals("log")) + { + ValueAxis domainAxis = new LogAxis(xlabel); + plot.setDomainAxis(domainAxis); + } else if (axis_x_type.equals("date")) { DateAxis domainAxis = new DateAxis(); @@ -334,6 +339,12 @@ if (axis_y_type.equals("logarithmic")) { + // + ValueAxis rangeAxis = new LogarithmicAxis(ylabel); + plot.setRangeAxis(rangeAxis); + } + else if (axis_y_type.equals("log")) + { ValueAxis rangeAxis = new LogAxis(ylabel); plot.setRangeAxis(rangeAxis); } From wozniak at ci.uchicago.edu Tue Sep 23 12:50:51 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Tue, 23 Sep 2014 12:50:51 -0500 (CDT) Subject: [Swift-commit] r8251 - www/Swift-T Message-ID: <20140923175051.F15419CCA1@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-23 12:50:51 -0500 (Tue, 23 Sep 2014) New Revision: 8251 Added: www/Swift-T/leaf__1.png Log: Adding leaf__1.png Added: www/Swift-T/leaf__1.png =================================================================== (Binary files differ) Property changes on: www/Swift-T/leaf__1.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream From wozniak at ci.uchicago.edu Tue Sep 23 12:51:28 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Tue, 23 Sep 2014 12:51:28 -0500 (CDT) Subject: [Swift-commit] r8252 - www Message-ID: <20140923175128.372669CCA1@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-23 12:51:28 -0500 (Tue, 23 Sep 2014) New Revision: 8252 Modified: www/push_to.sh Log: Include formula PNG Modified: www/push_to.sh =================================================================== --- www/push_to.sh 2014-09-23 17:50:51 UTC (rev 8251) +++ www/push_to.sh 2014-09-23 17:51:28 UTC (rev 8252) @@ -102,6 +102,7 @@ about/index.php Swift-T/index.php Swift-T/*.html +Swift-T/*.png Swift-T/images/*.png Swift-T/downloads/*.tar.gz index.html From ketan at ci.uchicago.edu Wed Sep 24 10:46:32 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Wed, 24 Sep 2014 10:46:32 -0500 (CDT) Subject: [Swift-commit] r8253 - SwiftApps/subjobs Message-ID: <20140924154632.855069CCA1@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-24 10:46:31 -0500 (Wed, 24 Sep 2014) New Revision: 8253 Modified: SwiftApps/subjobs/apps SwiftApps/subjobs/catsnsleepmpi.swift SwiftApps/subjobs/cf SwiftApps/subjobs/cobalt.xml SwiftApps/subjobs/runbash.sh SwiftApps/subjobs/runswift.sh SwiftApps/subjobs/subjob.sh Log: changes for experimentation Modified: SwiftApps/subjobs/apps =================================================================== --- SwiftApps/subjobs/apps 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/apps 2014-09-24 15:46:31 UTC (rev 8253) @@ -1,3 +1,3 @@ localhost cat /bin/cat null null null -cluster bgsh bg.sh null null null +cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null Modified: SwiftApps/subjobs/catsnsleepmpi.swift =================================================================== --- SwiftApps/subjobs/catsnsleepmpi.swift 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/catsnsleepmpi.swift 2014-09-24 15:46:31 UTC (rev 8253) @@ -2,7 +2,7 @@ app (file o, file sout, file serr) cat (file i) { - bgsh "/home/ketan/subjoblab/mpicatnap" @i @o arg("s","1") stdout=@sout stderr=@serr; + bgsh "/home/ketan/SwiftApps/subjobs/mpicatnap" @i @o arg("s","1") stdout=@sout stderr=@serr; } file out[]; Modified: SwiftApps/subjobs/cf =================================================================== --- SwiftApps/subjobs/cf 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/cf 2014-09-24 15:46:31 UTC (rev 8253) @@ -1,27 +1,6 @@ +use.provider.staging=false wrapperlog.always.transfer=false +execution.retries=0 provider.staging.pin.swiftfiles=false sitedir.keep=false -kickstart.always.transfer=false -replication.limit=3 -throttle.host.submit=2 -clustering.min.time=15 -kickstart.enabled=maybe -execution.retries=10 -pgraph=false -use.provider.staging=false -tracing.enabled=true -foreach.max.threads=1024 use.wrapper.staging=false -replication.enabled=false -throttle.submit=4 -throttle.score.job.factor=0.2 -lazy.errors=true -clustering.enabled=false -caching.algorithm=LRU -pgraph.node.options=color="seagreen", style="filled" -replication.min.queue.time=60 -clustering.queue.delay=4 -throttle.file.operations=8 -provenance.log=false -throttle.transfers=4 -pgraph.graph.options=splines="compound", rankdir="TB" Modified: SwiftApps/subjobs/cobalt.xml =================================================================== --- SwiftApps/subjobs/cobalt.xml 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/cobalt.xml 2014-09-24 15:46:31 UTC (rev 8253) @@ -12,9 +12,15 @@ 00:40:00 2050 -256 -256 -8 +512 +512 +16 +DEBUG +TRUE +ON +/home/ketan/workerlogs +DEBUG +/home/ketan/workerlogs 32 /home/ketan/swiftwork Modified: SwiftApps/subjobs/runbash.sh =================================================================== --- SwiftApps/subjobs/runbash.sh 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/runbash.sh 2014-09-24 15:46:31 UTC (rev 8253) @@ -1,5 +1,5 @@ #!/bin/bash #To run: -qsub -n 256 -t 50 --mode script subjob.sh +qsub -n 512 -t 02:00:00 --mode script subjob.sh Modified: SwiftApps/subjobs/runswift.sh =================================================================== --- SwiftApps/subjobs/runswift.sh 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/runswift.sh 2014-09-24 15:46:31 UTC (rev 8253) @@ -7,8 +7,7 @@ mpixlc mpicatnap.c -o mpicatnap #New method -/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=32 -#~/prebuilt/swift-devel/cog/modules/swift/dist/swift-svn/bin/swift catsnsleepmpi.swift -n=10 +/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt.xml -config cf -tc.file apps catsnsleepmpi.swift -n=300 -s=60 #A testblock run #qsub -A ATPESC2013 -n 32 -t 5 -q low --mode c16 --mode script testblock.sh # --disable_preboot Modified: SwiftApps/subjobs/subjob.sh =================================================================== --- SwiftApps/subjobs/subjob.sh 2014-09-23 17:51:28 UTC (rev 8252) +++ SwiftApps/subjobs/subjob.sh 2014-09-24 15:46:31 UTC (rev 8253) @@ -10,8 +10,9 @@ #build app mpixlc mpicatnap.c -o mpicatnap +bgxlc mysleep.c -o mysleep -SHAPE="2x2x2x2x2" +SHAPE="2x2x2x2x1" CORNERS=$(get-corners.py $COBALT_PARTNAME $SHAPE) @@ -20,7 +21,7 @@ MAXRUNJOB=64 i=0 -for j in $(seq 1 200) +for j in $(seq 1 1024) do for CORNER in $CORNERS do @@ -30,12 +31,11 @@ #runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 --timeout 30 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 & #without timeout - #(echo "About to use this corner: $CORNER"; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 1 --np 8 : mpicatnap in.data out.data $stime >RUNJOB.$j-$i 2>&1 ; echo $?) & - (echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 16 -n 512 : ./mysleep >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & + #(echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 16 -n 128 : ./mysleep 1 >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & + (echo "About to use this corner: $CORNER" >RUNJOB.$j-$i; runjob --block $COBALT_PARTNAME --corner $CORNER --shape $SHAPE -p 16 -n 64 : mpicatnap in.data out.data $stime >>RUNJOB.$j-$i 2>&1 ; echo Exit status: $? >>RUNJOB.$j-$i) & # Important - give some time for runjob to get initialized sleep 3 - i=$((i+1)) if [ $i -ge $MAXRUNJOB ]; then echo "Reached MAXRUNJOB $MAXRUNJOB" From wozniak at ci.uchicago.edu Mon Sep 29 08:28:26 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Mon, 29 Sep 2014 08:28:26 -0500 (CDT) Subject: [Swift-commit] r8254 - SwiftTutorials Message-ID: <20140929132827.04C399CC84@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-29 08:28:26 -0500 (Mon, 29 Sep 2014) New Revision: 8254 Added: SwiftTutorials/IIT_2014-09-29/ Log: Copy for IIT talk From wozniak at ci.uchicago.edu Mon Sep 29 09:52:51 2014 From: wozniak at ci.uchicago.edu (wozniak at ci.uchicago.edu) Date: Mon, 29 Sep 2014 09:52:51 -0500 (CDT) Subject: [Swift-commit] r8255 - SwiftTutorials/IIT_2014-09-29 Message-ID: <20140929145251.2CFD99CCA2@svn.ci.uchicago.edu> Author: wozniak Date: 2014-09-29 09:52:51 -0500 (Mon, 29 Sep 2014) New Revision: 8255 Modified: SwiftTutorials/IIT_2014-09-29/Swift-OHBM.2013.0616.pptx Log: Ready Modified: SwiftTutorials/IIT_2014-09-29/Swift-OHBM.2013.0616.pptx =================================================================== (Binary files differ) From ketan at ci.uchicago.edu Mon Sep 29 09:53:02 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 29 Sep 2014 09:53:02 -0500 (CDT) Subject: [Swift-commit] r8256 - SwiftApps/subjobs Message-ID: <20140929145302.D45B49CCA2@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-29 09:53:02 -0500 (Mon, 29 Sep 2014) New Revision: 8256 Modified: SwiftApps/subjobs/bg.sh SwiftApps/subjobs/runswift.sh Log: old changes Modified: SwiftApps/subjobs/bg.sh =================================================================== --- SwiftApps/subjobs/bg.sh 2014-09-29 14:52:51 UTC (rev 8255) +++ SwiftApps/subjobs/bg.sh 2014-09-29 14:53:02 UTC (rev 8256) @@ -28,7 +28,7 @@ export SWIFT_SUBBLOCKS=$(get-corners.py "$COBALT_PARTNAME" $SHAPE) export SWIFT_SUBBLOCK_ARRAY=($SWIFT_SUBBLOCKS) -echo "$0": SWIFT_SUBBLOCKS="$SWIFT_SUBBLOCKS" +#echo "$0": SWIFT_SUBBLOCKS="$SWIFT_SUBBLOCKS" if [ "_$SWIFT_SUBBLOCKS" = _ ]; then echo ERROR: "$0": SWIFT_SUBBLOCKS is null. @@ -36,10 +36,6 @@ fi nsb=${#SWIFT_SUBBLOCK_ARRAY[@]} -for ((sb=0;sb Author: ketan Date: 2014-09-29 10:14:31 -0500 (Mon, 29 Sep 2014) New Revision: 8257 Modified: SwiftApps/subjobs/README.txt SwiftApps/subjobs/setup Log: READMe and setup Modified: SwiftApps/subjobs/README.txt =================================================================== --- SwiftApps/subjobs/README.txt 2014-09-29 14:53:02 UTC (rev 8256) +++ SwiftApps/subjobs/README.txt 2014-09-29 15:14:31 UTC (rev 8257) @@ -3,25 +3,46 @@ Introduction ------------ -Sub-block jobs is a mode of running jobs on BlueGene systems wherein one can -allocate a larger block of compute nodes and repeatedly submit jobs of smaller -sized sub-blocks to this larger allocation. +This document describes an approach to run relatively smaller jobs over a +single large block on BlueGene systems. The technique, called sub-block jobs +lets users submit multiple, independent, smaller jobs within a single larger +cobalt block. Sub-block jobs is a mode of running jobs on BlueGene systems +wherein one can allocate a larger block of compute nodes and repeatedly submit +jobs of smaller sized sub-blocks to this larger allocation. -This package provides tools and scripts to run Swift applications in sub-block mode over the BlueGene resources. +This package provides tools and scripts to run Swift applications in sub-block +mode over the BlueGene resources. The benefit of this approach is that the +user does not have to invoke the sub-block specific routines involving the +details of the underlying node interconnect hardware. The approach +transparently allow user to run jobs directly via Swift. Additionally, users +can run multiple 'waves' of jobs asynchronously and in parallel without +restarting the outer block. Swift sub-block jobs --------------------- -To set up environment: +To download the package, checkout the code as follows: ---- +svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftApps/subjobs +---- + +followed by: + +---- +cd subjobs +---- + +To set up the environment: + +---- source setup ---- To run an example application ---- -./runswift +./runswift.sh ---- sub-block jobs from bash Modified: SwiftApps/subjobs/setup =================================================================== --- SwiftApps/subjobs/setup 2014-09-29 14:53:02 UTC (rev 8256) +++ SwiftApps/subjobs/setup 2014-09-29 15:14:31 UTC (rev 8257) @@ -1,4 +1,6 @@ #!/bin/bash +#put bg.sh in path + export PATH=$PWD:$PATH From ketan at ci.uchicago.edu Mon Sep 29 11:27:13 2014 From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu) Date: Mon, 29 Sep 2014 11:27:13 -0500 (CDT) Subject: [Swift-commit] r8258 - SwiftApps/subjobs Message-ID: <20140929162713.63DEB9CCA2@svn.ci.uchicago.edu> Author: ketan Date: 2014-09-29 11:27:13 -0500 (Mon, 29 Sep 2014) New Revision: 8258 Modified: SwiftApps/subjobs/README.txt Log: subblock limitations Modified: SwiftApps/subjobs/README.txt =================================================================== --- SwiftApps/subjobs/README.txt 2014-09-29 15:14:31 UTC (rev 8257) +++ SwiftApps/subjobs/README.txt 2014-09-29 16:27:13 UTC (rev 8258) @@ -45,19 +45,10 @@ ./runswift.sh ---- -sub-block jobs from bash -------------------------- - -To run the example application from bash: - ----- -./runbash ----- - Swift Sub-block jobs: HowTo ---------------------------- -In order to convert an ordinary Swift app run in sub-block mode, the following changes are required: +To convert an ordinary Swift application run in sub-block mode, the following changes are required: . Add bg.sh as the application invoker in place of sh. For example, if the app definition is as follows: @@ -108,4 +99,16 @@ ---- +Sub-block limitations +---------------------- +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 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. +