2010-11-11 02:56:14,607-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-9jiidf1k -jobdir 9 -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1J8R.pdb|4TRA.pdb -of 1J8R_001.dat -k -cdmfile -status provider -a -modulo 1:100 -root 1J8R -static 1J8R.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:14,607-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-10-8-2-2-1-1289432354376) is /bin/bash shared/_swiftwrap modftdock-9jiidf1k -jobdir 9 -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1J8R.pdb|4TRA.pdb -of 1J8R_001.dat -k -cdmfile -status provider -a -modulo 1:100 -root 1J8R -static 1J8R.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:15,306-0600 INFO LateBindingScheduler JobQueue: 333 2010-11-11 02:56:15,307-0600 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=sge, score=99.858 2010-11-11 02:56:15,307-0600 INFO vdl:execute END_SUCCESS thread=0-1-16-8-56-2 tr=modftdock 2010-11-11 02:56:15,308-0600 INFO vdl:createdirset START jobid=modftdock-ajiidf1k host=sge - Initializing directory structure 2010-11-11 02:56:15,950-0600 INFO vdl:createdirset END jobid=modftdock-ajiidf1k - Done initializing directory structure 2010-11-11 02:56:15,950-0600 INFO vdl:dostagein START jobid=modftdock-ajiidf1k - Staging in files 2010-11-11 02:56:15,952-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:15,952-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:15,952-0600 INFO vdl:dostagein END jobid=modftdock-ajiidf1k - Staging in finished 2010-11-11 02:56:15,953-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-ajiidf1k -jobdir a -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K77.pdb|4TRA.pdb -of 1K77_036.dat -k -cdmfile -status provider -a -modulo 36:100 -root 1K77 -static 1K77.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:15,953-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-19-8-37-2-1-1289432354382) is /bin/bash shared/_swiftwrap modftdock-ajiidf1k -jobdir a -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K77.pdb|4TRA.pdb -of 1K77_036.dat -k -cdmfile -status provider -a -modulo 36:100 -root 1K77 -static 1K77.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:20,042-0600 INFO SGEExecutor Job id from qsub: 4044702 2010-11-11 02:56:20,046-0600 INFO SGEExecutor Job id from qsub: 4044703 2010-11-11 02:56:23,179-0600 INFO AbstractQueuePoller Actively monitored: 513, New: 2, Done: 0 2010-11-11 02:56:33,478-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:56:44,033-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:56:54,405-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:54,407-0600 INFO vdl:dostageout START jobid=modftdock-d6iidf1k - Staging out files 2010-11-11 02:56:54,408-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,183-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,184-0600 INFO vdl:dostageout START jobid=modftdock-f3iidf1k - Staging out files 2010-11-11 02:56:55,185-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,197-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 2 2010-11-11 02:56:55,352-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,353-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,354-0600 INFO vdl:dostageout END jobid=modftdock-d6iidf1k - Staging out finished 2010-11-11 02:56:55,947-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,948-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:55,949-0600 INFO vdl:dostageout END jobid=modftdock-f3iidf1k - Staging out finished 2010-11-11 02:56:56,055-0600 INFO LateBindingScheduler JobQueue: 332 2010-11-11 02:56:56,055-0600 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=sge, score=99.858 2010-11-11 02:56:56,055-0600 INFO vdl:execute END_SUCCESS thread=0-1-16-8-45-2 tr=modftdock 2010-11-11 02:56:56,058-0600 INFO vdl:createdirset START jobid=modftdock-bjiidf1k host=sge - Initializing directory structure 2010-11-11 02:56:56,526-0600 INFO vdl:createdirset END jobid=modftdock-bjiidf1k - Done initializing directory structure 2010-11-11 02:56:56,527-0600 INFO vdl:dostagein START jobid=modftdock-bjiidf1k - Staging in files 2010-11-11 02:56:56,528-0600 INFO LateBindingScheduler JobQueue: 331 2010-11-11 02:56:56,528-0600 INFO LateBindingScheduler JobQueue: 331 2010-11-11 02:56:56,529-0600 INFO vdl:dostagein END jobid=modftdock-bjiidf1k - Staging in finished 2010-11-11 02:56:56,530-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-bjiidf1k -jobdir b -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1KYH.pdb|4TRA.pdb -of 1KYH_086.dat -k -cdmfile -status provider -a -modulo 86:100 -root 1KYH -static 1KYH.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:56,530-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-3-8-87-2-1-1289432354408) is /bin/bash shared/_swiftwrap modftdock-bjiidf1k -jobdir b -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1KYH.pdb|4TRA.pdb -of 1KYH_086.dat -k -cdmfile -status provider -a -modulo 86:100 -root 1KYH -static 1KYH.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:56,733-0600 INFO LateBindingScheduler JobQueue: 331 2010-11-11 02:56:56,734-0600 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=sge, score=99.858 2010-11-11 02:56:56,734-0600 INFO vdl:execute END_SUCCESS thread=0-1-17-8-65-2 tr=modftdock 2010-11-11 02:56:56,735-0600 INFO vdl:createdirset START jobid=modftdock-cjiidf1k host=sge - Initializing directory structure 2010-11-11 02:56:57,159-0600 INFO vdl:createdirset END jobid=modftdock-cjiidf1k - Done initializing directory structure 2010-11-11 02:56:57,159-0600 INFO vdl:dostagein START jobid=modftdock-cjiidf1k - Staging in files 2010-11-11 02:56:57,161-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:56:57,161-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:56:57,161-0600 INFO vdl:dostagein END jobid=modftdock-cjiidf1k - Staging in finished 2010-11-11 02:56:57,162-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-cjiidf1k -jobdir c -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1KTN.pdb|4TRA.pdb -of 1KTN_019.dat -k -cdmfile -status provider -a -modulo 19:100 -root 1KTN -static 1KTN.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:57,162-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-4-8-20-2-1-1289432354414) is /bin/bash shared/_swiftwrap modftdock-cjiidf1k -jobdir c -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1KTN.pdb|4TRA.pdb -of 1KTN_019.dat -k -cdmfile -status provider -a -modulo 19:100 -root 1KTN -static 1KTN.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:56:58,742-0600 INFO SGEExecutor Job id from qsub: 4044704 2010-11-11 02:56:58,743-0600 INFO SGEExecutor Job id from qsub: 4044705 2010-11-11 02:57:06,594-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:06,596-0600 INFO vdl:dostageout START jobid=modftdock-z5iidf1k - Staging out files 2010-11-11 02:57:06,597-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:06,764-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:06,764-0600 INFO vdl:dostageout START jobid=modftdock-94iidf1k - Staging out files 2010-11-11 02:57:06,765-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:06,856-0600 INFO AbstractQueuePoller Actively monitored: 513, New: 2, Done: 2 2010-11-11 02:57:07,229-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:07,230-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:07,230-0600 INFO vdl:dostageout END jobid=modftdock-z5iidf1k - Staging out finished 2010-11-11 02:57:07,662-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:07,663-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:07,664-0600 INFO vdl:dostageout END jobid=modftdock-94iidf1k - Staging out finished 2010-11-11 02:57:07,963-0600 INFO LateBindingScheduler JobQueue: 330 2010-11-11 02:57:07,964-0600 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=sge, score=99.858 2010-11-11 02:57:07,964-0600 INFO vdl:execute END_SUCCESS thread=0-1-3-8-66-2 tr=modftdock 2010-11-11 02:57:07,965-0600 INFO vdl:createdirset START jobid=modftdock-djiidf1k host=sge - Initializing directory structure 2010-11-11 02:57:08,226-0600 INFO LateBindingScheduler JobQueue: 329 2010-11-11 02:57:08,226-0600 INFO vdl:createdirset END jobid=modftdock-djiidf1k - Done initializing directory structure 2010-11-11 02:57:08,226-0600 INFO vdl:dostagein START jobid=modftdock-djiidf1k - Staging in files 2010-11-11 02:57:08,226-0600 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=sge, score=99.858 2010-11-11 02:57:08,227-0600 INFO vdl:execute END_SUCCESS thread=0-1-12-8-44-2 tr=modftdock 2010-11-11 02:57:08,228-0600 INFO vdl:createdirset START jobid=modftdock-ejiidf1k host=sge - Initializing directory structure 2010-11-11 02:57:08,229-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:57:08,475-0600 INFO vdl:createdirset END jobid=modftdock-ejiidf1k - Done initializing directory structure 2010-11-11 02:57:08,228-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:57:08,475-0600 INFO vdl:dostagein START jobid=modftdock-ejiidf1k - Staging in files 2010-11-11 02:57:08,476-0600 INFO vdl:dostagein END jobid=modftdock-djiidf1k - Staging in finished 2010-11-11 02:57:08,477-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:57:08,477-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-djiidf1k -jobdir d -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K7K.pdb|4TRA.pdb -of 1K7K_067.dat -k -cdmfile -status provider -a -modulo 67:100 -root 1K7K -static 1K7K.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:57:08,477-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-8-8-68-2-1-1289432354444) is /bin/bash shared/_swiftwrap modftdock-djiidf1k -jobdir d -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K7K.pdb|4TRA.pdb -of 1K7K_067.dat -k -cdmfile -status provider -a -modulo 67:100 -root 1K7K -static 1K7K.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:57:08,477-0600 INFO LateBindingScheduler JobQueue: 329 2010-11-11 02:57:08,477-0600 INFO vdl:dostagein END jobid=modftdock-ejiidf1k - Staging in finished 2010-11-11 02:57:08,478-0600 INFO Execute Submit: in: ftdock-20101110-1738-zyqtbmhc command: /bin/bash shared/_swiftwrap modftdock-ejiidf1k -jobdir e -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K6D.pdb|4TRA.pdb -of 1K6D_048.dat -k -cdmfile -status provider -a -modulo 48:100 -root 1K6D -static 1K6D.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:57:08,478-0600 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-1-20-8-49-2-1-1289432354446) is /bin/bash shared/_swiftwrap modftdock-ejiidf1k -jobdir e -scratch -e /cchome/mparis_x/swift/modftdock -out stdout.txt -err stderr.txt -i -d -if 1K6D.pdb|4TRA.pdb -of 1K6D_048.dat -k -cdmfile -status provider -a -modulo 48:100 -root 1K6D -static 1K6D.pdb -mobile 4TRA.pdb -calculate_grid 0.5 -angle_step 10 -keep 10 -noelec 2010-11-11 02:57:11,224-0600 INFO SGEExecutor Job id from qsub: 4044707 2010-11-11 02:57:11,225-0600 INFO SGEExecutor Job id from qsub: 4044706 2010-11-11 02:57:17,314-0600 INFO AbstractQueuePoller Actively monitored: 513, New: 2, Done: 0 2010-11-11 02:57:27,569-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:57:37,814-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:57:48,175-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:57:58,910-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:58:08,977-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:58:19,446-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 0 2010-11-11 02:58:31,483-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:58:31,484-0600 INFO vdl:dostageout START jobid=modftdock-u2iidf1k - Staging out files 2010-11-11 02:58:31,487-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:58:31,556-0600 INFO AbstractQueuePoller Actively monitored: 515, New: 0, Done: 2 2010-11-11 02:58:32,801-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:58:32,802-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:58:32,802-0600 INFO vdl:dostageout END jobid=modftdock-u2iidf1k - Staging out finished 2010-11-11 02:58:33,774-0600 INFO LateBindingScheduler JobQueue: 328 2010-11-11 02:58:33,777-0600 INFO vdl:execute END_FAILURE thread=0-1-7-8-32-2 tr=modftdock 2010-11-11 02:58:33,807-0600 DEBUG VDL2ExecutionContext sys:throw @ execute-default.k, line: 45: Exception in modftdock: Arguments: [-modulo, 31:100, -root, 1KS2, -static, 1KS2.pdb, -mobile, 4TRA.pdb, -calculate_grid, 0.5, -angle_step, 10, -keep, 10, -noelec] Host: sge Directory: ftdock-20101110-1738-zyqtbmhc/jobs/z/modftdock-z2iidf1k stderr.txt: stdout.txt: ---- Exception in modftdock: Arguments: [-modulo, 31:100, -root, 1KS2, -static, 1KS2.pdb, -mobile, 4TRA.pdb, -calculate_grid, 0.5, -angle_step, 10, -keep, 10, -noelec] Host: sge Directory: ftdock-20101110-1738-zyqtbmhc/jobs/z/modftdock-z2iidf1k stderr.txt: stdout.txt: ---- Caused by: Exception caught while reading exit code Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) at java.lang.Thread.run(Unknown Source) at org.globus.cog.karajan.workflow.nodes.functions.KException.function(KException.java:29) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:27) at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192) at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181) at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309) at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28) at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50) at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26) at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63) at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238) at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289) at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343) at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:230) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44) at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431) at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668) at java.lang.Thread.run(Unknown Source) Caused by: Exception caught while reading exit code Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) at java.lang.Thread.run(Unknown Source) at org.globus.cog.karajan.workflow.events.FailureNotificationEvent.(FailureNotificationEvent.java:36) at org.globus.cog.karajan.workflow.events.FailureNotificationEvent.(FailureNotificationEvent.java:42) at org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:153) at org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:373) at org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276) at org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:127) at org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168) at org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:675) at org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:422) at org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410) at org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:233) at org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:223) at org.globus.cog.abstraction.impl.common.AbstractDelegatedTaskHandler.failTask(AbstractDelegatedTaskHandler.java:54) at org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.processFailed(AbstractJobSubmissionTaskHandler.java:105) at org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.processFailed(AbstractExecutor.java:300) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:111) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) ... 1 more Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code ... 7 more Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) ... 6 more 2010-11-11 02:58:33,896-0600 INFO ExecutionContext Detailed exception: Exception in modftdock: Arguments: [-modulo, 31:100, -root, 1KS2, -static, 1KS2.pdb, -mobile, 4TRA.pdb, -calculate_grid, 0.5, -angle_step, 10, -keep, 10, -noelec] Host: sge Directory: ftdock-20101110-1738-zyqtbmhc/jobs/z/modftdock-z2iidf1k stderr.txt: stdout.txt: ---- Caused by: Exception caught while reading exit code Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) at java.lang.Thread.run(Unknown Source) at org.globus.cog.karajan.workflow.nodes.functions.KException.function(KException.java:29) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:27) at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192) at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181) at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309) at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28) at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50) at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26) at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63) at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238) at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289) at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343) at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:230) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44) at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431) at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668) at java.lang.Thread.run(Unknown Source) Caused by: Exception caught while reading exit code Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) at java.lang.Thread.run(Unknown Source) at org.globus.cog.karajan.workflow.events.FailureNotificationEvent.(FailureNotificationEvent.java:36) at org.globus.cog.karajan.workflow.events.FailureNotificationEvent.(FailureNotificationEvent.java:42) at org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:153) at org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:373) at org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276) at org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:127) at org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168) at org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:675) at org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:422) at org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410) at org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:233) at org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:223) at org.globus.cog.abstraction.impl.common.AbstractDelegatedTaskHandler.failTask(AbstractDelegatedTaskHandler.java:54) at org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.processFailed(AbstractJobSubmissionTaskHandler.java:105) at org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.processFailed(AbstractExecutor.java:300) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:111) at org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:81) at org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177) at org.globus.cog.abstraction.impl.scheduler.sge.QueuePoller.processStdout(QueuePoller.java:116) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169) at org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82) ... 1 more Caused by: org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Exception caught while reading exit code ... 7 more Caused by: java.lang.NumberFormatException: null at java.lang.Integer.parseInt(Unknown Source) at java.lang.Integer.parseInt(Unknown Source) at org.globus.cog.abstraction.impl.scheduler.common.Job.processExitCode(Job.java:93) ... 6 more 2010-11-11 02:58:33,896-0600 DEBUG Loader Swift finished with errors