[Swift-user] Argument list to long
Jonathan Monette
jon.monette at gmail.com
Mon Oct 4 18:39:40 CDT 2010
Yes. I have to make sure that all 4100 files are created before the
failing app can execute.
The writeData() way seems like a hack to get around the problem is Swift
but I will try it out and see if my script completes.
Mihael: pasted below is the stack trace that was generated in the log file.
2010-10-04 15:32:29,988-0500 WARN vdl:transferwrapperlog Failed to
transfer wrapper log from unrectified-20101004-1432-k89q8d3b/info/y on
localhost
2010-10-04 15:32:29,991-0500 INFO vdl:execute END_FAILURE thread=0-3
tr=mImgtbl
2010-10-04 15:32:29,996-0500 DEBUG VDL2ExecutionContext sys:throw @
execute-default.k, line: 45: Exception in mImgtbl:
Arguments: [proj_dir, images.tbl]
Host: localhost
Directory: unrectified-20101004-1432-k89q8d3b/jobs/y/mImgtbl-yuqc8ozj
stderr.txt:
stdout.txt:
----
Exception in mImgtbl:
Arguments: [proj_dir, images.tbl]
Host: localhost
Directory: unrectified-20101004-1432-k89q8d3b/jobs/y/mImgtbl-yuqc8ozj
stderr.txt:
stdout.txt:
----
Caused by: Cannot run program "/bin/bash" (in directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
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$Worker.run(ThreadPoolExecutor.java:668)
at java.lang.Thread.run(Thread.java:619)
Caused by: Cannot run program "/bin/bash" (in directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
at
org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
at
org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:42)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.failImmediately(FlowNode.java:153)
at
org.globus.cog.karajan.workflow.nodes.grid.GridExec.taskFailed(GridExec.java:373)
at
org.globus.cog.karajan.workflow.nodes.grid.AbstractGridNode.statusChanged(AbstractGridNode.java:276)
at org.griphyn.vdl.karajan.lib.Execute.statusChanged(Execute.java:127)
at
org.globus.cog.karajan.scheduler.AbstractScheduler.fireJobStatusChangeEvent(AbstractScheduler.java:168)
at
org.globus.cog.karajan.scheduler.LateBindingScheduler.statusChanged(LateBindingScheduler.java:675)
at
org.globus.cog.karajan.scheduler.WeightedHostScoreScheduler.statusChanged(WeightedHostScoreScheduler.java:422)
at
org.griphyn.vdl.karajan.VDSAdaptiveScheduler.statusChanged(VDSAdaptiveScheduler.java:410)
at
org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:233)
at
org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:223)
at
org.globus.cog.abstraction.impl.common.AbstractDelegatedTaskHandler.failTask(AbstractDelegatedTaskHandler.java:54)
at
org.globus.cog.abstraction.impl.execution.local.JobSubmissionTaskHandler.run(JobSubmissionTaskHandler.java:220)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
... 1 more
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at
org.globus.cog.abstraction.impl.execution.local.JobSubmissionTaskHandler.run(JobSubmissionTaskHandler.java:161)
... 6 more
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 8 more
2010-10-04 15:32:30,145-0500 INFO TaskNotifier Congestion queue size: 0
2010-10-04 15:32:30,193-0500 INFO ExecutionContext Detailed exception:
Exception in mImgtbl:
Arguments: [proj_dir, images.tbl]
Host: localhost
Directory: unrectified-20101004-1432-k89q8d3b/jobs/y/mImgtbl-yuqc8ozj
stderr.txt:
stdout.txt:
----
Caused by: Cannot run program "/bin/bash" (in directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
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(Thread.java:619)
Caused by: Cannot run program "/bin/bash" (in directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
at
org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(FailureNotificationEvent.java:36)
at
org.globus.cog.karajan.workflow.events.FailureNotificationEvent.<init>(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.execution.local.JobSubmissionTaskHandler.run(JobSubmissionTaskHandler.java:220)
at
java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
... 1 more
Caused by: java.io.IOException: Cannot run program "/bin/bash" (in
directory
"/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
java.io.IOException: error=7, Argument list too long
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at
org.globus.cog.abstraction.impl.execution.local.JobSubmissionTaskHandler.run(JobSubmissionTaskHandler.java:161)
... 6 more
Caused by: java.io.IOException: java.io.IOException: error=7, Argument
list too long
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 8 more
On 10/4/10 4:22 PM, Michael Wilde wrote:
> My guess is that you are calling one of your reduction jobs passing in a lot of files on the command line. Is that the case for the failing app?
>
> If so, you may be able to use the writeData() built in function to create a file containing a list of files names for say the input array, and pass just that one file on the command line. You'll still need to make sure that all the data dependencies are specified correctly and that all the required input files are arguments to the swift app() function for the reduction application, so that they get made available.
>
> This technique was proposed by Ben, but has not to my knowledge been heavily tested yet. So we may find more gotchas eg related to passing the IF or OF input and output file lists.
>
> - Mike
>
> ----- "Jonathan Monette"<jon.monette at gmail.com> wrote:
>
>> Hello,
>> What does this error mean?
>>
>> Failed to transfer wrapper log from
>> unrectified-20101004-1432-k89q8d3b/info/y on localhost
>> Execution failed:
>> Exception in mImgtbl:
>> Arguments: [proj_dir, images.tbl]
>> Host: localhost
>> Directory: unrectified-20101004-1432-k89q8d3b/jobs/y/mImgtbl-yuqc8ozj
>> stderr.txt:
>>
>> stdout.txt:
>>
>> ----
>>
>> Caused by:
>> Cannot run program "/bin/bash" (in directory
>> "/gpfs/pads/swift/jonmon/Swift/work/localhost/unrectified-20101004-1432-k89q8d3b"):
>>
>> java.io.IOException: error=7, Argument list too long
>>
>> When it says that it cannot run /bin/bash, is it talking about
>> _swiftwrap? Also, what does Argument list too long indicate? It
>> shows
>> that the arguments to the app mImgtbl are proj_dir and images.tbl.
>> That
>> is the correct number of arguments to mImgtbl. proj_dir is a
>> directory
>> that contains about 4100 files. Is there wrapper script in swift to
>> mImgtbl that cannot accept this many files?
>>
>> --
>> Jon
>>
>> Computers are incredibly fast, accurate, and stupid. Human beings are
>> incredibly slow, inaccurate, and brilliant. Together they are powerful
>> beyond imagination.
>> - Albert Einstein
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
--
Jon
Computers are incredibly fast, accurate, and stupid. Human beings are incredibly slow, inaccurate, and brilliant. Together they are powerful beyond imagination.
- Albert Einstein
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