[Swift-devel] gridftp issue in running oops swift script on queenbee
Wenjun Wu
wwj at ci.uchicago.edu
Thu Dec 3 14:31:51 CST 2009
Hello,
I got a weird issue in running the attached script on the TeraGrid
QueenBee.
The workflow fails after the ItFixInit.sh is done.
The InitFixInit.sh just copies some files to an output directory and
it finishes the copying successfully.
But when the swift engine tries to clean up the temp directory for the
ItFixInit task, it fails.
I also tries to set the sitedir.keep=true in the swift.properites to
avoid the removal of the temp files but got the same error.
Here is the description of QueenBeen in the site.xml file.
<pool handle="QueenBee">
<gridftp url="gsiftp://queenbee.loni-lsu.teragrid.org:2811" />
<execution provider="gt2" jobmanager="FORK"
url="queenbee.loni-lsu.teragrid.org" />
<workdirectory >/home/wwj/testjobs</workdirectory>
</pool>
And this is the tc.data file used for the workflow:
QueenBee PSim /home/wwj/tools/protlib2/bin/PSim.sh
null null null
QueenBee ItFixInit
/home/wwj/tools/protlib2/bin/ItFixInit.sh null null null
QueenBee RevisePData
/home/wwj/tools/protlib2/bin/RevisePData.sh null null null
Thanks!
Wenjun
Caused by:
org.globus.cog.abstraction.impl.file.IrrecoverableResourceException:
Exception in getFile
Caused by: org.globus.cog.abstraction.impl.file.FileResourceException:
Failed to retrieve file information about
/home/wwj/testjobs/oops-20091202-1700-vmh5dnd3/info/j/ItFixInit-jjpe3bkj-info
Caused by: org.globus.ftp.exception.ServerException: Server refused
performing the request. Custom message: Server refused MLST command
(error code 1) [Nested exception message: Custom message: Unexpected
reply: 500-Command failed : System error in stat: No such file or directory
500-A system call failed: No such file or directory
500-
500 End.] [Nested exception is
org.globus.ftp.exception.UnexpectedReplyCodeException: Custom message:
Unexpected reply: 500-Command failed : System error in stat: No such
file or directory
500-A system call failed: No such file or directory
500-
500 End.]
2009-12-02 17:01:33,938-0600 INFO vdl:execute END_FAILURE
thread=0-1-10-1-1-2-0-1-1 tr=ItFixInit
2009-12-02 17:01:33,942-0600 DEBUG VDL2ExecutionContext Exception in
ItFixInit:
Arguments: [sandbox/wwj/oops/input/fasta/T1af7.fasta,
output/T1af7/R00/T1af7.R00.fasta]
Host: QueenBee
Directory: oops-20091202-1700-vmh5dnd3/jobs/j/ItFixInit-jjpe3bkj
stderr.txt:
stdout.txt:
----
Exception in ItFixInit:
Arguments: [sandbox/wwj/oops/input/fasta/T1af7.fasta,
output/T1af7/R00/T1af7.R00.fasta]
Host: QueenBee
Directory: oops-20091202-1700-vmh5dnd3/jobs/j/ItFixInit-jjpe3bkj
stderr.txt:
stdout.txt:
----
Caused by: Failed to remove job directory
/home/wwj/testjobs/j/ItFixInit-jjpe3bkj
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:45)
at
org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
at
org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)
at
org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:176)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:296)
at
org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
at
org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
at
org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
at
org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)
at
org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren(AbstractFunction.java:40)
at
org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:233)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:278)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:391)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:329)
at
org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
at
org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:134)
at
org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:108)
at
org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:43)
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:595)
Caused by: Failed to remove job directory
/home/wwj/testjobs/j/ItFixInit-jjpe3bkj
at
org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:411)
at
org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:415)
at
org.globus.cog.karajan.workflow.nodes.GenerateErrorNode.post(GenerateErrorNode.java:28)
... 26 more
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