I see. Could this output be viewed as a sign?<br><br>Completed job cwtsmall-gt3062gi cwtsmall with arguments [scripts/runWaveletsAvg.R, 101, FB] on MIT_CMS<br>Staging out sid-wf1-3szhlhvg4seu0/shared//101-FBchannel15_cwt-avgResults.Rdata
to 101-FBchannel15_cwt-avgResults.Rdata from MIT_CMS<br><br>Thanks,<br>Jing<br><br><div><span class="gmail_quote">On 8/20/07, <b class="gmail_sendername">Mihael Hategan</b> <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Local empty files may be created even if the remote files don't exist.
<br>So don't take that as a sign that the application has run.<br><br>In the mean time I'll try to convince it to not create empty local<br>files, if they don't exist remotely.<br><br>Mihael<br><br>On Mon, 2007-08-20 at 13:43 -0500, Jing Tie wrote:
<br>> I think these files were from the job. Because I deleted all the<br>> *Results.Rdata before the job submitting, and found these empty files<br>> after the execution.<br>><br>> output of the process of execution:
<br>> RunID: 3szhlhvg4seu0<br>> cwtsmall started<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-1187633646429) setting status<br>> to Active<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-1187633646429) setting status
<br>> to Completed<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-1187633646432) setting status<br>> to Submitted<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-1187633646432) setting status<br>> to Active<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-1187633646432) setting status
<br>> to Completed<br>> ...<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-1-1187633646453) setting<br>> status to Completed<br>> Staged in scripts/runWaveletsAvg.R to<br>> sid-wf1-3szhlhvg4seu0/shared/scripts/ on MIT_CMS
<br>> Running job cwtsmall-gt3062gi cwtsmall with arguments<br>> [scripts/runWaveletsAvg.R, 101, FB] in<br>> sid-wf1-3szhlhvg4seu0/cwtsmall-gt3062gi on MIT_CMS<br>> Task(type=1, identity=urn:0-0-0-1-0-1-0-1187633646457) setting status
<br>> to Submitted<br>> Task(type=1, identity=urn:0-0-0-1-0-1-0-1187633646457) setting status<br>> to Active<br>> Task(type=1, identity=urn:0-0-0-1-0-1-0-1187633646457) setting status<br>> to Completed<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-1187633646459) setting status
<br>> to Active<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-1187633646459) setting status<br>> to Completed<br>> Completed job cwtsmall-gt3062gi cwtsmall with arguments<br>> [scripts/runWaveletsAvg.R, 101, FB] on MIT_CMS
<br>> Staging out<br>> sid-wf1-3szhlhvg4seu0/shared//101-FBchannel15_cwt-avgResults.Rdata to<br>> 101-FBchannel15_cwt-avgResults.Rdata from MIT_CMS<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-7-1187633646462) setting
<br>> status to Active<br>> Task(type=4, identity=urn:0-0-0-1-0-1-0-7-1187633646462) setting<br>> status to Completed<br>> ......<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-23-1187633646557) setting<br>> status to Active
<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-22-1187633646554) setting<br>> status to Failed Exception in getFile<br>> Task(type=2, identity=urn:0-0-0-1-0-1-0-2-1187633646560) setting<br>> status to Submitted
<br>> ......<br>><br>> Thanks,<br>> Jing<br>><br>> On 8/20/07, Mihael Hategan < <a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> But those are not from the same job.
<br>><br>> On Mon, 2007-08-20 at 12:28 -0500, Jing Tie wrote:<br>> > Yes. I saw 101-FBchannel1_cwt-avgResults.Rdata to<br>> > 101-FBchannel28_cwt-avgResults.Rdata 28 output files on the
<br>> swift<br>> > client, but all the files were empty.<br>> ><br>> > Jing<br>> ><br>> ><br>> > On 8/20/07, Mihael Hategan <
<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>> > On Mon, 2007-08-20 at 12:21 -0500, Jing Tie wrote:<br>> > > Yes. There is no * avgResults.Rdata
under shared<br>> directory,<br>> > only input<br>> > > file, scripts, wrapper.sh and seq.sh.<br>> ><br>> > Did the job actually run?
<br>> ><br>> > ><br>> > > Jing<br>> > ><br>> > > On 8/20/07, Mihael Hategan < <a href="mailto:hategan@mcs.anl.gov">
hategan@mcs.anl.gov</a>><br>> wrote:<br>> > > Not much we can do if the filesystem is<br>> broken.<br>> > > Did you check to confirm that the file is
<br>> not<br>> > there?<br>> > ><br>> > > Mihael<br>> > ><br>> > > On Mon, 2007-08-20 at 12:07 -0500, Jing
<br>> Tie wrote:<br>> > > > Hi,<br>> > > ><br>> > > > Here is another problem. It seems like<br>> something
<br>> > wrong with<br>> > > GFS<br>> > > > system.<br>> > > ><br>> > > > site: MIT_CMS
<br>> > > > gatekeeper: <a href="http://ce01.cmsaf.mit.edu">ce01.cmsaf.mit.edu</a><br>> > > > app_dir: /osg/app<br>> > > > data_dir: /osg/data
<br>> > > > condor_dir: /usr/local/condor/bin<br>> > > > R_dir: /osg/app/R- 2.5.1/bin/R<br>> > > ><br>> > > > output:
<br>> > > > Application exception: Exception in<br>> getFile<br>> > > > task:transfer @ vdl-int.k, line:<br>> 235<br>> > > > vdl:dostageout @
vdl-int.k,<br>> line: 378<br>> > > > vdl:execute2 @<br>> execute-default.k, line: 22<br>> > > > vdl:execute @ sid-wf1.kml
, line:<br>> 20<br>> > > > wavelettransf @ sid-wf1.kml,<br>> line: 362<br>> > > > batchtrials @ sid-wf1.kml, line:
<br>> 402<br>> > > > vdl:mains @ sid-wf1.kml , line:<br>> 399<br>> > > > Caused by:<br>> > ><br>
> ><br>> org.globus.cog.abstraction.impl.file.FileResourceException:<br>> > > > Exception in getFile<br>> > > > Caused by:<br>
> > org.globus.ftp.exception.ServerException : Server<br>> > > refused<br>> > > > performing the request. Custom<br>> message: (error
<br>> > code<br>> > > 1) cwtsmall<br>> > > > failed<br>> > > > Provenance graph saved in<br>> >
sid-wf1-7thy5mbfh09e1.dot<br>> > > > The following errors have occurred:<br>> > > > 1. Application "cwtsmall" failed<br>> (Exception in
<br>> > getFile<br>> > > > Caused by:<br>> > > > Server refused performing the request.<br>> Custom<br>> > > message: (error code
<br>> > > > 1)<br>> > > > [Nested exception message: Nested<br>> exception is<br>> > > ><br>> >
<br>> org.globus.ftp.exception.UnexpectedReplyCodeException :<br>> > > > Custom message: Unexpected reply:<br>> > > > 500-Command failed. :
<br>> > > ><br>> ><br>> globus_gridftp_server_file.c:globus_l_gfs_file_send:2190:<br>> > > > 500-globus_l_gfs_file_open failed.
<br>> > > ><br>> > ><br>> ><br>> 500-globus_gridftp_server_file.c:globus_l_gfs_file_open:1694:<br>> > > > 500-globus_xio_register_open failed.
<br>> > > ><br>> ><br>> 500-globus_xio_file_driver.c:globus_l_xio_file_open:438:<br>> > > > 500-Unable to open<br>> > > >
<br>> > ><br>> ><br>> file /osgfs/data/sid-wf1-7thy5mbfh09e1/shared//101-FBchannel16_cwt- avgResults.Rdata<br>> > > ><br>> >
<br>> 500-globus_xio_file_driver.c:globus_l_xio_file_open:381:<br>> > > > 500-System error in open: No such file<br>> or<br>> > directory<br>
> > > > 500-globus_xio: A system call failed: No<br>> such file<br>> > or<br>> > > directory<br>> > > > 500 End.])
<br>> > > > Arguments:<br>> "scripts/runWaveletsAvg.R, 101,<br>> > FB"<br>> > > > Host: UCSDT2
<br>> > > > Directory:<br>> > sid-wf1-7thy5mbfh09e1/cwtsmall-mb3l3rfi<br>> > > > STDERR:<br>> > > > STDOUT:
<br>> > > > Errors detected. Cleanup not done.<br>> > > > Execution completed with errors<br>> > > > sys:throw @
vdl.k, line: 140<br>> > > > vdl:mains @ sid-wf1.kml, line:<br>> 399<br>> > > > at<br>> > > >
<br>> > ><br>> > org.globus.cog.karajan.workflow.nodes.FlowNode.fail<br>> (FlowNode.java:413)<br>> > > > at<br>> > > >
<br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:417)<br>> > > > at<br>> > > >
<br>> ><br>> org.globus.cog.karajan.workflow.nodes.GenerateErrorNode.post<br>> > > > (GenerateErrorNode.java:28)<br>> > > > at
<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted<br>> > > > at
<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java :33)<br>> > > > at
<br>> > > ><br>> > ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.event<br>> > (FlowNode.java:334)<br>> > > > at
<br>> > > ><br>> > ><br>> > org.globus.cog.karajan.workflow.events.EventBus.send<br>> (EventBus.java:123)<br>> > > > at
<br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked<br>> > > > (EventBus.java:97)<br>> > > > at
<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent (FlowNode.java:172)<br>> > > > at
<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:298)<br>> > > > at
<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren (AbstractFunction.java
:37)<br>> > > > at<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowContainer.execute
(FlowContainer.java:63)<br>> > > > at<br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.restart<br>> > > > (
FlowNode.java :239)<br>> > > > at<br>> > > ><br>> > ><br>> > org.globus.cog.karajan.workflow.nodes.FlowNode.start
<br>> ( FlowNode.java :280)<br>> > > > at<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent
(FlowNode.java:392)<br>> > > > at<br>> > ><br>> > org.globus.cog.karajan.workflow.nodes.FlowNode.event<br>> > > > (
FlowNode.java:331)<br>> > > > at<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.FlowElementWrapper.event
(FlowElementWrapper.java:227)<br>> > > > at<br>> > > ><br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.events.EventBus.send
(EventBus.java:123)<br>> > > > at<br>> > ><br>> ><br>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked<br>> > > > (
EventBus.java:97)<br>> > > > at<br>> > > ><br>> ><br>> org.globus.cog.karajan.workflow.events.EventWorker.run<br>> > > (
EventWorker.java:69)<br>> > > ><br>> > > > Many thanks,<br>> > > > Jing<br>> > > >
<br>> _______________________________________________<br>> > > > Swift-user mailing list<br>> > > > <a href="mailto:Swift-user@ci.uchicago.edu">
Swift-user@ci.uchicago.edu</a><br>> > > ><br>> ><br>> <a href="http://mail.ci.uchicago.edu/mailman/listinfo/swift-user">http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
</a><br>> > ><br>> > ><br>> ><br>> ><br>><br>><br><br></blockquote></div><br>