[Swift-devel] script that returns bad parameter error
Mihael Hategan
hategan at mcs.anl.gov
Thu Dec 6 11:21:11 CST 2007
What does tc.data say?
Mihael
On Thu, 2007-12-06 at 09:15 -0800, Mike Kubal wrote:
> I took out the project tag and same results. Here's
> the section run_fred****.log where the failure occurs:
>
> 2007-12-06 10:44:14,968 DEBUG Loader Recompilation
> suppressed.
> 2007-12-06 10:44:19,096 INFO unknown Using sites
> file: sites-purdue-64-gram.xml
> 2007-12-06 10:44:19,097 INFO unknown Using tc.data:
> tc-purdue.data
> 2007-12-06 10:44:22,303 DEBUG GetFieldValue
> GetFieldValue(true)
> 2007-12-06 10:44:22,311 DEBUG GetFieldValue
> GetFieldValue(true)
> 2007-12-06 10:44:28,408 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457323) setting status to
> Active
> 2007-12-06 10:44:28,502 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457323) setting status to
> Completed
> 2007-12-06 10:44:28,553 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Submitted
> 2007-12-06 10:44:28,554 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Active
> 2007-12-06 10:44:29,022 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457326) setting status to
> Completed
> 2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Submitted
> 2007-12-06 10:44:29,026 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Active
> 2007-12-06 10:44:29,464 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1196959457330) setting status to
> Completed
> 2007-12-06 10:44:29,470 DEBUG vdl:execute2 Job
> run_fred-fqolp4li running in thread 0-0-1-0 run
> zh499u762hal2
> 2007-12-06 10:44:29,482 INFO vdl:execute2 Creating
> temporary directory
> run_fred-zh499u762hal2/run_fred-fqolp4li on Lear
> 2007-12-06 10:44:29,500 INFO vdl:createdirs Creating
> directory structure in run_fred-zh499u762hal2/shared
> (run_fred-zh499u762hal2/shared/)
> 2007-12-06 10:44:29,502 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457333) setting status to
> Active
> 2007-12-06 10:44:29,525 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1196959457333) setting status to
> Completed
> 2007-12-06 10:44:29,538 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-2-1196959457335) setting status
> to Active
> 2007-12-06 10:44:29,540 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1-1196959457338) setting status
> to Active
> 2007-12-06 10:44:29,542 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-2-1196959457335) setting status
> to Completed
> 2007-12-06 10:44:29,551 DEBUG TaskImpl Task(type=4,
> identity=urn:0-0-1-0-1-1196959457338) setting status
> to Completed
> 2007-12-06 10:44:29,566 INFO vdl:dostagein Staging in
> Marsha_lig_1.mol2 ( - Marsha_lig_1.mol2 to
> run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:29,567 INFO vdl:dostagein Staging in
> 1beh.oeb.gz ( - 1beh.oeb.gz to
> run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:29,570 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Submitted
> 2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Active
> 2007-12-06 10:44:29,571 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Submitted
> 2007-12-06 10:44:29,572 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Active
> 2007-12-06 10:44:30,005 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-1-1196959457342) setting status
> to Completed
> 2007-12-06 10:44:30,007 INFO vdl:dostagein Staged in
> Marsha_lig_1.mol2 to run_fred-zh499u762hal2/shared/ on
> Lear
> 2007-12-06 10:44:31,703 DEBUG TaskImpl Task(type=2,
> identity=urn:0-0-1-0-2-1196959457345) setting status
> to Completed
> 2007-12-06 10:44:31,705 INFO vdl:dostagein Staged in
> 1beh.oeb.gz to run_fred-zh499u762hal2/shared/ on Lear
> 2007-12-06 10:44:31,707 INFO vdl:execute2 Running job
> run_fred-fqolp4li run_fred with arguments [-rec,
> 1beh.oeb.gz, -dbase, Marsha_lig_1.mol2, -prefix,
> Marsha_li\
> g_1] in run_fred-zh499u762hal2/run_fred-fqolp4li on
> Lear
> 2007-12-06 10:44:32,925 DEBUG TaskImpl Task(type=1,
> identity=urn:0-0-1-0-1196959457349) setting status to
> Failed Parameter not supported
> 2007-12-06 10:44:32,938 DEBUG vdl:execute2 Application
> exception: Parameter not supported
> task:execute @ vdl-int.k, line: 328
> sys:sequential @ vdl-int.k, line: 316
> sys:try @ vdl-int.k, line: 315
> task:allocatehost @ vdl-int.k, line: 298
> vdl:execute2 @ execute-default.k, line: 22
> sys:restartonerror @ execute-default.k, line:
> 20
> sys:sequential @ execute-default.k, line: 19
> sys:try @ execute-default.k, line: 18
> sys:if @ execute-default.k, line: 17
> sys:then @ execute-default.k, line: 16
> sys:if @ execute-default.k, line: 15
> vdl:execute @ run_fred.kml, line: 20
> run_fred @ run_fred.kml, line: 151
> sys:parallel @ run_fred.kml, line: 150
> sys:parallelfor @ run_fred.kml, line: 80
> sys:parallel @ run_fred.kml, line: 79
> vdl:mainp @ run_fred.kml, line: 78
> mainp @ vdl.k, line: 141
> vdl:mains @ run_fred.kml, line: 77
> vdl:mains @ run_fred.kml, line: 77
> rlog:restartlog @ run_fred.kml, line: 75
> kernel:project @ run_fred.kml, line: 2
> run_fred-zh499u762hal2
> Caused by: org.globus.gram.GramException: Parameter
> not supported
>
>
> --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
>
> > I think I've seen fork complaining about "project"
> > before. Can you try
> > to comment that profile tag out and run with fork
> > again?
> >
> > It may also be useful to post the logs since they
> > may contain stack
> > traces that point more accurately towards the
> > problem.
> >
> > Mihael
> >
> > On Thu, 2007-12-06 at 08:15 -0800, Mike Kubal wrote:
> > > Hi Mihael,
> > >
> > > No need to apologize, I appreciate your feedback.
> > >
> > > Here is the sites file.
> > >
> > > <?xml version="1.0" encoding="UTF-8"?>
> > > <config
> > >
> >
> xmlns="http://www.griphyn.org/chimera/GVDS-PoolConfig"
> > >
> >
> xsi:schemaLocation="http://www.griphyn.org/chimera/GVDS
> > >
> > http://www.griphyn.org/chimera/gvds-poolcfg-1.5.xsd"
> > >
> >
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> > > version="1.5">
> > >
> > > <pool handle="Lear" sysinfo="INTEL64::LINUX">
> > > <gridftp
> > > url="gsiftp://gridftp.purdue.teragrid.org"
> > > storage="/autohome/u102/mkubal/SWIFT_working_dir"
> > > major="2" minor="2" patch="4">
> > > </gridftp>
> > > <profile namespace="globus"
> > > key="project">UC-MCA01S018</profile>
> > > <jobmanager universe="vanilla"
> > >
> >
> url="tg-gatekeeper.purdue.teragrid.org:2119/jobmanager-fork"
> > > major="2" minor="0" patch="0"/>
> > >
> > >
> >
> <workdirectory>/autohome/u102/mkubal/SWIFT_working_dir</workdirectory>
> > > </pool>
> > > </config>
> > >
> > > I have also tried the condor job manager at
> > Purdue
> > > that has the same url except that it ends in
> > '-condor'
> > > instead of '-fork' . I get the same error.
> > >
> > > Cheers,
> > >
> > > Mike
> > >
> > >
> > >
> > >
> > >
> > > --- Mihael Hategan <hategan at mcs.anl.gov> wrote:
> > >
> > > > Sorry. My email wasn't very friendly. I was
> > trying
> > > > to type less :)
> > > >
> > > > On Wed, 2007-12-05 at 17:42 -0600, Michael Wilde
> > > > wrote:
> > > > > Mike,
> > > > >
> > > > > Mihael suspects that a bad globus parameter in
> > > > your sites.xml file is
> > > > > causing this error message. So please send
> > that
> > > > so we can take a look.
> > > > >
> > > > > Thanks,
> > > > >
> > > > > MikeW
> > > > >
> > > > > On 12/5/07 4:45 PM, Mihael Hategan wrote:
> > > > > > Post the sites file.
> > > > > >
> > > > > > On Wed, 2007-12-05 at 14:33 -0800, Mike
> > Kubal
> > > > wrote:
> > > > > >> Unfortunately I still get the same error:
> > > > > >>
> > > > > >> run_fred failed
> > > > > >> The following errors have occurred:
> > > > > >> 1. Application "run_fred" failed (Parameter
> > not
> > > > > >> supported)
> > > > > >> Arguments: "-rec, 1beh.oeb.gz,
> > -dbase,
> > > > > >> Marsha_lig_1.mol2, -prefix, Marsha_lig_1"
> > > > > >> Host: Lear
> > > > > >> Directory:
> > > > > >> run_fred-2k0629rvbffz0/run_fred-r81pg3li
> > > > > >> STDERR:
> > > > > >> STDOUT:
> > > > > >>
> > > > > >> Does 'Parameter not supported' usually
> > refer to
> > > > an
> > > > > >> argument of the remote application? I
> > wonder if
> > > > it
> > > > > >> does not like the .oeb.gz file?
> > > > > >>
> > > > > >>
> > > > > >>
> > > > > >> --- Ben Clifford <benc at hawaga.org.uk>
> > wrote:
> > > > > >>
> > > > > >>>
> > > > > >>> On Wed, 5 Dec 2007, Mike Kubal wrote:
> > > > > >>>
> > > > > >>>> run_fred "-rec"
> > receptor_file
> > > > > >>> "-dbase"
> > > > > >>>> ligand_file "-prefix" ligand_prefix;
> > > > > >>> In here, take the filenames of each file
> > by
> > > > saying
> > > > > >>> @filenmame(receptor_file), like this:
> > > > > >>>
> > > > > >>>> run_fred "-rec"
> > > > > >>> @filename(receptor_file) "-dbase"
> > > > > >>>> @filename(ligand_file) "-prefix"
> > > > ligand_prefix;
> > > > > >>> --
> > > > > >>>
> > > > _______________________________________________
> > > > > >>> Swift-devel mailing list
> > > > > >>> Swift-devel at ci.uchicago.edu
> > > > > >>>
> > > > > >>
> > > >
> > >
> >
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > > >>>
> > > > > >>
> > > > > >>
> > > > > >>
> > > >
> > >
> >
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