[Swift-devel] script that returns bad parameter error
Mike Kubal
mikekubal at yahoo.com
Thu Dec 6 11:15:45 CST 2007
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
> > > > >>>
> > > > >>
> > > > >>
> > > > >>
> > >
> >
>
____________________________________________________________________________________
> > > > >> Be a better friend, newshound, and
> > > > >> know-it-all with Yahoo! Mobile. Try it
> now.
> > >
> >
>
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> > >
> > > > >>
> > > > >>
> _______________________________________________
> > > > >> Swift-devel mailing list
> > > > >> Swift-devel at ci.uchicago.edu
> > > > >>
> > >
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > >>
> > > > >
> > > > >
> _______________________________________________
> > > > > Swift-devel mailing list
> > > > > Swift-devel at ci.uchicago.edu
> > > > >
> > >
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > > > >
> > > > >
> > > >
> > >
> > > _______________________________________________
> > > Swift-devel mailing list
> > > Swift-devel at ci.uchicago.edu
> > >
> >
>
http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >
> > >
> >
> >
> >
> >
>
____________________________________________________________________________________
> > Looking for last minute shopping deals?
> > Find them fast with Yahoo! Search.
>
http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> >
>
> _______________________________________________
> Swift-devel mailing list
>
=== message truncated ===
____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping
More information about the Swift-devel
mailing list