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Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job
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From: Stefan Z. <ste...@uc...> - 2007-02-16 11:09:01
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Hi, In the previous Util.pm I put the CPUCount element after the posix block, but from the error you got Mark, it could be that GridSAM is looking for CPUCount directly after wallTimeLimit? I've updated Util.pm to put CPUCount directly after wallTimeLimit at the end of the MPIApplication block (it's at the same url). Could you try giving this a go? Also, could you send the JSDL generated? Cheers, Stefan. Gordon Stewart wrote: > Well, the error has changed a little, but I'm not sure whether it's for > the better or worse... > > The GGF give an example MPI JSDL file for GridSAM > (http://www.ggf.org/GGF17/materials/253/gridsam-jsdl-mpi-sample.pdf): > > ... > <JobDescription> > <Application > xmlns:posix="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"> > <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> > <posix:Executable>/bin/some-parallel-app</posix:Executable> > <posix:Argument>hello world</posix:Argument> > <posix:Environment name="ABC">DEF</posix:Environment> > <mpi:ProcessorCount>10</mpi:ProcessorCount> > <xyz:OtherExtension xmlns:xyz="urn:xyz">My > Extension</xyz:OtherExtension> > </mpi:MPIApplication> > </Application> > </JobDescription> > ... > > Assuming that the generated JSDL now has this form, I'm not really sure > what could be causing these errors. It now seems to be complaining > about the existence of the POSIX elements within the MPIApplication > element, but they are clearly allowed. Perhaps you could post the new > JSDL to see if that provides any further inspiration? > > Gordon > > -----Original Message----- > From: gri...@li... > [mailto:gri...@li...] On Behalf Of Mark > HB > Sent: 16 February 2007 09:28 > To: Stefan Zasada > Cc: cax...@gm...; gri...@li... > Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job > > > Dear Stefan, > > Unfortunately it doesn't seem to fix it for me. > I did this: > 1) Copied new Util.pm to OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE > 2) restarted OMII server > 3) ran the ahe_destroy....... & ahe_create.... scripts (just in case) > 4) Run the ahe-client as before, but got the error as before > > Error: > Description: Invalid JSDL v1.0 job description: [error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' > here in element MPIApplication@urn:gridsam:mpi, error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' > here in element MPIApplication@urn:gridsam:mpi, error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here > in element MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: > > Expected element 'ProcessorCount@urn:gridsam:mpi' instead of > 'Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here in element > MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: Expected > element 'ProcessorCount@urn:gridsam:mpi' instead of > 'WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here > in element MPIApplication@urn:gridsam:mpi] > > > Stefan Zasada wrote: > Dear Mark and Carlos, > > I've modified Util.pm to put the <mpi:ProcessorCount> > element after the JSDL posix stuff. Get it from: > > http://ccs.chem.ucl.ac.uk/~stefan/Util.pm > > Replace the Util.pm in your AHE distribution with it and let me know >> if > it works. > > Cheers, > > Stefan. > > Gordon Stewart wrote: > >>>> There's a file called Util.pm.mpi in the >>>> $OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE directory of the OMII >>>> 3.2.0 installation (and also in the ahe.war file within the >> installation >>>> bundle) that, at a brief glance, appears to contain the code which >>>> builds the JSDL. >>>> >>>> I'm not sure what changes you would have to make in order to modify >> the >>>> order of elements. >>>> >>>> Gordon >>>> >>>> >>>> -----Original Message----- >>>> From: Carlos Alexandre Queiroz [mailto:cax...@gm...] >>>> Sent: 16 February 2007 08:57 >>>> To: Gordon Stewart >>>> Cc: Mark HB >>>> Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>> >>>> Humm, it is a good guess, however, AHE-Server is generating this >>>> jsdl, anyone knows where we have to change it in order to >>>> generate a different jsdl file ?? >>>> >>>> >>>> thx, >>>> >>>> cax >>>> >>>> >>>> On 16/02/2007, at 7:49 PM, Gordon Stewart wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Looking at the error message, it would appear to be the JSDL which >>>>> is at >>>>> fault. I've had errors in the past where the order of elements >>>>> differs >>>>> from what the parser is expecting. According to the GridSAM >>>>> documentation for the MPIApplication element at >>>>> http://gridsam.sourceforge.net/2.0.0/gridsam-client/jsdl.html, the >>>>> definition is: >>>>> >>>> >>>>> <jsdl:Application> >>>>> .. >>>>> <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> >>>>> <jsdl-posix:*/>* >>>>> <mpi:ProcessorCount>xsd:positiveInteger</mpi:ProcessorCount> >>>>> </mpi:MPIApplication> >>>>> .. >>>>> </jsdl:Application> >>>>> >>>> >>>>> The POSIX application type (the jsdl-posix: element above) is >>>>> defined in >>>>> the XML schema as a sequence, which requires the child elements to >>>>> appear in the order specified. My guess (and it's only a guess as >>>>> I've >>>>> never used the MPI extensions) would be that this is the same with >>>>> MPIApplication, and that it is objecting to the ProcessorCount >> element >>>>> appearing before the POSIX stuff; relocating this after the >>>>> WallTimeLimit element may help. >>>>> >>>> >>>>> Gordon >>>>> >>>> >>>>> -----Original Message----- >>>>> From: gri...@li... >>>>> [mailto:gri...@li...] On Behalf Of > >>>>> Mark >>>>> HB >>>>> Sent: 16 February 2007 07:11 >>>>> To: gri...@li... >>>>> Subject: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>>> >>>>> Hey, >>>>> Sincere apologies if this has sent twice! >>>>> >>>>> I am using AHE bundled with OMII server and have created a gridsam >>>>> instance to point at the Manchester node of the NGS (thanks list for >>>>> helping sort that out). >>>>> This GRIDSam instance was installed by following the instructions >>>>> found >>>>> at: >>>>> omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/ >>>>> index.htm >>>>> l >>>>> >>>>> However when I try to run a job, it all goes wrong. >>>>> Please find below the error I get, my jobmanger.xml and then the >> JSDL >>>>> message itself. >>>>> Can anyone help? >>>>> >>>>> Cheers >>>>> Mark >>>>> >>>>> ############## ERROR ############## >>>>> >>>>> 12:37:20 INFO (StartCall.java:182) - AHE Job Owner: >>>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: pending >>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description:job >> is >>>>> being scheduled >>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>> 2007-02-15T12:37:19.840Z >>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>> 2007-02-15T12:37:19.840Z >>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: failed >>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description: >>>>> Invalid JSDL v1.0 job description: [error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>> element MPIApplication@urn:gridsam:mpi, error: >> cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> WallTimeLimit@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>> element >>>>> MPIApplication@urn:gridsam:mpi] >>>>> >>>>> ################ JOBMANAGER.XML ################ >>>>> <?xml version="1.0" encoding="UTF-8"?> >>>>> <module id="jobmanager.globus" version="1.0.0"> >>>>> <!-- dependent modules --> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/common.xml"/> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/embedded.xml"/> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/globus.xml"/> >>>>> <sub-module descriptor="database.xml"/> >>>>> <sub-module descriptor="authorisation.xml"/> >>>>> <!-- override the factory defaults here --> >>>>> <contribution configuration-id="hivemind.ApplicationDefaults"> >>>>> <!-- The job manager location --> >>>>> <default symbol="globus.JobManager" value="grid-data.man.ac.uk"/> >>>>> >>>>> <!-- The root file system for staging files >>>>> --> >>>>> <default symbol="globus.RootFileSystemURI" >>>>> value="gsiftp://grid-data.man.ac.uk"/> >>>>> <!-- How often the status of the job is polled >>>>> --> >>>>> <default symbol="globus.MonitoringPeriod" value="20000"/> >>>>> <!-- the default location of the classad generation script >>>>> WEB-INF/classes/rsl.groovy --> <default >>>>> symbol="globus.ScriptResource" value="rsl.groovy"/> >>>>> </contribution> >>>>> </module> >>>>> >>>>> #################### JSDL ######################## >>>>> <JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl"> >>>>> <JobDescription> >>>>> <JobIdentification> >>>>> <JobName>NAMD_NGS_MAN</JobName> >>>>> <Description>THIS IS FOR NAMD ON THE >> NGS</Description> >>>>> <JobAnnotation>NAMD Annotation</JobAnnotation> >>>>> <JobProject>AHE Project</JobProject> >>>>> </JobIdentification> >>>>> <Application> >>>>> <mpi:MPIApplication >>>>> xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" >>>>> xmlns:mpi="urn:gridsam:mpi"> >>>>> <mpi:ProcessorCount>1</mpi:ProcessorCount> >>>>> <Executable>/home/ngs0386/bin/cimmsim</Executable> >>>>> <Argument>datPlain12</Argument> >>>>> <Output>stdout.txt</Output> >>>>> <Error>stderr.txt</Error> >>>>> <WorkingDirectory>195914151107445079635</WorkingDirectory> >>>>> <WallTimeLimit>720</WallTimeLimit> >>>>> </mpi:MPIApplication> >>>>> </Application> >>>>> >>>>> <DataStaging> >>>>> <FileName>datPlain12</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Source><URI>http://test:to...@ig...:18080/ >>>>> filestage/19 >>>>> 5914151107445079635/datPlain12</URI></Source> >>>>> </DataStaging><DataStaging><FileName>stdout.txt</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/stdout.txt</URI></Target> >>>>> </DataStaging> >>>>> <DataStaging> >>>>> <FileName>stderr.txt</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/stderr.txt</URI></Target> >>>>> >>>> >>>>> </DataStaging> >>>>> <DataStaging> >>>>> <FileName>_th-details.out</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/_th-details.out</URI></Target> >>>>> </DataStaging> >>>>> </JobDescription> >>>>> <myproxy:MyProxy >>>>> >> xmlns:myproxy="urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid- >>>>> >>>>> su >>>>> pport.ac.uk</myproxy:ProxyServer> >>>>> <myproxy:ProxyServerDN>/C=UK/O=eScience/OU=CLRC/L=DL/CN=host/ >>>>> myproxy.gri >>>>> d-support.ac.uk/E=a...@dl...</myproxy:ProxyServerDN> >>>>> <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> >>>>> <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> >>>>> <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</ >>>>> myproxy:ProxyServerPassPhra >>>>> se> >>>>> <myproxy:ProxyServerLifetime>7512</myproxy:ProxyServerLifetime></ >>>>> myproxy >>>>> :MyProxy> >>>>> </JobDefinition> >>>>> >>>> >>>>> -- >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> --- >>>>> Mark Halling-Brown | Tel: +44-20-7631-6839 >>>>> Research Associate | >>>>> Room 359 | Fax: +44-20-7631-6803 >>>>> School of Crystallography | >>>>> Birkbeck College | Email: >>>>> Malet Street | >> gh...@ma... >>>>> London WC1E 7HX | ma...@gm... >>>>> UK | >>>>> http://people.cryst.bbk.ac.uk/~ghall04 >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> --- >>>>> >>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> - >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>> share >>>>> your >>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>> http://www.techsay.com/default.php? >>>>> page=join.php&p=sourceforge&CID=DEVDE >>>>> V >>>>> _______________________________________________ >>>>> GridSAM-Discuss mailing list >>>>> Gri...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>> >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> --- >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>> share your >>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>> http://www.techsay.com/default.php? >>>>> page=join.php&p=sourceforge&CID=DEVDEV >>>>> _______________________________________________ >>>>> GridSAM-Discuss mailing list >>>>> Gri...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>> >>>> cax >>>> ----------------------------- >>>> Think outside the box >>>> >>>> >>>> >>>> >>>> >>>> >>>> > - >> ------------------------------------------------------------------------ >> - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to >> share your > opinions on IT & business topics through brief surveys-and earn cash > >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE >> V > _______________________________________________ > GridSAM-Discuss mailing list > Gri...@li... > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss > -- Stefan Zasada <ste...@uc...> Centre for Computational Science Chemistry Department, University College London, 20 Gordon Street, London, WC1H 0AJ, UK. Tel: +44 (0)20 7679 5300 |
