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From: Gordon S. <g.s...@ne...> - 2007-02-16 10:49:03
|
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=3D"http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"> <mpi:MPIApplication xmlns:mpi=3D"urn:gridsam:mpi"> <posix:Executable>/bin/some-parallel-app</posix:Executable> <posix:Argument>hello world</posix:Argument> <posix:Environment name=3D"ABC">DEF</posix:Environment> <mpi:ProcessorCount>10</mpi:ProcessorCount> <xyz:OtherExtension xmlns:xyz=3D"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:=20 cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' instead of 'Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix'=20 here in element MPIApplication@urn:gridsam:mpi, error:=20 cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' instead of 'Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix'=20 here in element MPIApplication@urn:gridsam:mpi, error:=20 cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' instead of 'Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here=20 in element MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' instead of=20 'Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here in element=20 MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: Expected=20 element 'ProcessorCount@urn:gridsam:mpi' instead of=20 'WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here=20 in element MPIApplication@urn:gridsam:mpi] Stefan Zasada wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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: > =20 >> 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...]=20 >> 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 =20 >> jsdl, anyone knows where we have to change it in order to =20 >> generate a different jsdl file ?? >> >> >> thx, >> >> cax >> >> >> On 16/02/2007, at 7:49 PM, Gordon Stewart wrote: >> >> =20 >>> Hi, >>> =20 >>> Looking at the error message, it would appear to be the JSDL which =20 >>> is at >>> fault. I've had errors in the past where the order of elements =20 >>> 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: >>> =20 >> =20 >>> <jsdl:Application> >>> .. >>> <mpi:MPIApplication xmlns:mpi=3D"urn:gridsam:mpi"> >>> <jsdl-posix:*/>* >>> <mpi:ProcessorCount>xsd:positiveInteger</mpi:ProcessorCount> >>> </mpi:MPIApplication> >>> .. >>> </jsdl:Application> >>> =20 >> =20 >>> The POSIX application type (the jsdl-posix: element above) is =20 >>> 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 =20 >>> 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. >>> =20 >> =20 >>> Gordon >>> =20 >> =20 >>> -----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 >>> =20 >>> Hey, >>> Sincere apologies if this has sent twice! >>> =20 >>> 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 =20 >>> found >>> at: >>> omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/=20 >>> index.htm >>> l >>> =20 >>> 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? >>> =20 >>> Cheers >>> Mark >>> =20 >>> ############## ERROR ############## >>> =20 >>> 12:37:20 INFO (StartCall.java:182) - AHE Job Owner: >>> /C=3DUK/O=3DeScience/OU=3DImperial/L=3DLeSC/CN=3Dmark 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 =20 >>> element >>> MPIApplication@urn:gridsam:mpi] >>> =20 >>> ################ JOBMANAGER.XML ################ >>> <?xml version=3D"1.0" encoding=3D"UTF-8"?> >>> <module id=3D"jobmanager.globus" version=3D"1.0.0"> >>> <!-- dependent modules --> >>> <sub-module >>> descriptor=3D"org/icenigrid/gridsam/resource/config/common.xml"/> >>> <sub-module >>> descriptor=3D"org/icenigrid/gridsam/resource/config/embedded.xml"/> >>> <sub-module >>> descriptor=3D"org/icenigrid/gridsam/resource/config/globus.xml"/> >>> <sub-module descriptor=3D"database.xml"/> >>> <sub-module descriptor=3D"authorisation.xml"/> >>> <!-- override the factory defaults here --> >>> <contribution configuration-id=3D"hivemind.ApplicationDefaults"> >>> <!-- The job manager location --> >>> <default symbol=3D"globus.JobManager" = value=3D"grid-data.man.ac.uk"/> >>> =20 >>> <!-- The root file system for staging files >>> --> >>> <default symbol=3D"globus.RootFileSystemURI" >>> value=3D"gsiftp://grid-data.man.ac.uk"/> >>> <!-- How often the status of the job is polled >>> --> >>> <default symbol=3D"globus.MonitoringPeriod" value=3D"20000"/> >>> <!-- the default location of the classad generation script >>> WEB-INF/classes/rsl.groovy --> <default >>> symbol=3D"globus.ScriptResource" value=3D"rsl.groovy"/> >>> </contribution> >>> </module> >>> =20 >>> #################### JSDL ######################## >>> <JobDefinition xmlns=3D"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=3D"http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" >>> xmlns:mpi=3D"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> >>> =20 >>> <DataStaging> >>> <FileName>datPlain12</FileName> >>> <CreationFlag>overwrite</CreationFlag> >>> <DeleteOnTermination>false</DeleteOnTermination> >>> =20 >>> <Source><URI>http://test:to...@ig...:18080/=20 >>> filestage/19 >>> 5914151107445079635/datPlain12</URI></Source> >>> </DataStaging><DataStaging><FileName>stdout.txt</FileName> >>> <CreationFlag>overwrite</CreationFlag> >>> <DeleteOnTermination>false</DeleteOnTermination> >>> =20 >>> <Target><URI>webdav://test:to...@ig...:18080/=20 >>> filestage/ >>> 195914151107445079635/stdout.txt</URI></Target> >>> </DataStaging> >>> <DataStaging> >>> <FileName>stderr.txt</FileName> >>> <CreationFlag>overwrite</CreationFlag> >>> <DeleteOnTermination>false</DeleteOnTermination> >>> =20 >>> <Target><URI>webdav://test:to...@ig...:18080/=20 >>> filestage/ >>> 195914151107445079635/stderr.txt</URI></Target> >>> =20 >> =20 >>> </DataStaging> >>> <DataStaging> >>> <FileName>_th-details.out</FileName> >>> <CreationFlag>overwrite</CreationFlag> >>> <DeleteOnTermination>false</DeleteOnTermination> >>> =20 >>> <Target><URI>webdav://test:to...@ig...:18080/=20 >>> filestage/ >>> 195914151107445079635/_th-details.out</URI></Target> >>> </DataStaging> >>> </JobDescription> >>> <myproxy:MyProxy >>> xmlns:myproxy=3D"urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid- >>> =20 >>> su >>> pport.ac.uk</myproxy:ProxyServer> >>> = <myproxy:ProxyServerDN>/C=3DUK/O=3DeScience/OU=3DCLRC/L=3DDL/CN=3Dhost/=20 >>> myproxy.gri >>> d-support.ac.uk/E=3Da...@dl...</myproxy:ProxyServerDN> >>> <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> >>> <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> >>> <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</=20 >>> myproxy:ProxyServerPassPhra >>> se> >>> <myproxy:ProxyServerLifetime>7512</myproxy:ProxyServerLifetime></=20 >>> myproxy >>> :MyProxy> >>> </JobDefinition> >>> =20 >> =20 >>> --=20 >>> ---------------------------------------------------------------------- >>> =20 >>> -- >>> --- >>> 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 >>> ---------------------------------------------------------------------- >>> =20 >>> -- >>> --- >>> =20 >> =20 >>> ---------------------------------------------------------------------- >>> =20 >>> -- >>> - >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >>> share >>> your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?=20 >>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDE >>> V >>> _______________________________________________ >>> GridSAM-Discuss mailing list >>> Gri...@li... >>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>> =20 >>> ---------------------------------------------------------------------- >>> =20 >>> --- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >>> share your >>> opinions on IT & business topics through brief surveys-and earn cash >>> http://www.techsay.com/default.php?=20 >>> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >>> _______________________________________________ >>> GridSAM-Discuss mailing list >>> Gri...@li... >>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>> =20 >> cax >> ----------------------------- >> Think outside the box >> >> >> >> >> >> >> =20 > > - ------------------------------------------------------------------------ - > 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=3Djoin.php&p=3Dsourceforge&CID=3D= 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.3 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFF1YOSoR/fdCmliYMRAkfoAKDJFZIg7OsI/9mB2KtTsotT2syG0ACg2KJ5 > BYz6D2OV3k3DkfF/SwC09tY=3D > =3D/Iqm > -----END PGP SIGNATURE----- > =20 --=20 ------------------------------------------------------------------------ --- 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss |
|
From: Mark HB <m.h...@ma...> - 2007-02-16 10:22:24
|
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: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > 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.j...@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=DEVDEV > _______________________________________________ > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.3 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFF1YOSoR/fdCmliYMRAkfoAKDJFZIg7OsI/9mB2KtTsotT2syG0ACg2KJ5 > BYz6D2OV3k3DkfF/SwC09tY= > =/Iqm > -----END PGP SIGNATURE----- > -- --------------------------------------------------------------------------- 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 --------------------------------------------------------------------------- |
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From: Stefan Z. <ste...@uc...> - 2007-02-16 10:12:52
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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.j...@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=DEVDEV _______________________________________________ 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.3 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFF1YOSoR/fdCmliYMRAkfoAKDJFZIg7OsI/9mB2KtTsotT2syG0ACg2KJ5 BYz6D2OV3k3DkfF/SwC09tY= =/Iqm -----END PGP SIGNATURE----- |
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From: Gordon S. <g.s...@ne...> - 2007-02-16 09:14:06
|
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...]=20 Sent: 16 February 2007 08:57 To: Gordon Stewart Cc: Mark HB Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Humm, it is a good guess, however, AHE-Server is generating this =20 jsdl, anyone knows where we have to change it in order to =20 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 =20 > is at > fault. I've had errors in the past where the order of elements =20 > 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=3D"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 =20 > 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 =20 > 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 =20 > 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 =20 > found > at: > omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/=20 > 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=3DUK/O=3DeScience/OU=3DImperial/L=3DLeSC/CN=3Dmark 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 =20 > element > MPIApplication@urn:gridsam:mpi] > > ################ JOBMANAGER.XML ################ > <?xml version=3D"1.0" encoding=3D"UTF-8"?> > <module id=3D"jobmanager.globus" version=3D"1.0.0"> > <!-- dependent modules --> > <sub-module > descriptor=3D"org/icenigrid/gridsam/resource/config/common.xml"/> > <sub-module > descriptor=3D"org/icenigrid/gridsam/resource/config/embedded.xml"/> > <sub-module > descriptor=3D"org/icenigrid/gridsam/resource/config/globus.xml"/> > <sub-module descriptor=3D"database.xml"/> > <sub-module descriptor=3D"authorisation.xml"/> > <!-- override the factory defaults here --> > <contribution configuration-id=3D"hivemind.ApplicationDefaults"> > <!-- The job manager location --> > <default symbol=3D"globus.JobManager" value=3D"grid-data.man.ac.uk"/> > > <!-- The root file system for staging files > --> > <default symbol=3D"globus.RootFileSystemURI" > value=3D"gsiftp://grid-data.man.ac.uk"/> > <!-- How often the status of the job is polled > --> > <default symbol=3D"globus.MonitoringPeriod" value=3D"20000"/> > <!-- the default location of the classad generation script > WEB-INF/classes/rsl.groovy --> <default > symbol=3D"globus.ScriptResource" value=3D"rsl.groovy"/> > </contribution> > </module> > > #################### JSDL ######################## > <JobDefinition xmlns=3D"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=3D"http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" > xmlns:mpi=3D"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/=20 > 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/=20 > 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/=20 > 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/=20 > filestage/ > 195914151107445079635/_th-details.out</URI></Target> > </DataStaging> > </JobDescription> > <myproxy:MyProxy > = xmlns:myproxy=3D"urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid- > su > pport.ac.uk</myproxy:ProxyServer> > = <myproxy:ProxyServerDN>/C=3DUK/O=3DeScience/OU=3DCLRC/L=3DDL/CN=3Dhost/=20 > myproxy.gri > d-support.ac.uk/E=3Da...@dl...</myproxy:ProxyServerDN> > <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> > <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> > <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</=20 > myproxy:ProxyServerPassPhra > se> > <myproxy:ProxyServerLifetime>7512</myproxy:ProxyServerLifetime></=20 > myproxy > :MyProxy> > </JobDefinition> > > > --=20 > ---------------------------------------------------------------------- > -- > --- > 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 =20 > share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDE > 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 =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV > _______________________________________________ > GridSAM-Discuss mailing list > Gri...@li... > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss cax - ----------------------------- Think outside the box -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (Darwin) iD8DBQFF1XHlFRQXwtwLTD0RAod6AJwOyczxnLkUF4C/IBioNUKl0Qlm2ACgpeG8 JjW/t+XWoD+zFi518YngNlI=3D =3DFGFg -----END PGP SIGNATURE----- |
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From: Gordon S. <g.s...@ne...> - 2007-02-16 08:49:04
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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=3D"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=3DUK/O=3DeScience/OU=3DImperial/L=3DLeSC/CN=3Dmark 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=3D"1.0" encoding=3D"UTF-8"?> <module id=3D"jobmanager.globus" version=3D"1.0.0"> <!-- dependent modules --> <sub-module descriptor=3D"org/icenigrid/gridsam/resource/config/common.xml"/> <sub-module descriptor=3D"org/icenigrid/gridsam/resource/config/embedded.xml"/> <sub-module descriptor=3D"org/icenigrid/gridsam/resource/config/globus.xml"/> <sub-module descriptor=3D"database.xml"/> <sub-module descriptor=3D"authorisation.xml"/> <!-- override the factory defaults here --> <contribution configuration-id=3D"hivemind.ApplicationDefaults"> <!-- The job manager location --> <default symbol=3D"globus.JobManager" value=3D"grid-data.man.ac.uk"/> <!-- The root file system for staging files --> <default symbol=3D"globus.RootFileSystemURI" value=3D"gsiftp://grid-data.man.ac.uk"/> <!-- How often the status of the job is polled --> <default symbol=3D"globus.MonitoringPeriod" value=3D"20000"/> <!-- the default location of the classad generation script WEB-INF/classes/rsl.groovy --> <default symbol=3D"globus.ScriptResource" value=3D"rsl.groovy"/> </contribution> </module> #################### JSDL ######################## <JobDefinition xmlns=3D"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=3D"http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" xmlns:mpi=3D"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>=20 </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=3D"urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid-s= u pport.ac.uk</myproxy:ProxyServer> <myproxy:ProxyServerDN>/C=3DUK/O=3DeScience/OU=3DCLRC/L=3DDL/CN=3Dhost/my= proxy.gri d-support.ac.uk/E=3Da...@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> --=20 ------------------------------------------------------------------------ --- 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V _______________________________________________ GridSAM-Discuss mailing list Gri...@li... https://lists.sourceforge.net/lists/listinfo/gridsam-discuss |
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From: Mark HB <m.h...@ma...> - 2007-02-16 08:05:52
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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.html 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/195914151107445079635/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-support.ac.uk</myproxy:ProxyServer> <myproxy:ProxyServerDN>/C=UK/O=eScience/OU=CLRC/L=DL/CN=host/myproxy.grid-support.ac.uk/E=a.j...@dl...</myproxy:ProxyServerDN> <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</myproxy:ProxyServerPassPhrase> <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 --------------------------------------------------------------------------- |
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From: Gordon S. <g.s...@ne...> - 2007-02-15 10:22:10
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Hi all, We're using GridSAM 2.0.0 as supplied with the OMII-UK server release version 3.2.0, and are experiencing problems. We first saw these on an installation on Ubuntu (Dapper) and now find the same things happening under CentOS 4.4. GridSAM appears to run correctly to begin with: jobs appear to be submitted and retrieved successfully. After about half a dozen submissions, however, jobs fail, either when staging in or out, and no further jobs will complete until the container is restarted. I've copied a section of the log file into the end of this message, beginning at the point when staging-in completes. In this example, files are staged from and to the same directory. The fact that it works some of the time suggests to me that this is likely a problem with the GridSAM / VFS interactions. Does anyone have any experience with this or similar problems, or any further ideas as to what might be causing this? I have submitted this as a bug (1655009) at present. Thanks, Gordon P.S. Apologies if this appears twice; I think the original expired while awaiting moderation, but I'm not certain! ******************************************************************* Gordon Stewart (Research Assistant) National e-Science Centre University of Glasgow E-Mail: g DOT stewart AT nesc.gla.ac.uk ******************************************************************* - state {staged-in} reached WseSourceProcessor: No destinations to route the event - Job ff808081109b9f4e01109bbcb53c0025.3b0b1adf:1109ba09693:-7fdd threw a JobExecutionException:=20 org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Stage Task.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java :516) - state {active} reached WseSourceProcessor: No destinations to route the event - executing shell script /project/omii-server/omii-server-3.2.0/jakarta-tomcat-5.0.25/temp/exec-1 6475.sh - executable completed - 0 - state {executed} reached WseSourceProcessor: No destinations to route the event - Job ff808081109b9f4e01109bbcb53c0025.3b0b1adf:1109ba09693:-7fdc threw a JobExecutionException:=20 org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Stage Task.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java :516) - state {staging-out} reached WseSourceProcessor: No destinations to route the event - staging file file:///tmp/gridsam-ff808081109b9f4e01109bbcb53c0025/download.archive -> sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3. 2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.Au roraServiceGridSAM/8c0260b0-b695-11db-af8c-a424a8974f08/download.archive - Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.A uroraServiceGridSAM/8c0260b0-b695-11db-af8c-a424a8974f08/download.archiv e" is writeable. org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.A uroraServiceGridSAM/8c0260b0-b695-11db-af8c-a424a8974f08/download.archiv e" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.getOutputStream(Abstr actFileObject.java:1127) at org.apache.commons.vfs.provider.DefaultFileContent.getOutputStream(Defau ltFileContent.java:367) at org.icenigrid.gridsam.core.plugin.connector.data.VFSSupport.copyFileToFi le(VFSSupport.java:186) at org.icenigrid.gridsam.core.plugin.connector.data.VFSSupport.copy(VFSSupp ort.java:127) at org.icenigrid.gridsam.core.plugin.connector.data.StageOutStage$1.run(Sta geOutStage.java:162) at org.icenigrid.gridsam.core.plugin.manager.DefaultJobContext$1.run(Defaul tJobContext.java:111) at java.lang.Thread.run(Thread.java:595) Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.A uroraServiceGridSAM/8c0260b0-b695-11db-af8c-a424a8974f08" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 7 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.A uroraServiceGridSAM" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 8 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 9 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 10 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 11 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 12 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 13 more Caused by: org.apache.commons.vfs.FileSystemException: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/" is writeable. at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:475) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:468) ... 14 more Caused by: java.lang.NullPointerException at org.apache.commons.vfs.provider.AbstractFileSystem.resolveFile(AbstractF ileSystem.java:267) at org.apache.commons.vfs.provider.AbstractFileSystem.resolveFile(AbstractF ileSystem.java:262) at org.apache.commons.vfs.provider.AbstractFileObject.getParent(AbstractFil eObject.java:503) at org.apache.commons.vfs.provider.AbstractFileObject.isWriteable(AbstractF ileObject.java:465) ... 15 more - download.archive fails to be staged: Could not determine if file "sftp://<<USER>>:<<PASSWORD>>@<<HOST>>/project/omii-server/omii-server-3 .2.0/jakarta-tomcat-5.0.25/temp/uk.ac.gla.nesc.project.services.aurora.A uroraServiceGridSAM/8c0260b0-b695-11db-af8c-a424a8974f08/download.archiv e" is writeable. - state {failed} reached - failed 1170843940156 1170843940289 1170843940370 1170843940411 1170844145834 1170844145879 1170844145942=09 WseSourceProcessor: No destinations to route the event - Job ff808081109b9f4e01109bbcb53c0025.3b0b1adf:1109ba09693:-7fdb threw a JobExecutionException:=20 org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Stage Task.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java :516) WseSourceProcessor: No destinations to route the event - Job ff808081109b9f4e01109bbcb53c0025.3b0b1adf:1109ba09693:-7fda threw a JobExecutionException:=20 org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Stage Task.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java :516) |
|
From: Gordon S. <g.s...@ne...> - 2007-02-15 10:17:40
|
Hi, I experienced similar problems with GridSAM under OMII 3.2.0 a while back which I raised as a bug (1610199, the report for which can be found at http://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D1610199&grou= p_i d=3D141177&atid=3D748732). This occurred when trying to deploy a new instance of GridSAM using the latest builds from this site. I found that replacing the contents of WEB-INF/classes/org in the new GridSAM directory with the contents from the instance shipped with the OMII server caused these errors to go away. I am, however, experiencing other issues under OMII 3.2.0 detailed in another bug report (1655009) and another post. Hope this helps. Gordon |
|
From: Mark HB <m.h...@ma...> - 2007-02-13 13:09:27
|
Hey,
I am trying to install multiple instances of gridsam 2.0 on Tomcat. I am
using the OMII-server 3.2.0. I am trying to install four, gridsam_leeds,
gridsam_man, gridsam_oesc, gridsam_rl. I have followed the instructions
found on:
omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/index.html
However, when I restart the server, I get the following error in the
localhost_*date*.log: Incompatible magic value
I get the same error each gridsam, but have only pasted one below
Can you help?
Cheers
Mark
2007-02-07 09:24:29 StandardContext[/gridsam_man]Error configuring
application listener of class
org.icenigrid.gridsam.webservice.servlet.JobManagerConfigurator
java.lang.ClassFormatError: Incompatible magic value -272646673 in class
file org/icenigrid/gridsam/webservice/servlet/JobManagerConfigurator
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at
org.apache.catalina.loader.WebappClassLoader.findClassInternal(WebappClassLoader.java:1634)
at
org.apache.catalina.loader.WebappClassLoader.findClass(WebappClassLoader.java:860)
at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1307)
at
org.apache.catalina.loader.WebappClassLoader.loadClass(WebappClassLoader.java:1189)
at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:3753)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4321)
at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:823)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:807)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:595)
at
org.apache.catalina.core.StandardHostDeployer.install(StandardHostDeployer.java:277)
at org.apache.catalina.core.StandardHost.install(StandardHost.java:832)
at
org.apache.catalina.startup.HostConfig.deployDirectories(HostConfig.java:683)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:432)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:964)
at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:349)
at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:119)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1091)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:789)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1083)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:478)
at org.apache.catalina.core.StandardService.start(StandardService.java:476)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:2298)
at org.apache.catalina.startup.Catalina.start(Catalina.java:556)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:284)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:422)
--
---------------------------------------------------------------------------
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
---------------------------------------------------------------------------
|
|
From: Stefan Z. <ste...@uc...> - 2007-01-30 17:01:32
|
Dear All, According to the GridSAM 2.0 documentation at: http://gridsam.sourceforge.net/2.0.0/gridsam-service/gt2.html when deploying multiple GridSAM instances in the same container, the following jars need to be to $TOMCAT_HOME/shared/lib and removed from each instance's lib directory (as was the case with previous GridSAM versions): bouncycastle-jce-jdk13-119.jar, cryptix32.jar, cryptix-asn1.jar, cryptix.jar, puretls.jar In the 2.0 deployment there is no bouncycastle jar, and the versions of cryptix* and puretls are named differently. Are these steps are no longer needed, or do the different versions of the jars need to be moved? Thanks, Stefan. |
|
From: Carlos A. Q. <cqu...@vp...> - 2007-01-23 00:25:39
|
Hi, Please does anyone know why I am getting this error ? I am using gridsam 2 and I get this error every time I try to submit a mpi job to grid. GridSAM state is: failed Time: 2007-01-23T11:13:42.109+11:00 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] ---------------------------------------- thx, Carlos Alexandre Queiroz |
|
From: Carlos A. Q. <cqu...@vp...> - 2007-01-02 04:45:40
|
Hi, I am trying to test gridsam installation. I am using gridsam as part of omii package. After have installed omii and gridsam, I am able to see the wsdl file, but when I try to submit a simple job to gridsam, for instance, sleep.jsdl or helloworld.jsdl, by executing gridsam-submit -s "http:// ngahe.vpac.org:18080/gridsam/services/gridsam?wsdl" -j helloworld.jsdl I've got the following error on catalina.out file: WseSourceHandler**Received SOAPMessage from Application** WseSourceProcessor: No destinations to route the event WseSubscriptionManagerHandler: UnknownExchangeException : - >WseSubscriptionManagerProcessor: Action missing. Processor only deals with WS-Eventing exchanges. Anyone knows what is going on ? thx so much, Carlos Alexandre Queiroz |
|
From: Vesselin N. <ve...@do...> - 2006-12-13 20:22:55
|
Dawid, If you want to deny everything to everyone you should put 'true' for <deny> and 'false' for <allow>. If you put 'false' in both than all submission will be allowed - that's how it is expected to work (and it is explain in the documentation). I've just made some changes to the documentation of the authorization.xml examples. The changes affect the examples where you'd have a specific XPath string - it needs to have the namspaces declared according to XQuery syntax for namespace declarations in query strings. Check the new documentation and let me know if you still have problems with authorization. --Vesso dejw wrote: >Hi all, > >doeas anyone knows why authorisation could not work? what could be cause >of this? I changed it many times also according to the docs and nothing. >Even if I deny everything and to everyone I can still submit jobs >without problems to my service. > >Cheers, >Dawid > > >------------------------------------------------------------------------- >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 > > -- ----------------------------------------------------------------- Vesso A. Novov -- Research Assistant -- ----------------------------------------------------------------- London e-Science Centre http://www.lesc.doc.ic.ac.uk Imperial College London, Department of Computing 180 Queen's Gate, London SW7 2RH, UK tel: +44 (0)207-594-8399 fax: +44 (0)207-581-8024 ----------------------------------------------------------------- |
|
From: dejw <de...@ma...> - 2006-11-23 08:13:15
|
sorry I'm resending it also to the list > Hi Steve, > > I have omii server and client 3.1.0 from omii web site, I have also > GridSAM server and client 2.0.0 embedded in this install bundle. > > Everything was installed according to docs on the omii page with defaul= t > omii temporary certificates set during installation (BTW I tried once t= o > chnge temporary certificates to some others but I never succeeded with > this, even support tips couldn't help me with this). > > For job submission I have my own java client besed on the GridSAM jars. > And also gridsam-submit - in both cases I have the same behaviour and > results. > > Dawid > > > A.S.McGough napisa=B3(a): > =20 >> Hi Dawid, >> >> It's not clear at all at the moment why this seems to be happening. In >> order to see what is going on I could do with knowing some informatio= n: >> >> 1) Which version of GridSAM are you using, where did you download it >> from and which version of the OMII container are you using? >> >> 2) What are you using to submit jobs? the gridsam-submit command or >> your own client? >> >> 3) What certificate are you using? The one from the OMII website or a >> more secure one? >> >> If you let me know I'll see if I can reproduce your problem. >> >> steve.. >> >> dejw wrote: >> =20 >>> Hi all, >>> >>> doeas anyone knows why authorisation could not work? what could be ca= use >>> of this? I changed it many times also according to the docs and nothi= ng. >>> Even if I deny everything and to everyone I can still submit jobs >>> without problems to my service. >>> >>> Cheers, >>> Dawid >>> >>> >>> ---------------------------------------------------------------------= ---- >>> >>> 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 cas= h >>> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CI= D=3DDEVDEV >>> >>> _______________________________________________ >>> GridSAM-Discuss mailing list >>> Gri...@li... >>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>> =20 >>> =20 >> =20 > > > =20 |
|
From: A.S.McGough <as...@do...> - 2006-11-22 15:04:38
|
Hi Dawid, It's not clear at all at the moment why this seems to be happening. In order to see what is going on I could do with knowing some information: 1) Which version of GridSAM are you using, where did you download it from and which version of the OMII container are you using? 2) What are you using to submit jobs? the gridsam-submit command or your own client? 3) What certificate are you using? The one from the OMII website or a more secure one? If you let me know I'll see if I can reproduce your problem. steve.. dejw wrote: > Hi all, > > doeas anyone knows why authorisation could not work? what could be cause > of this? I changed it many times also according to the docs and nothing. > Even if I deny everything and to everyone I can still submit jobs > without problems to my service. > > Cheers, > Dawid > > > ------------------------------------------------------------------------- > 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 > -- ------------------------------------------------------------------------ Dr A. Stephen McGough http://www.doc.ic.ac.uk/~asm ------------------------------------------------------------------------ Technical Coordinator, London e-Science Centre, Imperial College London, Department of Computing, 180 Queen's Gate, London SW7 2BZ, UK tel: +44 (0)207-594-8409 fax: +44 (0)207-581-8024 ------------------------------------------------------------------------ |
|
From: dejw <de...@ma...> - 2006-11-22 14:37:24
|
Hi all, doeas anyone knows why authorisation could not work? what could be cause of this? I changed it many times also according to the docs and nothing. Even if I deny everything and to everyone I can still submit jobs without problems to my service. Cheers, Dawid |
|
From: dejw <de...@ma...> - 2006-11-22 12:32:50
|
Hi Garry, thanks for this, I used your authorisation.xml without changes and ... it doesn't work for me ! :) I don't understand this. I can still submit jobs, even when I use /bin/sleep and I have other DN than in your file. Should I change the GridSAM configuration somwhere else? It is weird. Dawid Garry Smith napisa=B3(a): > Hi Dawid, > > =20 >> I did some experiment - I changed in authorization.xml deny and allow=20 >> rules to <false/>. So I understad that nobody should be able to submit= =20 >> jobs? >> But after I changed this and restart server I still can submit jobs.=20 >> So maybe I have something wrong with my configuration? It works for yo= u? >> =20 > > Yes I had this working. Check the file at=20 > http://acet.rdg.ac.uk/~gms/authorisation.xml > I remember experiencing some problems so kept the badguys group defined= .=20 > Don't quite remember what the issue was now. > > =20 >> And the question about this authorization mechanism: >> >> What is taken into account? The principle DN from the keystore used to= =20 >> create connection between client and server? or the DN is taken from=20 >> user's globus proxy? >> =20 > > Should be the DN from user's globus proxy. > > Garry > > > -----------------------------------------------------------------------= -- > 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > _______________________________________________ > GridSAM-Discuss mailing list > Gri...@li... > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss > =20 |
|
From: Garry S. <gar...@co...> - 2006-11-22 12:07:29
|
Hi Dawid, > > I did some experiment - I changed in authorization.xml deny and allow > rules to <false/>. So I understad that nobody should be able to submit > jobs? > But after I changed this and restart server I still can submit jobs. > So maybe I have something wrong with my configuration? It works for you? Yes I had this working. Check the file at http://acet.rdg.ac.uk/~gms/authorisation.xml I remember experiencing some problems so kept the badguys group defined. Don't quite remember what the issue was now. > > And the question about this authorization mechanism: > > What is taken into account? The principle DN from the keystore used to > create connection between client and server? or the DN is taken from > user's globus proxy? Should be the DN from user's globus proxy. Garry |
|
From: dejw <de...@ma...> - 2006-11-22 11:54:59
|
Hi Garry, I did some experiment - I changed in authorization.xml deny and allow rules to <false/>. So I understad that nobody should be able to submit jo= bs? But after I changed this and restart server I still can submit jobs. So maybe I have something wrong with my configuration? It works for you? And the question about this authorization mechanism: What is taken into account? The principle DN from the keystore used to create connection between client and server? or the DN is taken from user's globus proxy? But what if the target system is not globus based? fork, condor or something? then if you have information about myproxy server where user stores its credentials its useless? Or maybe it is used by GridSAM internally to check user's DN and authorize him without bothering about what is below GridSAM service (i.e. fork, condor etc.) ? Dawid Garry Smith napisa=B3(a): > Hi Dawid, > > =20 >> The question is how to recognize >> each portal user in GridSAM service - I mean how to authenticate and >> authorize them. Because now every user can use portal access without >> restriction because GridSAM server can see only client with given >> keystore. What option do I have? Can I send for example user DN and >> resolve it on the server side? something like GSI where I can provid= e >> user's proxy credentials? Maybe I should use some omii server >> technology? I saw there some account service or something? >> >> =20 > I normally include the myproxy element in the JSDL and insert the user'= s=20 > DN into the GridSAM's authorization.xml. See the following link > > http://gridsam.sourceforge.net/1.1/deploymentguide/auth.html > > regards > Garry > > > > dejw wrote: > > =20 >> Hi Steve, >> >> thanks for replay, I didn't find any William Lee message concerning >> WS-Security. Have you any exmaples of codes or something? How to use=20 >> gridsam API and use WS-Security with it? I wonder if I can use maybe >> globus proxy certificate inside WM-Security somehow. I would like to t= ry >> to do this, what do you think? So I should wait until Vesso will be >> available ? >> >> Dawid >> >> >> A.S.McGough napisa=B3(a): >> =20 >> >> =20 >>> Dear Dawid, >>> >>> Unfortunately Vesso who would know more about the security side is on >>> holiday at the moment, so I'll try to answer as best I can. >>> >>> GridSAM supports communication to the service through HTTPS - I'm >>> assuming that this is what you are using at the moment? It also >>> supports the use of WS-Security - which will allow you to use user >>> certificates when submitting jobs. This will allow you to perform use= r >>> Authentication and Authorisation. >>> >>> As for how to enable WS-Security if you look in the old archive of >>> this list I beleve William Lee explained this. >>> >>> Hope this is of help - if not feel free to get back in touch, >>> >>> steve.. >>> >>> dejw wrote: >>> =20 >>> >>> =20 >>>> Hi, >>>> >>>> I am interesting to provide portal access to the GridSAM service. I = have >>>> ready working client. I'm using omii stuff with keystore to create S= SL >>>> connection between portal and service. The question is how to recogn= ize >>>> each portal user in GridSAM service - I mean how to authenticate and >>>> authorize them. Because now every user can use portal access without >>>> restriction because GridSAM server can see only client with given >>>> keystore. What option do I have? Can I send for example user DN and >>>> resolve it on the server side? something like GSI where I can prov= ide >>>> user's proxy credentials? Maybe I should use some omii server >>>> technology? I saw there some account service or something? >>>> >>>> Best Regards, >>>> Dawid Szejnfeld, PSNC >>>> >>>> >>>> --------------------------------------------------------------------= ----- >>>> >>>> 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 ca= sh >>>> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&C= ID=3DDEVDEV >>>> >>>> _______________________________________________ >>>> GridSAM-Discuss mailing list >>>> Gri...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>> =20 >>>> =20 >>>> >>>> =20 >>> =20 >>> >>> =20 >> >> ----------------------------------------------------------------------= --- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to shar= e your >> opinions on IT & business topics through brief surveys - and earn cash >> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV >> _______________________________________________ >> GridSAM-Discuss mailing list >> Gri...@li... >> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >> >> >> =20 >> >> =20 > > > -----------------------------------------------------------------------= -- > 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=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > _______________________________________________ > GridSAM-Discuss mailing list > Gri...@li... > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss > =20 |
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From: Garry S. <gar...@co...> - 2006-11-22 11:19:04
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Hi Dawid, >The question is how to recognize >each portal user in GridSAM service - I mean how to authenticate and >authorize them. Because now every user can use portal access without >restriction because GridSAM server can see only client with given >keystore. What option do I have? Can I send for example user DN and >resolve it on the server side? something like GSI where I can provide >user's proxy credentials? Maybe I should use some omii server >technology? I saw there some account service or something? > I normally include the myproxy element in the JSDL and insert the user's DN into the GridSAM's authorization.xml. See the following link http://gridsam.sourceforge.net/1.1/deploymentguide/auth.html regards Garry dejw wrote: >Hi Steve, > >thanks for replay, I didn't find any William Lee message concerning >WS-Security. Have you any exmaples of codes or something? How to use >gridsam API and use WS-Security with it? I wonder if I can use maybe >globus proxy certificate inside WM-Security somehow. I would like to try >to do this, what do you think? So I should wait until Vesso will be >available ? > >Dawid > > >A.S.McGough napisał(a): > > >>Dear Dawid, >> >>Unfortunately Vesso who would know more about the security side is on >>holiday at the moment, so I'll try to answer as best I can. >> >>GridSAM supports communication to the service through HTTPS - I'm >>assuming that this is what you are using at the moment? It also >>supports the use of WS-Security - which will allow you to use user >>certificates when submitting jobs. This will allow you to perform user >>Authentication and Authorisation. >> >>As for how to enable WS-Security if you look in the old archive of >>this list I beleve William Lee explained this. >> >>Hope this is of help - if not feel free to get back in touch, >> >>steve.. >> >>dejw wrote: >> >> >>>Hi, >>> >>>I am interesting to provide portal access to the GridSAM service. I have >>>ready working client. I'm using omii stuff with keystore to create SSL >>>connection between portal and service. The question is how to recognize >>>each portal user in GridSAM service - I mean how to authenticate and >>>authorize them. Because now every user can use portal access without >>>restriction because GridSAM server can see only client with given >>>keystore. What option do I have? Can I send for example user DN and >>>resolve it on the server side? something like GSI where I can provide >>>user's proxy credentials? Maybe I should use some omii server >>>technology? I saw there some account service or something? >>> >>>Best Regards, >>>Dawid Szejnfeld, PSNC >>> >>> >>>------------------------------------------------------------------------- >>> >>>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 >>> >>> >>> >> >> > > > >------------------------------------------------------------------------- >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 > > > > |
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From: dejw <de...@ma...> - 2006-11-22 08:34:45
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Hi Steve, thanks for replay, I didn't find any William Lee message concerning WS-Security. Have you any exmaples of codes or something? How to use=20 gridsam API and use WS-Security with it? I wonder if I can use maybe globus proxy certificate inside WM-Security somehow. I would like to try to do this, what do you think? So I should wait until Vesso will be available ? Dawid A.S.McGough napisa=B3(a): > Dear Dawid, > > Unfortunately Vesso who would know more about the security side is on > holiday at the moment, so I'll try to answer as best I can. > > GridSAM supports communication to the service through HTTPS - I'm > assuming that this is what you are using at the moment? It also > supports the use of WS-Security - which will allow you to use user > certificates when submitting jobs. This will allow you to perform user > Authentication and Authorisation. > > As for how to enable WS-Security if you look in the old archive of > this list I beleve William Lee explained this. > > Hope this is of help - if not feel free to get back in touch, > > steve.. > > dejw wrote: >> Hi, >> >> I am interesting to provide portal access to the GridSAM service. I ha= ve >> ready working client. I'm using omii stuff with keystore to create SSL >> connection between portal and service. The question is how to recogniz= e >> each portal user in GridSAM service - I mean how to authenticate and >> authorize them. Because now every user can use portal access without >> restriction because GridSAM server can see only client with given >> keystore. What option do I have? Can I send for example user DN and >> resolve it on the server side? something like GSI where I can provid= e >> user's proxy credentials? Maybe I should use some omii server >> technology? I saw there some account service or something? >> >> Best Regards, >> Dawid Szejnfeld, PSNC >> >> >> ----------------------------------------------------------------------= --- >> >> 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=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV >> >> _______________________________________________ >> GridSAM-Discuss mailing list >> Gri...@li... >> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >> =20 > > |
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From: A.S.McGough <as...@do...> - 2006-11-21 18:24:53
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Dear Dawid, Unfortunately Vesso who would know more about the security side is on holiday at the moment, so I'll try to answer as best I can. GridSAM supports communication to the service through HTTPS - I'm assuming that this is what you are using at the moment? It also supports the use of WS-Security - which will allow you to use user certificates when submitting jobs. This will allow you to perform user Authentication and Authorisation. As for how to enable WS-Security if you look in the old archive of this list I beleve William Lee explained this. Hope this is of help - if not feel free to get back in touch, steve.. dejw wrote: > Hi, > > I am interesting to provide portal access to the GridSAM service. I have > ready working client. I'm using omii stuff with keystore to create SSL > connection between portal and service. The question is how to recognize > each portal user in GridSAM service - I mean how to authenticate and > authorize them. Because now every user can use portal access without > restriction because GridSAM server can see only client with given > keystore. What option do I have? Can I send for example user DN and > resolve it on the server side? something like GSI where I can provide > user's proxy credentials? Maybe I should use some omii server > technology? I saw there some account service or something? > > Best Regards, > Dawid Szejnfeld, PSNC > > > ------------------------------------------------------------------------- > 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 > -- ------------------------------------------------------------------------ Dr A. Stephen McGough http://www.doc.ic.ac.uk/~asm ------------------------------------------------------------------------ Technical Coordinator, London e-Science Centre, Imperial College London, Department of Computing, 180 Queen's Gate, London SW7 2BZ, UK tel: +44 (0)207-594-8409 fax: +44 (0)207-581-8024 ------------------------------------------------------------------------ |
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From: dejw <de...@ma...> - 2006-11-21 10:03:58
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Hi, I am interesting to provide portal access to the GridSAM service. I have ready working client. I'm using omii stuff with keystore to create SSL connection between portal and service. The question is how to recognize each portal user in GridSAM service - I mean how to authenticate and authorize them. Because now every user can use portal access without restriction because GridSAM server can see only client with given keystore. What option do I have? Can I send for example user DN and resolve it on the server side? something like GSI where I can provide user's proxy credentials? Maybe I should use some omii server technology? I saw there some account service or something? Best Regards, Dawid Szejnfeld, PSNC |
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From: dejw <de...@ma...> - 2006-09-27 15:13:32
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Hi all, I have question about JSDL support for different connectors. Can I found somewhere some summary with all GridSAM connectors i.e. fork, globus, dramaa etc. and the subset of JSDL they support? I want to have a complete list of JSDL elements supported by every connector and maybe if its possible how they are interpreted internally - how they are translated into language, job submission schema of the target system. Is it possible to have something like this? Regards, Dawid Szejnfeld, PSNC |
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From: dejw <de...@ma...> - 2006-09-22 09:12:02
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Hi, I have to write my own client for gridsam and I'm wondering if it is possible somehow to load crypto.properties not from classloader but from some specified directory? I think that wss4j tries to load it only as resource from classloader. I'm using now libraries and sources of gridsam client 2.0.0 rc1. Is it possible to set some system variable like for client-config.wsdd ( 'axis.ClientConfigFile') in the code? The problem is I could have a few clients for different systems in the same classloader and some of them can have its own crypto.properties file. Regards, Dawid Szejnfeld, PSNC |
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