|
From: Mark HB <m.h...@ma...> - 2007-02-16 11:19:26
|
Dear Stefan, That worked! excellent. Just in case you still want it, the jsdl is below Regards Mark <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:m pi="urn:gridsam:mpi"> <Executable>/home/ngs0386/bin/cimmsim</Executable><Argument>datPlain12</Argument>< Output>stdout.txt</Output><Error>stderr.txt</Error><WorkingDirectory>24141116110754609957</Wor kingDirectory><WallTimeLimit>720</WallTimeLimit><mpi:ProcessorCount>1</mpi:ProcessorCount></mp i:MPIApplication> </Application> <DataStaging><FileName>datPlain12</FileName><CreationFlag>overwrite</CreationFlag><DeleteO nTermination>false</DeleteOnTermination><Source><URI>http://test:to...@ig...: 18080/filestage/24141116110754609957/datPlain12</URI></Source></DataStaging><DataStaging><File Name>stdout.txt</FileName><CreationFlag>overwrite</CreationFlag><DeleteOnTermination>false</De leteOnTermination><Target><URI>webdav://test:to...@ig...:18080/filestage/2414 1116110754609957/stdout.txt</URI></Target></DataStaging><DataStaging><FileName>stderr.txt</Fil eName><CreationFlag>overwrite</CreationFlag><DeleteOnTermination>false</DeleteOnTermination><T arget><URI>webdav://test:to...@ig...:18080/filestage/24141116110754609957/std err.txt</URI></Target></DataStaging><DataStaging><FileName>_th-details.out</FileName><Creation Flag>overwrite</CreationFlag><DeleteOnTermination>false</DeleteOnTermination><Target><URI>webd av://test:to...@ig...:18080/filestage/24141116110754609957/_th-details.out</U RI></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/mypro xy.grid-support.ac.uk/E=a...@dl...</myproxy:ProxyServerDN><myproxy:ProxyServerPort> 7512</myproxy:ProxyServerPort><myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserNam e><myproxy:ProxyServerPassPhrase>any1any1</myproxy:ProxyServerPassPhrase><myproxy:ProxyServerL ifetime>7512</myproxy:ProxyServerLifetime></myproxy:MyProxy></JobDefinition> Stefan Zasada wrote: > Hi, > > In the previous Util.pm I put the CPUCount element after the posix > block, but from the error you got Mark, it could be that GridSAM is > looking for CPUCount directly after wallTimeLimit? I've updated Util.pm > to put CPUCount directly after wallTimeLimit at the end of the > MPIApplication block (it's at the same url). Could you try giving this a go? > > Also, could you send the JSDL generated? > > Cheers, > > Stefan. > > Gordon Stewart wrote: > >> Well, the error has changed a little, but I'm not sure whether it's for >> the better or worse... >> >> The GGF give an example MPI JSDL file for GridSAM >> (http://www.ggf.org/GGF17/materials/253/gridsam-jsdl-mpi-sample.pdf): >> >> ... >> <JobDescription> >> <Application >> xmlns:posix="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"> >> <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> >> <posix:Executable>/bin/some-parallel-app</posix:Executable> >> <posix:Argument>hello world</posix:Argument> >> <posix:Environment name="ABC">DEF</posix:Environment> >> <mpi:ProcessorCount>10</mpi:ProcessorCount> >> <xyz:OtherExtension xmlns:xyz="urn:xyz">My >> Extension</xyz:OtherExtension> >> </mpi:MPIApplication> >> </Application> >> </JobDescription> >> ... >> >> Assuming that the generated JSDL now has this form, I'm not really sure >> what could be causing these errors. It now seems to be complaining >> about the existence of the POSIX elements within the MPIApplication >> element, but they are clearly allowed. Perhaps you could post the new >> JSDL to see if that provides any further inspiration? >> >> Gordon >> >> -----Original Message----- >> From: gri...@li... >> [mailto:gri...@li...] On Behalf Of Mark >> HB >> Sent: 16 February 2007 09:28 >> To: Stefan Zasada >> Cc: cax...@gm...; gri...@li... >> Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >> >> >> Dear Stefan, >> >> Unfortunately it doesn't seem to fix it for me. >> I did this: >> 1) Copied new Util.pm to OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE >> 2) restarted OMII server >> 3) ran the ahe_destroy....... & ahe_create.... scripts (just in case) >> 4) Run the ahe-client as before, but got the error as before >> >> Error: >> Description: Invalid JSDL v1.0 job description: [error: >> cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' >> >> instead of 'Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' >> here in element MPIApplication@urn:gridsam:mpi, error: >> cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' >> >> instead of 'Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' >> here in element MPIApplication@urn:gridsam:mpi, error: >> cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' >> >> instead of 'Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here >> in element MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: >> >> Expected element 'ProcessorCount@urn:gridsam:mpi' instead of >> 'Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here in element >> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: Expected >> element 'ProcessorCount@urn:gridsam:mpi' instead of >> 'WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here >> in element MPIApplication@urn:gridsam:mpi] >> >> >> Stefan Zasada wrote: >> Dear Mark and Carlos, >> >> I've modified Util.pm to put the <mpi:ProcessorCount> >> element after the JSDL posix stuff. Get it from: >> >> http://ccs.chem.ucl.ac.uk/~stefan/Util.pm >> >> Replace the Util.pm in your AHE distribution with it and let me know >> >>> if >>> >> it works. >> >> Cheers, >> >> Stefan. >> >> Gordon Stewart wrote: >> >> >>>>> There's a file called Util.pm.mpi in the >>>>> $OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE directory of the OMII >>>>> 3.2.0 installation (and also in the ahe.war file within the >>>>> >>> installation >>> >>>>> bundle) that, at a brief glance, appears to contain the code which >>>>> builds the JSDL. >>>>> >>>>> I'm not sure what changes you would have to make in order to modify >>>>> >>> the >>> >>>>> order of elements. >>>>> >>>>> Gordon >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Carlos Alexandre Queiroz [mailto:cax...@gm...] >>>>> Sent: 16 February 2007 08:57 >>>>> To: Gordon Stewart >>>>> Cc: Mark HB >>>>> Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>>> >>>>> Humm, it is a good guess, however, AHE-Server is generating this >>>>> jsdl, anyone knows where we have to change it in order to >>>>> generate a different jsdl file ?? >>>>> >>>>> >>>>> thx, >>>>> >>>>> cax >>>>> >>>>> >>>>> On 16/02/2007, at 7:49 PM, Gordon Stewart wrote: >>>>> >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> Looking at the error message, it would appear to be the JSDL which >>>>>> is at >>>>>> fault. I've had errors in the past where the order of elements >>>>>> differs >>>>>> from what the parser is expecting. According to the GridSAM >>>>>> documentation for the MPIApplication element at >>>>>> http://gridsam.sourceforge.net/2.0.0/gridsam-client/jsdl.html, the >>>>>> definition is: >>>>>> >>>>>> >>>>> >>>>> >>>>>> <jsdl:Application> >>>>>> .. >>>>>> <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> >>>>>> <jsdl-posix:*/>* >>>>>> <mpi:ProcessorCount>xsd:positiveInteger</mpi:ProcessorCount> >>>>>> </mpi:MPIApplication> >>>>>> .. >>>>>> </jsdl:Application> >>>>>> >>>>>> >>>>> >>>>> >>>>>> The POSIX application type (the jsdl-posix: element above) is >>>>>> defined in >>>>>> the XML schema as a sequence, which requires the child elements to >>>>>> appear in the order specified. My guess (and it's only a guess as >>>>>> I've >>>>>> never used the MPI extensions) would be that this is the same with >>>>>> MPIApplication, and that it is objecting to the ProcessorCount >>>>>> >>> element >>> >>>>>> appearing before the POSIX stuff; relocating this after the >>>>>> WallTimeLimit element may help. >>>>>> >>>>>> >>>>> >>>>> >>>>>> Gordon >>>>>> >>>>>> >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: gri...@li... >>>>>> [mailto:gri...@li...] On Behalf Of >>>>>> >>>>>> Mark >>>>>> HB >>>>>> Sent: 16 February 2007 07:11 >>>>>> To: gri...@li... >>>>>> Subject: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>>>> >>>>>> Hey, >>>>>> Sincere apologies if this has sent twice! >>>>>> >>>>>> I am using AHE bundled with OMII server and have created a gridsam >>>>>> instance to point at the Manchester node of the NGS (thanks list for >>>>>> helping sort that out). >>>>>> This GRIDSam instance was installed by following the instructions >>>>>> found >>>>>> at: >>>>>> omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/ >>>>>> index.htm >>>>>> l >>>>>> >>>>>> However when I try to run a job, it all goes wrong. >>>>>> Please find below the error I get, my jobmanger.xml and then the >>>>>> >>> JSDL >>> >>>>>> message itself. >>>>>> Can anyone help? >>>>>> >>>>>> Cheers >>>>>> Mark >>>>>> >>>>>> ############## ERROR ############## >>>>>> >>>>>> 12:37:20 INFO (StartCall.java:182) - AHE Job Owner: >>>>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: pending >>>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description:job >>>>>> >>> is >>> >>>>>> being scheduled >>>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>>> 2007-02-15T12:37:19.840Z >>>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>>> 2007-02-15T12:37:19.840Z >>>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: failed >>>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description: >>>>>> Invalid JSDL v1.0 job description: [error: cvc-complex-type.2.4b: >>>>>> Element not allowed: >>>>>> Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>>> Element not allowed: >>>>>> Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>>> Element not allowed: >>>>>> Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>>> Element not allowed: >>>>>> Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>>> Element not allowed: >>>>>> WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>>> element MPIApplication@urn:gridsam:mpi, error: >>>>>> >>> cvc-complex-type.2.4b: >>> >>>>>> Element not allowed: >>>>>> WallTimeLimit@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>>> element >>>>>> MPIApplication@urn:gridsam:mpi] >>>>>> >>>>>> ################ JOBMANAGER.XML ################ >>>>>> <?xml version="1.0" encoding="UTF-8"?> >>>>>> <module id="jobmanager.globus" version="1.0.0"> >>>>>> <!-- dependent modules --> >>>>>> <sub-module >>>>>> descriptor="org/icenigrid/gridsam/resource/config/common.xml"/> >>>>>> <sub-module >>>>>> descriptor="org/icenigrid/gridsam/resource/config/embedded.xml"/> >>>>>> <sub-module >>>>>> descriptor="org/icenigrid/gridsam/resource/config/globus.xml"/> >>>>>> <sub-module descriptor="database.xml"/> >>>>>> <sub-module descriptor="authorisation.xml"/> >>>>>> <!-- override the factory defaults here --> >>>>>> <contribution configuration-id="hivemind.ApplicationDefaults"> >>>>>> <!-- The job manager location --> >>>>>> <default symbol="globus.JobManager" value="grid-data.man.ac.uk"/> >>>>>> >>>>>> <!-- The root file system for staging files >>>>>> --> >>>>>> <default symbol="globus.RootFileSystemURI" >>>>>> value="gsiftp://grid-data.man.ac.uk"/> >>>>>> <!-- How often the status of the job is polled >>>>>> --> >>>>>> <default symbol="globus.MonitoringPeriod" value="20000"/> >>>>>> <!-- the default location of the classad generation script >>>>>> WEB-INF/classes/rsl.groovy --> <default >>>>>> symbol="globus.ScriptResource" value="rsl.groovy"/> >>>>>> </contribution> >>>>>> </module> >>>>>> >>>>>> #################### JSDL ######################## >>>>>> <JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl"> >>>>>> <JobDescription> >>>>>> <JobIdentification> >>>>>> <JobName>NAMD_NGS_MAN</JobName> >>>>>> <Description>THIS IS FOR NAMD ON THE >>>>>> >>> NGS</Description> >>> >>>>>> <JobAnnotation>NAMD Annotation</JobAnnotation> >>>>>> <JobProject>AHE Project</JobProject> >>>>>> </JobIdentification> >>>>>> <Application> >>>>>> <mpi:MPIApplication >>>>>> xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" >>>>>> xmlns:mpi="urn:gridsam:mpi"> >>>>>> <mpi:ProcessorCount>1</mpi:ProcessorCount> >>>>>> <Executable>/home/ngs0386/bin/cimmsim</Executable> >>>>>> <Argument>datPlain12</Argument> >>>>>> <Output>stdout.txt</Output> >>>>>> <Error>stderr.txt</Error> >>>>>> <WorkingDirectory>195914151107445079635</WorkingDirectory> >>>>>> <WallTimeLimit>720</WallTimeLimit> >>>>>> </mpi:MPIApplication> >>>>>> </Application> >>>>>> >>>>>> <DataStaging> >>>>>> <FileName>datPlain12</FileName> >>>>>> <CreationFlag>overwrite</CreationFlag> >>>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>>> >>>>>> <Source><URI>http://test:to...@ig...:18080/ >>>>>> filestage/19 >>>>>> 5914151107445079635/datPlain12</URI></Source> >>>>>> </DataStaging><DataStaging><FileName>stdout.txt</FileName> >>>>>> <CreationFlag>overwrite</CreationFlag> >>>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>>> >>>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>>> filestage/ >>>>>> 195914151107445079635/stdout.txt</URI></Target> >>>>>> </DataStaging> >>>>>> <DataStaging> >>>>>> <FileName>stderr.txt</FileName> >>>>>> <CreationFlag>overwrite</CreationFlag> >>>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>>> >>>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>>> filestage/ >>>>>> 195914151107445079635/stderr.txt</URI></Target> >>>>>> >>>>>> >>>>> >>>>> >>>>>> </DataStaging> >>>>>> <DataStaging> >>>>>> <FileName>_th-details.out</FileName> >>>>>> <CreationFlag>overwrite</CreationFlag> >>>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>>> >>>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>>> filestage/ >>>>>> 195914151107445079635/_th-details.out</URI></Target> >>>>>> </DataStaging> >>>>>> </JobDescription> >>>>>> <myproxy:MyProxy >>>>>> >>>>>> >>> xmlns:myproxy="urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid- >>> >>>>>> >>>>>> su >>>>>> pport.ac.uk</myproxy:ProxyServer> >>>>>> <myproxy:ProxyServerDN>/C=UK/O=eScience/OU=CLRC/L=DL/CN=host/ >>>>>> myproxy.gri >>>>>> d-support.ac.uk/E=a...@dl...</myproxy:ProxyServerDN> >>>>>> <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> >>>>>> <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> >>>>>> <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</ >>>>>> myproxy:ProxyServerPassPhra >>>>>> se> >>>>>> <myproxy:ProxyServerLifetime>7512</myproxy:ProxyServerLifetime></ >>>>>> myproxy >>>>>> :MyProxy> >>>>>> </JobDefinition> >>>>>> >>>>>> >>>>> >>>>> >>>>>> -- >>>>>> >>>>>> >>> ---------------------------------------------------------------------- >>> >>>>>> >>>>>> -- >>>>>> --- >>>>>> Mark Halling-Brown | Tel: +44-20-7631-6839 >>>>>> Research Associate | >>>>>> Room 359 | Fax: +44-20-7631-6803 >>>>>> School of Crystallography | >>>>>> Birkbeck College | Email: >>>>>> Malet Street | >>>>>> >>> gh...@ma... >>> >>>>>> London WC1E 7HX | ma...@gm... >>>>>> UK | >>>>>> http://people.cryst.bbk.ac.uk/~ghall04 >>>>>> >>>>>> >>> ---------------------------------------------------------------------- >>> >>>>>> >>>>>> -- >>>>>> --- >>>>>> >>>>>> >>>>> >>>>> >>> ---------------------------------------------------------------------- >>> >>>>>> >>>>>> -- >>>>>> - >>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>>> share >>>>>> your >>>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>>> http://www.techsay.com/default.php? >>>>>> page=join.php&p=sourceforge&CID=DEVDE >>>>>> V >>>>>> _______________________________________________ >>>>>> GridSAM-Discuss mailing list >>>>>> Gri...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>>> >>>>>> >>>>>> >>> ---------------------------------------------------------------------- >>> >>>>>> >>>>>> --- >>>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>>> share your >>>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>>> http://www.techsay.com/default.php? >>>>>> page=join.php&p=sourceforge&CID=DEVDEV >>>>>> _______________________________________________ >>>>>> GridSAM-Discuss mailing list >>>>>> Gri...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>>> >>>>>> >>>>> cax >>>>> ----------------------------- >>>>> Think outside the box >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >> - >> >>> ------------------------------------------------------------------------ >>> - >>> >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to >> >>> share your >>> >> opinions on IT & business topics through brief surveys-and earn cash >> >> >>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE >>> V >>> >> _______________________________________________ >> GridSAM-Discuss mailing list >> Gri...@li... >> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >> >> > > -- --------------------------------------------------------------------------- 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 --------------------------------------------------------------------------- |