Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job

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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
>> ----------------------------------------------------------------------
> 
>> --
>> ---
> 
> 
>> ----------------------------------------------------------------------
> 
>> --
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>> _______________________________________________
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>> Gri...@li...
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> 
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> 
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> 
> cax
> -----------------------------
> Think outside the box
> 
> 
> 
> 
> 
> 

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- --
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
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