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From: Bharathi K. <Bha...@ma...> - 2007-07-02 15:49:38
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Hi, I am using omii-client 3.4.0, and omii-server3.4.0. I am using omii-certificates. On rpc326 (desktop) I installed omii client and server, and on biruni (another machine) i installed omii client only. I am submitting sleep.jsdl file, as follows. gridsam-submit -s http://rpc326.cs.man.ac.uk:8080/gridsam/services/gridsam -j /home/biruni/bharathi/sleep.jsdl If I submit from rpc326 which is a local client it is working fine. But, if I submit from biruni i am getting an error. 2007-07-02 15:42:06,504 FATAL [GridSAMSubmit] (main:) unable to submit job: failed to submit job: No jsdl:JobDefinition element can be found in the request. Please check your input and the namespace declarations. <JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl"> <JobDescription> <JobIdentification> <JobProject>gridsam</JobProject> </JobIdentification> <Application> <POSIXApplication xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"> <Executable>/bin/sleep</Executable> <Argument>5</Argument> </POSIXApplication> </Application> </JobDescription> </JobDefinition> regards, Bharathi |
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From: Bharathi K. <Bha...@ma...> - 2007-06-27 14:57:58
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Hi, I am trying to submit jobs to gridsam server using omii client. I got couple of errors . 1) I am trying to configure OMII client to use escience certificate, and i followed the tutorial avaialble at http://www.omii.ac.uk/docs/3.4.0/installation_guide/security/replacing_the_omii_temporary_certificate/nonomii_with_client_omii.htm. ./bin/cmtool -I -d . -ca certs/cacert.pem -alias oldcert Importing trusted CA's certificate certs/cacert.pem into the new keystore omii.ks java.security.cert.CertificateParsingException: invalid DER-encoded certificate data 2) when i am submitting a job gridsam-submit -s http://gridsam.besc.ac.uk:18080/gridsam-manchester/services/gridsam -j /home/bharathi/downloads/hello.jsdl and getting error: 2007-06-27 14:45:46,671 FATAL [GridSAMSubmit] (main:) unable to submit job: failed to submit job: SecurityContextInitHandler: security processing failed; nested exception is: org.apache.ws.security.WSSecurityException: An error was discovered processing the <wsse:Security> header. (WSSecurityEngine: Invalid timestamp {0}); nested exception is: java.text.ParseException: Unparseable date: "2007-06-27T13:45:46.357Z" Any help is appreciated. regards, Bharathi. |
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From: Vesselin N. <ve...@do...> - 2007-05-21 17:00:38
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dejw wrote: >Hi, > >simple question - which version of BES is implemented within GridSAM? >the latest v33 ? > > No. The BES version supported in GridSAM is the one finalized for the HPCProfile demo at SuperComputing'06 in Tampa, FL in November 2006. >Regards, >Dawid Szejnfeld > > >------------------------------------------------------------------------- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >_______________________________________________ >GridSAM-Discuss mailing list >Gri...@li... >https://lists.sourceforge.net/lists/listinfo/gridsam-discuss > > |
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From: dejw <de...@ma...> - 2007-05-18 11:59:36
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Hi, simple question - which version of BES is implemented within GridSAM? the latest v33 ? Regards, Dawid Szejnfeld |
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From: Mark HB <m.h...@ma...> - 2007-05-14 15:09:26
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Dear Jos, Thank very much for your reply. Success! I had moved/deleted all the required jar files except: bcprov-jdk*.jar Once I had deleted these, it all works!! Thanks again, Mark Koetsier wrote: > Hi, > > I experienced the same problem (I posted a bug report about it). In my case it > occurred when multiple GridSAM instances were running in one container. I > think it has to do with a known problem with the Globus Cog kit and its use > of classloaders. > > According to the Cog Kit FAQ: > http://wiki.cogkit.org/index.php/FAQ#While_developing_Grid_Portals_with_Java_COG_Kit.2C_I_get_a_ClassCastException_for_BouncyCastle_classes._Why.3F > > The solution in the cogkit FAQ worked for me - i.e. move the cryptix*.jar and > puretls.jar libraries to $OMII/shared/lib and make sure they are removed from > the GridSAM instances. > > Regards, > > Jos. > > On Monday 14 May 2007 11:09:43 Mark HB wrote: > >> Dear Vesselin, >> >> I am sending this query again as I have not yet received a reply. If you >> need anymore info from me to help diagnose this error, then please ask. >> >> Thanks for your reply. After looking into this further, I think we have >> boiled it down to the exact problem. I am now certain that it is not a >> certificate problem, as I have successfully run a job on one of the grid >> nodes using my set-up on Friday. However the error below is still a >> problem. I will elaborate on my setup. >> >> I am running four instances of grid-sam. One points to the local system, >> and the other three point to respective NGS nodes (man, leeds & oesc). >> When I restart the OMII server, I am then able to submit a job to ONE of >> the NGS nodes successfully, however, the other two respond with the same >> error as before! >> >> "Description: cannot initialise working directory: Could not connect to >> FTP server on"gsiftp://grid-data.man.ac.uk/ - User globus credential is >> required but not specified in the context". >> >> It CANNOT be credentials, as I have just successfully run a job on the >> leeds node, but the exact same job fails on the man and oesc nodes. >> >> I set up the multiple instances exactly as instructed on the gridsam >> site (moving jar files etc). >> >> Have you any ideas >> Regards >> Mark >> >> Vesselin Novov wrote: >> >>> Mark, >>> >>> I should have pointed out, I have never used the AHE in OMII. >>> All my tests use directly installed/managed GridSAM instance. >>> It's worth checking with the AHE developers what exactly goes on >>> when AHE instantiates/manages a GridSAM instance with regard to any >>> security credentials. >>> >>> -Vesso >>> >>> Mark HB wrote: >>> >>>> Vesselin, >>>> >>>> Yes, sorry about that. The error is exactly the same no matter which >>>> node I send the job to, and hence I just grabbed the first log file to >>>> hand. >>>> >>>> Cheers >>>> Mark >>>> >>>> Novov wrote: >>>> >>>>> Mark, >>>>> >>>>> I recently had this exact error, but, in my case missing proxy >>>>> credentials were definitely >>>>> the cause of it. >>>>> >>>>> I am also a bit confused: >>>>> >>>>> - the pasted "GridSAM state is . . ." below indicates the job was >>>>> attempted on the 27th March >>>>> and it was Not submitted because no connection was established with >>>>> grid-compute.leeds.ac.uk. >>>>> - the gram_job_mgr_9570.log entries are from 13th March and indicate >>>>> that job Was at least submitted. >>>>> - the catalina.out section below also indicates a job Was submitted, >>>>> the staging-in of input files was successful >>>>> but failed at staging-out(after execution) phase and the machine is >>>>> grid-data.man.ac.uk. >>>>> >>>>> regards >>>>> Vesso >>>>> >>>>> Mark HB wrote: >>>>> >>>>>> Dear GRIDSam list, >>>>>> >>>>>> I am attempting to run an application on the NGS using AHE/GRIDSam >>>>>> bundled with the OMII-stack. I get the following error when trying to >>>>>> run the job: >>>>>> >>>>>> GridSAM state is: failed >>>>>> Time: 2007-03-22T08:23:48.172Z >>>>>> Description: cannot initialise working directory: Could not connect >>>>>> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >>>>>> credential is required but not specified in the context". >>>>>> >>>>>> I can assure you that I have both a GRIDSam proxy certificate and >>>>>> proxy user certificate running. >>>>>> >>>>>> The GRAM log file found on the NGS machine can be found here: >>>>>> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >>>>>> >>>>>> The main point in this log is "GRAM_SCRIPT_ERROR = 26" >>>>>> >>>>>> ABelow you will find the output produced in the catalina.log file. >>>>>> >>>>>> Has anyone come across this error before? I would appreciate any >>>>>> comments? >>>>>> >>>>>> Cheers >>>>>> Mark >>>>>> >>>>>> - principal obtained from Axis transport - >>>>>> EMA...@ma..., >>>>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>>>> - principal obtained from Axis transport - >>>>>> EMA...@ma..., >>>>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>>>> - state {pending} reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - principal obtained from Axis transport - >>>>>> EMA...@ma..., >>>>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>>>> - principal obtained from Axis transport - >>>>>> EMA...@ma..., >>>>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - state {staging-in} reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Proxy Credentials received : >>>>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>>>> - basic authentication scheme selected >>>>>> - staging (copy) file >>>>>> http://test:to...@ig...:18080/filestage/5512182021072 >>>>>> 78041688/datPlain12 >>>>>> >>>>>> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >>>>>> - basic authentication scheme selected >>>>>> - total byte write 2508 >>>>>> - datPlain12 staged >>>>>> - state {staged-in} reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - executing groovy script >>>>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>>>> - executed groovy script >>>>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - RSL &( arguments = "-f" "datPlain12" )( directory = >>>>>> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >>>>>> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( >>>>>> jobType = "mpi" ) >>>>>> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >>>>>> - Globus job submitted >>>>>> https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) WseSourceProcessor: No destinations to route the event >>>>>> - globus job is active - >>>>>> https://grid-data.man.ac.uk:64304/25112/1174414409/ - state {active} >>>>>> reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - state {staging-out} reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - staging file >>>>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >>>>>> webdav://test:to...@ig...:18080/filestage/55121820210 >>>>>> 7278041688/stdout.txt [Fatal Error] :-1:-1: Premature end of file. >>>>>> - total byte write 4353 >>>>>> [Fatal Error] :-1:-1: Premature end of file. >>>>>> - stdout.txt staged >>>>>> - staging file >>>>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >>>>>> webdav://test:to...@ig...:18080/filestage/55121820210 >>>>>> 7278041688/stderr.txt [Fatal Error] :-1:-1: Premature end of file. >>>>>> - total byte write 194 >>>>>> [Fatal Error] :-1:-1: Premature end of file. >>>>>> - stderr.txt staged >>>>>> - staging file >>>>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >>>>>> webdav://test:to...@ig...:18080/filestage/55121820210 >>>>>> 7278041688/_th-details.out [Fatal Error] :-1:-1: Premature end of file. >>>>>> - total byte write 32075 >>>>>> [Fatal Error] :-1:-1: Premature end of file. >>>>>> - _th-details.out staged >>>>>> - state {staged-out} reached >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) - state {done} reached >>>>>> - done 1174414390889 1174414391097 1174414406236 1174414430046 >>>>>> 1174414449984 1174414470047 1174414482532 1174414482572 >>>>>> WseSourceProcessor: No destinations to route the event >>>>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 >>>>>> threw a JobExecutionException: >>>>>> org.quartz.JobExecutionException >>>>>> at >>>>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta >>>>>> geTask.execute(DefaultJobManagerContext.java:525) at >>>>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at >>>>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja >>>>>> va:516) >>>>>> > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > 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 --------------------------------------------------------------------------- |
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From: Jos K. <jo...@ne...> - 2007-05-14 10:59:49
|
Hi, I experienced the same problem (I posted a bug report about it). In my case it occurred when multiple GridSAM instances were running in one container. I think it has to do with a known problem with the Globus Cog kit and its use of classloaders. According to the Cog Kit FAQ: http://wiki.cogkit.org/index.php/FAQ#While_developing_Grid_Portals_with_Java_COG_Kit.2C_I_get_a_ClassCastException_for_BouncyCastle_classes._Why.3F The solution in the cogkit FAQ worked for me - i.e. move the cryptix*.jar and puretls.jar libraries to $OMII/shared/lib and make sure they are removed from the GridSAM instances. Regards, Jos. On Monday 14 May 2007 11:09:43 Mark HB wrote: > Dear Vesselin, > > I am sending this query again as I have not yet received a reply. If you > need anymore info from me to help diagnose this error, then please ask. > > Thanks for your reply. After looking into this further, I think we have > boiled it down to the exact problem. I am now certain that it is not a > certificate problem, as I have successfully run a job on one of the grid > nodes using my set-up on Friday. However the error below is still a > problem. I will elaborate on my setup. > > I am running four instances of grid-sam. One points to the local system, > and the other three point to respective NGS nodes (man, leeds & oesc). > When I restart the OMII server, I am then able to submit a job to ONE of > the NGS nodes successfully, however, the other two respond with the same > error as before! > > "Description: cannot initialise working directory: Could not connect to > FTP server on"gsiftp://grid-data.man.ac.uk/ - User globus credential is > required but not specified in the context". > > It CANNOT be credentials, as I have just successfully run a job on the > leeds node, but the exact same job fails on the man and oesc nodes. > > I set up the multiple instances exactly as instructed on the gridsam > site (moving jar files etc). > > Have you any ideas > Regards > Mark > > Vesselin Novov wrote: > > Mark, > > > > I should have pointed out, I have never used the AHE in OMII. > > All my tests use directly installed/managed GridSAM instance. > > It's worth checking with the AHE developers what exactly goes on > > when AHE instantiates/manages a GridSAM instance with regard to any > > security credentials. > > > > -Vesso > > > > Mark HB wrote: > >> Vesselin, > >> > >> Yes, sorry about that. The error is exactly the same no matter which > >> node I send the job to, and hence I just grabbed the first log file to > >> hand. > >> > >> Cheers > >> Mark > >> > >> Novov wrote: > >>> Mark, > >>> > >>> I recently had this exact error, but, in my case missing proxy > >>> credentials were definitely > >>> the cause of it. > >>> > >>> I am also a bit confused: > >>> > >>> - the pasted "GridSAM state is . . ." below indicates the job was > >>> attempted on the 27th March > >>> and it was Not submitted because no connection was established with > >>> grid-compute.leeds.ac.uk. > >>> - the gram_job_mgr_9570.log entries are from 13th March and indicate > >>> that job Was at least submitted. > >>> - the catalina.out section below also indicates a job Was submitted, > >>> the staging-in of input files was successful > >>> but failed at staging-out(after execution) phase and the machine is > >>> grid-data.man.ac.uk. > >>> > >>> regards > >>> Vesso > >>> > >>> Mark HB wrote: > >>>> Dear GRIDSam list, > >>>> > >>>> I am attempting to run an application on the NGS using AHE/GRIDSam > >>>> bundled with the OMII-stack. I get the following error when trying to > >>>> run the job: > >>>> > >>>> GridSAM state is: failed > >>>> Time: 2007-03-22T08:23:48.172Z > >>>> Description: cannot initialise working directory: Could not connect > >>>> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus > >>>> credential is required but not specified in the context". > >>>> > >>>> I can assure you that I have both a GRIDSam proxy certificate and > >>>> proxy user certificate running. > >>>> > >>>> The GRAM log file found on the NGS machine can be found here: > >>>> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log > >>>> > >>>> The main point in this log is "GRAM_SCRIPT_ERROR = 26" > >>>> > >>>> ABelow you will find the output produced in the catalina.log file. > >>>> > >>>> Has anyone come across this error before? I would appreciate any > >>>> comments? > >>>> > >>>> Cheers > >>>> Mark > >>>> > >>>> - principal obtained from Axis transport - > >>>> EMA...@ma..., > >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK > >>>> - principal obtained from Axis transport - > >>>> EMA...@ma..., > >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK > >>>> - state {pending} reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - principal obtained from Axis transport - > >>>> EMA...@ma..., > >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK > >>>> - principal obtained from Axis transport - > >>>> EMA...@ma..., > >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - state {staging-in} reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Proxy Credentials received : > >>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown > >>>> - basic authentication scheme selected > >>>> - staging (copy) file > >>>> http://test:to...@ig...:18080/filestage/5512182021072 > >>>>78041688/datPlain12 > >>>> > >>>> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 > >>>> - basic authentication scheme selected > >>>> - total byte write 2508 > >>>> - datPlain12 staged > >>>> - state {staged-in} reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - executing groovy script > >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy > >>>> - executed groovy script > >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - RSL &( arguments = "-f" "datPlain12" )( directory = > >>>> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( > >>>> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( > >>>> jobType = "mpi" ) > >>>> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs > >>>> - Globus job submitted > >>>> https://grid-data.man.ac.uk:64304/25112/1174414409/ > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) WseSourceProcessor: No destinations to route the event > >>>> - globus job is active - > >>>> https://grid-data.man.ac.uk:64304/25112/1174414409/ - state {active} > >>>> reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - state {staging-out} reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> - staging file > >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> > >>>> webdav://test:to...@ig...:18080/filestage/55121820210 > >>>>7278041688/stdout.txt [Fatal Error] :-1:-1: Premature end of file. > >>>> - total byte write 4353 > >>>> [Fatal Error] :-1:-1: Premature end of file. > >>>> - stdout.txt staged > >>>> - staging file > >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> > >>>> webdav://test:to...@ig...:18080/filestage/55121820210 > >>>>7278041688/stderr.txt [Fatal Error] :-1:-1: Premature end of file. > >>>> - total byte write 194 > >>>> [Fatal Error] :-1:-1: Premature end of file. > >>>> - stderr.txt staged > >>>> - staging file > >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> > >>>> webdav://test:to...@ig...:18080/filestage/55121820210 > >>>>7278041688/_th-details.out [Fatal Error] :-1:-1: Premature end of file. > >>>> - total byte write 32075 > >>>> [Fatal Error] :-1:-1: Premature end of file. > >>>> - _th-details.out staged > >>>> - state {staged-out} reached > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) - state {done} reached > >>>> - done 1174414390889 1174414391097 1174414406236 1174414430046 > >>>> 1174414449984 1174414470047 1174414482532 1174414482572 > >>>> WseSourceProcessor: No destinations to route the event > >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 > >>>> threw a JobExecutionException: > >>>> org.quartz.JobExecutionException > >>>> at > >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$Sta > >>>>geTask.execute(DefaultJobManagerContext.java:525) at > >>>> org.quartz.core.JobRunShell.run(JobRunShell.java:191) at > >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.ja > >>>>va:516) |
|
From: Mark HB <m.h...@ma...> - 2007-05-14 10:09:02
|
Dear Vesselin, I am sending this query again as I have not yet received a reply. If you need anymore info from me to help diagnose this error, then please ask. Thanks for your reply. After looking into this further, I think we have boiled it down to the exact problem. I am now certain that it is not a certificate problem, as I have successfully run a job on one of the grid nodes using my set-up on Friday. However the error below is still a problem. I will elaborate on my setup. I am running four instances of grid-sam. One points to the local system, and the other three point to respective NGS nodes (man, leeds & oesc). When I restart the OMII server, I am then able to submit a job to ONE of the NGS nodes successfully, however, the other two respond with the same error as before! "Description: cannot initialise working directory: Could not connect to FTP server on"gsiftp://grid-data.man.ac.uk/ - User globus credential is required but not specified in the context". It CANNOT be credentials, as I have just successfully run a job on the leeds node, but the exact same job fails on the man and oesc nodes. I set up the multiple instances exactly as instructed on the gridsam site (moving jar files etc). Have you any ideas Regards Mark Vesselin Novov wrote: > Mark, > > I should have pointed out, I have never used the AHE in OMII. > All my tests use directly installed/managed GridSAM instance. > It's worth checking with the AHE developers what exactly goes on > when AHE instantiates/manages a GridSAM instance with regard to any > security credentials. > > -Vesso > > Mark HB wrote: > > >> Vesselin, >> >> Yes, sorry about that. The error is exactly the same no matter which >> node I send the job to, and hence I just grabbed the first log file to hand. >> >> Cheers >> Mark >> >> >> Novov wrote: >> >> >> >>> Mark, >>> >>> I recently had this exact error, but, in my case missing proxy >>> credentials were definitely >>> the cause of it. >>> >>> I am also a bit confused: >>> >>> - the pasted "GridSAM state is . . ." below indicates the job was >>> attempted on the 27th March >>> and it was Not submitted because no connection was established with >>> grid-compute.leeds.ac.uk. >>> - the gram_job_mgr_9570.log entries are from 13th March and indicate >>> that job Was at least submitted. >>> - the catalina.out section below also indicates a job Was submitted, the >>> staging-in of input files was successful >>> but failed at staging-out(after execution) phase and the machine is >>> grid-data.man.ac.uk. >>> >>> regards >>> Vesso >>> >>> Mark HB wrote: >>> >>> >>> >>> >>> >>>> Dear GRIDSam list, >>>> >>>> I am attempting to run an application on the NGS using AHE/GRIDSam >>>> bundled with the OMII-stack. I get the following error when trying to >>>> run the job: >>>> >>>> GridSAM state is: failed >>>> Time: 2007-03-22T08:23:48.172Z >>>> Description: cannot initialise working directory: Could not connect >>>> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >>>> credential is required but not specified in the context". >>>> >>>> I can assure you that I have both a GRIDSam proxy certificate and proxy >>>> user certificate running. >>>> >>>> The GRAM log file found on the NGS machine can be found here: >>>> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >>>> >>>> The main point in this log is "GRAM_SCRIPT_ERROR = 26" >>>> >>>> ABelow you will find the output produced in the catalina.log file. >>>> >>>> Has anyone come across this error before? I would appreciate any comments? >>>> >>>> Cheers >>>> Mark >>>> >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - state {pending} reached >>>> WseSourceProcessor: No destinations to route the event >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Proxy Credentials received : >>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>> - basic authentication scheme selected >>>> - staging (copy) file >>>> http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 >>>> >>>> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >>>> - basic authentication scheme selected >>>> - total byte write 2508 >>>> - datPlain12 staged >>>> - state {staged-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - executing groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> - executed groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - RSL &( arguments = "-f" "datPlain12" )( directory = >>>> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >>>> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >>>> = "mpi" ) >>>> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >>>> - Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> - state {active} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 4353 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stdout.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 194 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stderr.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 32075 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - _th-details.out staged >>>> - state {staged-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {done} reached >>>> - done 1174414390889 1174414391097 1174414406236 1174414430046 >>>> 1174414449984 1174414470047 1174414482532 1174414482572 >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> > > -- --------------------------------------------------------------------------- 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: Mark HB <m.h...@ma...> - 2007-04-17 08:42:07
|
Dear Vesselin, Apologies if you have already replied to me (I have been on holiday and was ruthless in deleting my spammed mail). I was wondering if you had a chance to look into the problem I am having with running multiple gridsam instances (see below) Cheers Mark ########################### Dear Vesselin, Thanks for your reply. After looking into this further, I think we have boiled it down to the exact problem. I am now certain that it is not a certificate problem, as I have successfully run a job on one of the grid nodes using my set-up on Friday. However the error below is still a problem. I will elaborate on my setup. I am running four instances of grid-sam. One points to the local system, and the other three point to respective NGS nodes (man, leeds & oesc). When I restart the OMII server, I am then able to submit a job to ONE of the NGS nodes successfully, however, the other two respond with the same error as before! "Description: cannot initialise working directory: Could not connect to FTP server on"gsiftp://grid-data.man.ac.uk/ - User globus credential is required but not specified in the context". It CANNOT be credentials, as I have just successfully run a job on the leeds node, but the exact same job fails on the man and oesc nodes. I set up the multiple instances exactly as instructed on the gridsam site (moving jar files etc). Have you any ideas Regards Mark Vesselin Novov wrote: > Mark, > > I should have pointed out, I have never used the AHE in OMII. > All my tests use directly installed/managed GridSAM instance. > It's worth checking with the AHE developers what exactly goes on > when AHE instantiates/manages a GridSAM instance with regard to any > security credentials. > > -Vesso > > Mark HB wrote: > > >> Vesselin, >> >> Yes, sorry about that. The error is exactly the same no matter which >> node I send the job to, and hence I just grabbed the first log file to hand. >> >> Cheers >> Mark >> >> >> Novov wrote: >> >> >> >>> Mark, >>> >>> I recently had this exact error, but, in my case missing proxy >>> credentials were definitely >>> the cause of it. >>> >>> I am also a bit confused: >>> >>> - the pasted "GridSAM state is . . ." below indicates the job was >>> attempted on the 27th March >>> and it was Not submitted because no connection was established with >>> grid-compute.leeds.ac.uk. >>> - the gram_job_mgr_9570.log entries are from 13th March and indicate >>> that job Was at least submitted. >>> - the catalina.out section below also indicates a job Was submitted, the >>> staging-in of input files was successful >>> but failed at staging-out(after execution) phase and the machine is >>> grid-data.man.ac.uk. >>> >>> regards >>> Vesso >>> >>> Mark HB wrote: >>> >>> >>> >>> >>> >>>> Dear GRIDSam list, >>>> >>>> I am attempting to run an application on the NGS using AHE/GRIDSam >>>> bundled with the OMII-stack. I get the following error when trying to >>>> run the job: >>>> >>>> GridSAM state is: failed >>>> Time: 2007-03-22T08:23:48.172Z >>>> Description: cannot initialise working directory: Could not connect >>>> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >>>> credential is required but not specified in the context". >>>> >>>> I can assure you that I have both a GRIDSam proxy certificate and proxy >>>> user certificate running. >>>> >>>> The GRAM log file found on the NGS machine can be found here: >>>> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >>>> >>>> The main point in this log is "GRAM_SCRIPT_ERROR = 26" >>>> >>>> ABelow you will find the output produced in the catalina.log file. >>>> >>>> Has anyone come across this error before? I would appreciate any comments? >>>> >>>> Cheers >>>> Mark >>>> >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - state {pending} reached >>>> WseSourceProcessor: No destinations to route the event >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Proxy Credentials received : >>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>> - basic authentication scheme selected >>>> - staging (copy) file >>>> http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 >>>> >>>> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >>>> - basic authentication scheme selected >>>> - total byte write 2508 >>>> - datPlain12 staged >>>> - state {staged-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - executing groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> - executed groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - RSL &( arguments = "-f" "datPlain12" )( directory = >>>> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >>>> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >>>> = "mpi" ) >>>> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >>>> - Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> - state {active} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 4353 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stdout.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 194 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stderr.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 32075 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - _th-details.out staged >>>> - state {staged-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {done} reached >>>> - done 1174414390889 1174414391097 1174414406236 1174414430046 >>>> 1174414449984 1174414470047 1174414482532 1174414482572 >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> > > -- --------------------------------------------------------------------------- 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: Vesselin N. <ve...@do...> - 2007-04-12 12:20:47
|
Stian, I've had similar experience with Maven2 - when it works it is a very useful product, but when something goes wrong it's a pain to figure out what, where and why. regards Vesso Stian Soiland wrote: >On 4 Apr 2007, at 10:59, Stian Soiland wrote: > > > >>I just downloaded the GridSAM 2.0.1 source release, and I can't >>succeed in compiling it. >> >>I believe there is some issues with the dependencies, such as: >> >> >>[WARNING] POM for 'axis:axis-1.2.1:pom:itinnov-1:provided' is >>invalid. It will be ignored for artifact resolution. Reason: Not a >>v4.0.0 POM. >> >> > >I cleared my $HOME/.m2/repository, waited patiently, and then it >seemed to build fine. I tried both with the 2.0.1 download and the >latest CVS > >I don't know why, maybe these crazy maven people updated something in >the repository, and I had some old version..? Or GridSAM is using >something from other repositories without changing the version? > >-- >Stian Soiland, myGrid team >School of Computer Science >The University of Manchester >http://www.cs.man.ac.uk/~ssoiland/ > > > >------------------------------------------------------------------------- >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 > > |
|
From: Stian S. <sso...@cs...> - 2007-04-04 10:30:32
|
On 4 Apr 2007, at 10:59, Stian Soiland wrote: > I just downloaded the GridSAM 2.0.1 source release, and I can't > succeed in compiling it. > > I believe there is some issues with the dependencies, such as: > > > [WARNING] POM for 'axis:axis-1.2.1:pom:itinnov-1:provided' is > invalid. It will be ignored for artifact resolution. Reason: Not a > v4.0.0 POM. I cleared my $HOME/.m2/repository, waited patiently, and then it seemed to build fine. I tried both with the 2.0.1 download and the latest CVS I don't know why, maybe these crazy maven people updated something in the repository, and I had some old version..? Or GridSAM is using something from other repositories without changing the version? -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ |
|
From: Stian S. <sso...@cs...> - 2007-04-04 09:59:43
|
I just downloaded the GridSAM 2.0.1 source release, and I can't
succeed in compiling it.
I believe there is some issues with the dependencies, such as:
[WARNING] POM for 'axis:axis-1.2.1:pom:itinnov-1:provided' is
invalid. It will be ignored for artifact resolution. Reason: Not a
v4.0.0 POM.
: stain@mira ~/download/GridSAM-2.0.1-src;mvn install
[INFO] Scanning for projects...
[INFO] Reactor build order:
[INFO] GridSAM
[INFO] GridSAM Schema
[INFO] GridSAM Core Engine
[INFO] GridSAM Client
[INFO] GridSAM Broker Plugin
[INFO] GridSAM Service
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from ibiblio-repo
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from apache-repo
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from codehaus
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from mevenide
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from gridsam
[INFO] artifact org.apache.maven.wagon:wagon-ssh-external: checking
for updates from central
[INFO]
------------------------------------------------------------------------
----
[INFO] Building GridSAM
[INFO] task-segment: [install]
[INFO]
------------------------------------------------------------------------
----
[INFO] [site:attach-descriptor]
[INFO] [install:install]
[INFO] Installing /Users/stain/download/GridSAM-2.0.1-src/pom.xml to /
Users/stain/.m2/repository/org/icenigrid/gridsam/2.0.1/gridsam-2.0.1.pom
[INFO]
------------------------------------------------------------------------
----
[INFO] Building GridSAM Schema
[INFO] task-segment: [install]
[INFO]
------------------------------------------------------------------------
----
[WARNING] While downloading xml-apis:xml-apis:2.0.2
This artifact has been relocated to xml-apis:xml-apis:1.0.b2.
[INFO] [xmlbeans:xmlbeans {execution: default}]
[INFO] Either nothing to generate or all schema objects are up to date.
[INFO] [resources:resources]
[INFO] Using default encoding to copy filtered resources.
[INFO] [compiler:compile]
[INFO] Nothing to compile - all classes are up to date
[INFO] [resources:testResources]
[INFO] Using default encoding to copy filtered resources.
[INFO] [compiler:testCompile]
[INFO] No sources to compile
[INFO] [surefire:test]
[INFO] Tests are skipped.
[INFO] [surefire:test {execution: unit-test}]
[INFO] No tests to run.
[INFO] [jar:jar]
[INFO] Building jar: /Users/stain/download/GridSAM-2.0.1-src/modules/
schema/target/gridsam-schema-2.0.1.jar
[INFO] [install:install]
[INFO] Installing /Users/stain/download/GridSAM-2.0.1-src/modules/
schema/target/gridsam-schema-2.0.1.jar to /Users/stain/.m2/repository/
org/icenigrid/gridsam-schema/2.0.1/gridsam-schema-2.0.1.jar
[INFO]
------------------------------------------------------------------------
----
[INFO] Building GridSAM Core Engine
[INFO] task-segment: [install]
[INFO]
------------------------------------------------------------------------
----
[INFO] [resources:resources]
[INFO] Using default encoding to copy filtered resources.
[INFO] snapshot commons-vfs:commons-vfs:1.0-SNAPSHOT: checking for
updates from ibiblio-repo
[INFO] snapshot commons-vfs:commons-vfs:1.0-SNAPSHOT: checking for
updates from apache-repo
[INFO] snapshot commons-vfs:commons-vfs:1.0-SNAPSHOT: checking for
updates from codehaus
[INFO] snapshot commons-vfs:commons-vfs:1.0-SNAPSHOT: checking for
updates from mevenide
[INFO] snapshot commons-vfs:commons-vfs:1.0-SNAPSHOT: checking for
updates from gridsam
[WARNING] POM for 'hivemind:hivemind:pom:1.1.1:compile' is invalid.
It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM.
[WARNING] POM for 'axis:axis-1.2.1:pom:itinnov-1:provided' is
invalid. It will be ignored for artifact resolution. Reason: Not a
v4.0.0 POM.
[WARNING] POM for 'slide:slide-webdavlib:pom:2.1:compile' is invalid.
It will be ignored for artifact resolution. Reason: Not a v4.0.0 POM.
[WARNING] POM for 'jsch:jsch:pom:0.1.25:compile' is invalid. It will
be ignored for artifact resolution. Reason: Not a v4.0.0 POM.
[INFO] [compiler:compile]
[INFO] Compiling 125 source files to /Users/stain/download/
GridSAM-2.0.1-src/modules/core/target/classes
[INFO]
------------------------------------------------------------------------
[ERROR] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Compilation failure
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/support/GridSAMSupport.java:[22,23]
package org.apache.axis does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/persistence/hibernate/
HibernatePersistenceStore.java:[23,34] package
org.apache.hivemind.events does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/persistence/hibernate/
HibernatePersistenceStore.java:[43,37] cannot find symbol
symbol: class RegistryShutdownListener
implements PersistenceStore, RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/DRMConnectorDescriptor.java:
[18,27] package org.apache.hivemind does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/DRMConnectorDescriptor.java:
[113,44] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DRMConnectorDescriptor
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[29,34]
package org.apache.hivemind.events does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[36,23]
package com.jcraft.jsch does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[37,23]
package com.jcraft.jsch does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[38,23]
package com.jcraft.jsch does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[39,23]
package com.jcraft.jsch does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[40,23]
package com.jcraft.jsch does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[45,52]
cannot find symbol
symbol: class RegistryShutdownListener
public class SSHShell extends POSIXShell implements
RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[55,12]
cannot find symbol
symbol : class Session
location: class org.icenigrid.gridsam.core.plugin.shell.ssh.SSHShell
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[291,30]
cannot find symbol
symbol : class UserInfo
location: class org.icenigrid.gridsam.core.plugin.shell.ssh.SSHShell
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[455,16]
cannot find symbol
symbol : class ChannelExec
location: class
org.icenigrid.gridsam.core.plugin.shell.ssh.SSHShell.ProcessWrapper
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[473,30]
cannot find symbol
symbol : class ChannelExec
location: class
org.icenigrid.gridsam.core.plugin.shell.ssh.SSHShell.ProcessWrapper
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/DefaultJobContext.java:
[23,27] package org.apache.hivemind does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/
DefaultJobManagerContext.java:[24,27] package org.apache.hivemind
does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/DefaultJobContext.java:
[67,32] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DefaultJobContext
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/
DefaultJobManagerContext.java:[62,12] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/
DefaultJobManagerContext.java:[80,39] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/
DefaultJobManagerContext.java:[87,31] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/
DefaultJobManagerContext.java:[97,14] cannot find symbol
symbol : class Registry
location: class
org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/connector/condor/
ShellBasedCondorDRMConnectorManager.java:[27,34] package
org.apache.hivemind.events does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/connector/condor/
ShellBasedCondorDRMConnectorManager.java:[51,47] cannot find symbol
symbol: class RegistryShutdownListener
AbstractDRMConnectorManager implements
RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/scheduler/SchedulerDelegate.java:
[24,34] package org.apache.hivemind.events does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/scheduler/SchedulerDelegate.java:
[43,53] cannot find symbol
symbol: class RegistryShutdownListener
public class SchedulerDelegate implements Scheduler,
RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[25,46] package org.globus.cog.abstraction.impl.common does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[26,51] package org.globus.cog.abstraction.impl.common.task does not
exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[27,45] package org.globus.cog.abstraction.interfaces does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[28,45] package org.globus.cog.abstraction.interfaces does not exist
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[40,12] cannot find symbol
symbol : class FileResource
location: class
org.icenigrid.gridsam.core.plugin.vfs.gsiftp.GSIFTPFileSystem
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[81,19] cannot find symbol
symbol : class FileResource
location: class
org.icenigrid.gridsam.core.plugin.vfs.gsiftp.GSIFTPFileSystem
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
[153,27] cannot find symbol
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location: class
org.icenigrid.gridsam.core.plugin.vfs.gsiftp.GSIFTPFileSystem
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/connector/fork/
ForkDRMConnectorManager.java:[17,34] package
org.apache.hivemind.events does not exist
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org/icenigrid/gridsam/core/plugin/connector/fork/
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symbol: class RegistryShutdownListener
implements RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/manager/auth/simple/
DefaultAuthorisation.java:[13,34] package org.apache.hivemind.events
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org/icenigrid/gridsam/core/plugin/manager/auth/simple/
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public class DefaultAuthorisation implements Authorisation,
RegistryShutdownListener {
/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileObject.java:
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org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileObject.java:
[33,45] package org.globus.cog.abstraction.interfaces does not exist
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org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileObject.java:
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org/icenigrid/gridsam/core/plugin/manager/ManagedRegistry.java:
[21,27] package org.apache.hivemind does not exist
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org/icenigrid/gridsam/core/plugin/manager/ManagedRegistry.java:
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org/icenigrid/gridsam/core/plugin/manager/ManagedRegistry.java:
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org/icenigrid/gridsam/core/plugin/manager/ManagedRegistry.java:
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org/icenigrid/gridsam/core/plugin/connector/drmaa/
DrmaaDRMConnectorManager.java:[17,34] package
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implements RegistryShutdownListener {
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org/icenigrid/gridsam/core/plugin/manager/DefaultJobManager.java:
[30,27] package org.apache.hivemind does not exist
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/Users/stain/download/GridSAM-2.0.1-src/modules/core/src/main/java/
org/icenigrid/gridsam/core/plugin/shell/local/LocalShell.java:[30,34]
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org/icenigrid/gridsam/core/plugin/shell/local/LocalShell.java:[39,54]
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public class LocalShell extends POSIXShell implements
RegistryShutdownListener {
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org/icenigrid/gridsam/core/plugin/manager/ResourceRegistry.java:
[24,27] package org.apache.hivemind does not exist
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[27,27] package org.apache.hivemind does not exist
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[28,32] package org.apache.hivemind.impl does not exist
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[29,32] package org.apache.hivemind.impl does not exist
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[30,32] package org.apache.hivemind.impl does not exist
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[31,32] package org.apache.hivemind.util does not exist
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[32,32] package org.apache.hivemind.util does not exist
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org/icenigrid/gridsam/core/support/GridSAMSupport.java:[267,18]
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access org.apache.xmlbeans.xml.stream.XMLInputStream
file org/apache/xmlbeans/xml/stream/XMLInputStream.class not found
xJSDL = JobDefinitionDocument.Factory.parse(pReader);
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org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[206,16]
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org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[308,17]
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org/icenigrid/gridsam/core/plugin/shell/ssh/SSHShell.java:[408,8]
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org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext.Stage
Task
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org/icenigrid/gridsam/core/plugin/vfs/gsiftp/GSIFTPFileSystem.java:
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org/icenigrid/gridsam/core/plugin/manager/ResourceRegistry.java:
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[INFO]
------------------------------------------------------------------------
[INFO] For more information, run Maven with the -e switch
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 28 seconds
[INFO] Finished at: Wed Apr 04 09:30:37 WEST 2007
[INFO] Final Memory: 9M/18M
[INFO]
------------------------------------------------------------------------
--
Stian Soiland, myGrid team
School of Computer Science
The University of Manchester
http://www.cs.man.ac.uk/~ssoiland/
|
|
From: Mark HB <m.h...@ma...> - 2007-04-02 09:14:35
|
Dear Vesselin, Thanks for your reply. After looking into this further, I think we have boiled it down to the exact problem. I am now certain that it is not a certificate problem, as I have successfully run a job on one of the grid nodes using my set-up on Friday. However the error below is still a problem. I will elaborate on my setup. I am running four instances of grid-sam. One points to the local system, and the other three point to respective NGS nodes (man, leeds & oesc). When I restart the OMII server, I am then able to submit a job to ONE of the NGS nodes successfully, however, the other two respond with the same error as before! "Description: cannot initialise working directory: Could not connect to FTP server on"gsiftp://grid-data.man.ac.uk/ - User globus credential is required but not specified in the context". It CANNOT be credentials, as I have just successfully run a job on the leeds node, but the exact same job fails on the man and oesc nodes. I set up the multiple instances exactly as instructed on the gridsam site (moving jar files etc). Have you any ideas Regards Mark Vesselin Novov wrote: > Mark, > > I should have pointed out, I have never used the AHE in OMII. > All my tests use directly installed/managed GridSAM instance. > It's worth checking with the AHE developers what exactly goes on > when AHE instantiates/manages a GridSAM instance with regard to any > security credentials. > > -Vesso > > Mark HB wrote: > > >> Vesselin, >> >> Yes, sorry about that. The error is exactly the same no matter which >> node I send the job to, and hence I just grabbed the first log file to hand. >> >> Cheers >> Mark >> >> >> Novov wrote: >> >> >> >>> Mark, >>> >>> I recently had this exact error, but, in my case missing proxy >>> credentials were definitely >>> the cause of it. >>> >>> I am also a bit confused: >>> >>> - the pasted "GridSAM state is . . ." below indicates the job was >>> attempted on the 27th March >>> and it was Not submitted because no connection was established with >>> grid-compute.leeds.ac.uk. >>> - the gram_job_mgr_9570.log entries are from 13th March and indicate >>> that job Was at least submitted. >>> - the catalina.out section below also indicates a job Was submitted, the >>> staging-in of input files was successful >>> but failed at staging-out(after execution) phase and the machine is >>> grid-data.man.ac.uk. >>> >>> regards >>> Vesso >>> >>> Mark HB wrote: >>> >>> >>> >>> >>> >>>> Dear GRIDSam list, >>>> >>>> I am attempting to run an application on the NGS using AHE/GRIDSam >>>> bundled with the OMII-stack. I get the following error when trying to >>>> run the job: >>>> >>>> GridSAM state is: failed >>>> Time: 2007-03-22T08:23:48.172Z >>>> Description: cannot initialise working directory: Could not connect >>>> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >>>> credential is required but not specified in the context". >>>> >>>> I can assure you that I have both a GRIDSam proxy certificate and proxy >>>> user certificate running. >>>> >>>> The GRAM log file found on the NGS machine can be found here: >>>> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >>>> >>>> The main point in this log is "GRAM_SCRIPT_ERROR = 26" >>>> >>>> ABelow you will find the output produced in the catalina.log file. >>>> >>>> Has anyone come across this error before? I would appreciate any comments? >>>> >>>> Cheers >>>> Mark >>>> >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - state {pending} reached >>>> WseSourceProcessor: No destinations to route the event >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> - principal obtained from Axis transport - >>>> EMA...@ma..., >>>> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Proxy Credentials received : >>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>> - basic authentication scheme selected >>>> - staging (copy) file >>>> http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 >>>> >>>> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >>>> - basic authentication scheme selected >>>> - total byte write 2508 >>>> - datPlain12 staged >>>> - state {staged-in} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - executing groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> - executed groovy script >>>> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - RSL &( arguments = "-f" "datPlain12" )( directory = >>>> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >>>> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >>>> = "mpi" ) >>>> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >>>> - Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> WseSourceProcessor: No destinations to route the event >>>> - globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>> - state {active} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {staging-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 4353 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stdout.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 194 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - stderr.txt staged >>>> - staging file >>>> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >>>> webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - total byte write 32075 >>>> [Fatal Error] :-1:-1: Premature end of file. >>>> - _th-details.out staged >>>> - state {staged-out} reached >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> - state {done} reached >>>> - done 1174414390889 1174414391097 1174414406236 1174414430046 >>>> 1174414449984 1174414470047 1174414482532 1174414482572 >>>> WseSourceProcessor: No destinations to route the event >>>> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >>>> a JobExecutionException: >>>> org.quartz.JobExecutionException >>>> at >>>> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>>> at >>>> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> >> >> >> > > -- --------------------------------------------------------------------------- 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: Vesselin N. <ve...@do...> - 2007-03-22 12:11:14
|
Mark, I should have pointed out, I have never used the AHE in OMII. All my tests use directly installed/managed GridSAM instance. It's worth checking with the AHE developers what exactly goes on when AHE instantiates/manages a GridSAM instance with regard to any security credentials. -Vesso Mark HB wrote: >Vesselin, > >Yes, sorry about that. The error is exactly the same no matter which >node I send the job to, and hence I just grabbed the first log file to hand. > >Cheers >Mark > > > Novov wrote: > > >>Mark, >> >>I recently had this exact error, but, in my case missing proxy >>credentials were definitely >>the cause of it. >> >>I am also a bit confused: >> >>- the pasted "GridSAM state is . . ." below indicates the job was >>attempted on the 27th March >>and it was Not submitted because no connection was established with >>grid-compute.leeds.ac.uk. >>- the gram_job_mgr_9570.log entries are from 13th March and indicate >>that job Was at least submitted. >>- the catalina.out section below also indicates a job Was submitted, the >>staging-in of input files was successful >>but failed at staging-out(after execution) phase and the machine is >>grid-data.man.ac.uk. >> >>regards >>Vesso >> >>Mark HB wrote: >> >> >> >> >>>Dear GRIDSam list, >>> >>>I am attempting to run an application on the NGS using AHE/GRIDSam >>>bundled with the OMII-stack. I get the following error when trying to >>>run the job: >>> >>>GridSAM state is: failed >>> Time: 2007-03-22T08:23:48.172Z >>> Description: cannot initialise working directory: Could not connect >>>to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >>>credential is required but not specified in the context". >>> >>>I can assure you that I have both a GRIDSam proxy certificate and proxy >>>user certificate running. >>> >>>The GRAM log file found on the NGS machine can be found here: >>>http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >>> >>>The main point in this log is "GRAM_SCRIPT_ERROR = 26" >>> >>>ABelow you will find the output produced in the catalina.log file. >>> >>>Has anyone come across this error before? I would appreciate any comments? >>> >>>Cheers >>>Mark >>> >>>- principal obtained from Axis transport - >>>EMA...@ma..., >>>CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>- principal obtained from Axis transport - >>>EMA...@ma..., >>>CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>- state {pending} reached >>>WseSourceProcessor: No destinations to route the event >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- principal obtained from Axis transport - >>>EMA...@ma..., >>>CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>- principal obtained from Axis transport - >>>EMA...@ma..., >>>CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- state {staging-in} reached >>>WseSourceProcessor: No destinations to route the event >>>- Proxy Credentials received : >>>/C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>- basic authentication scheme selected >>>- staging (copy) file >>>http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 >>> >>>-> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >>>- basic authentication scheme selected >>>- total byte write 2508 >>>- datPlain12 staged >>>- state {staged-in} reached >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- executing groovy script >>>org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>- executed groovy script >>>org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- RSL &( arguments = "-f" "datPlain12" )( directory = >>>"551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >>>stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >>>= "mpi" ) >>>- Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >>>- Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>WseSourceProcessor: No destinations to route the event >>>- globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >>>- state {active} reached >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- state {staging-out} reached >>>WseSourceProcessor: No destinations to route the event >>>- staging file >>>gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >>>webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >>>[Fatal Error] :-1:-1: Premature end of file. >>>- total byte write 4353 >>>[Fatal Error] :-1:-1: Premature end of file. >>>- stdout.txt staged >>>- staging file >>>gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >>>webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >>>[Fatal Error] :-1:-1: Premature end of file. >>>- total byte write 194 >>>[Fatal Error] :-1:-1: Premature end of file. >>>- stderr.txt staged >>>- staging file >>>gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >>>webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >>>[Fatal Error] :-1:-1: Premature end of file. >>>- total byte write 32075 >>>[Fatal Error] :-1:-1: Premature end of file. >>>- _th-details.out staged >>>- state {staged-out} reached >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>>- state {done} reached >>>- done 1174414390889 1174414391097 1174414406236 1174414430046 >>>1174414449984 1174414470047 1174414482532 1174414482572 >>>WseSourceProcessor: No destinations to route the event >>>- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >>>a JobExecutionException: >>>org.quartz.JobExecutionException >>> at >>>org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >>> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >>> at >>>org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >>> >>> >>> >>> >>> >>> >>> >>> >> >> >> > > > > -- ----------------------------------------------------------------- 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 ----------------------------------------------------------------- |
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From: Mark HB <m.h...@ma...> - 2007-03-22 12:02:10
|
Vesselin, Yes, sorry about that. The error is exactly the same no matter which node I send the job to, and hence I just grabbed the first log file to hand. Cheers Mark Novov wrote: > Mark, > > I recently had this exact error, but, in my case missing proxy > credentials were definitely > the cause of it. > > I am also a bit confused: > > - the pasted "GridSAM state is . . ." below indicates the job was > attempted on the 27th March > and it was Not submitted because no connection was established with > grid-compute.leeds.ac.uk. > - the gram_job_mgr_9570.log entries are from 13th March and indicate > that job Was at least submitted. > - the catalina.out section below also indicates a job Was submitted, the > staging-in of input files was successful > but failed at staging-out(after execution) phase and the machine is > grid-data.man.ac.uk. > > regards > Vesso > > Mark HB wrote: > > >> Dear GRIDSam list, >> >> I am attempting to run an application on the NGS using AHE/GRIDSam >> bundled with the OMII-stack. I get the following error when trying to >> run the job: >> >> GridSAM state is: failed >> Time: 2007-03-22T08:23:48.172Z >> Description: cannot initialise working directory: Could not connect >> to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >> credential is required but not specified in the context". >> >> I can assure you that I have both a GRIDSam proxy certificate and proxy >> user certificate running. >> >> The GRAM log file found on the NGS machine can be found here: >> http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log >> >> The main point in this log is "GRAM_SCRIPT_ERROR = 26" >> >> ABelow you will find the output produced in the catalina.log file. >> >> Has anyone come across this error before? I would appreciate any comments? >> >> Cheers >> Mark >> >> - principal obtained from Axis transport - >> EMA...@ma..., >> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >> - principal obtained from Axis transport - >> EMA...@ma..., >> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >> - state {pending} reached >> WseSourceProcessor: No destinations to route the event >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - principal obtained from Axis transport - >> EMA...@ma..., >> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >> - principal obtained from Axis transport - >> EMA...@ma..., >> CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - state {staging-in} reached >> WseSourceProcessor: No destinations to route the event >> - Proxy Credentials received : >> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >> - basic authentication scheme selected >> - staging (copy) file >> http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 >> >> -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >> - basic authentication scheme selected >> - total byte write 2508 >> - datPlain12 staged >> - state {staged-in} reached >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - executing groovy script >> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >> - executed groovy script >> org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - RSL &( arguments = "-f" "datPlain12" )( directory = >> "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >> stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >> = "mpi" ) >> - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >> - Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> WseSourceProcessor: No destinations to route the event >> - globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >> - state {active} reached >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - state {staging-out} reached >> WseSourceProcessor: No destinations to route the event >> - staging file >> gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >> [Fatal Error] :-1:-1: Premature end of file. >> - total byte write 4353 >> [Fatal Error] :-1:-1: Premature end of file. >> - stdout.txt staged >> - staging file >> gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >> [Fatal Error] :-1:-1: Premature end of file. >> - total byte write 194 >> [Fatal Error] :-1:-1: Premature end of file. >> - stderr.txt staged >> - staging file >> gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >> webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >> [Fatal Error] :-1:-1: Premature end of file. >> - total byte write 32075 >> [Fatal Error] :-1:-1: Premature end of file. >> - _th-details.out staged >> - state {staged-out} reached >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> - state {done} reached >> - done 1174414390889 1174414391097 1174414406236 1174414430046 >> 1174414449984 1174414470047 1174414482532 1174414482572 >> WseSourceProcessor: No destinations to route the event >> - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >> a JobExecutionException: >> org.quartz.JobExecutionException >> at >> org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) >> at org.quartz.core.JobRunShell.run(JobRunShell.java:191) >> at >> org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >> >> >> >> >> >> > > -- --------------------------------------------------------------------------- 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: Vesselin N. <ve...@do...> - 2007-03-22 11:55:26
|
Mark, I recently had this exact error, but, in my case missing proxy credentials were definitely the cause of it. I am also a bit confused: - the pasted "GridSAM state is . . ." below indicates the job was attempted on the 27th March and it was Not submitted because no connection was established with grid-compute.leeds.ac.uk. - the gram_job_mgr_9570.log entries are from 13th March and indicate that job Was at least submitted. - the catalina.out section below also indicates a job Was submitted, the staging-in of input files was successful but failed at staging-out(after execution) phase and the machine is grid-data.man.ac.uk. regards Vesso Mark HB wrote: >Dear GRIDSam list, > >I am attempting to run an application on the NGS using AHE/GRIDSam >bundled with the OMII-stack. I get the following error when trying to >run the job: > >GridSAM state is: failed > Time: 2007-03-22T08:23:48.172Z > Description: cannot initialise working directory: Could not connect >to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus >credential is required but not specified in the context". > >I can assure you that I have both a GRIDSam proxy certificate and proxy >user certificate running. > >The GRAM log file found on the NGS machine can be found here: >http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log > >The main point in this log is "GRAM_SCRIPT_ERROR = 26" > >ABelow you will find the output produced in the catalina.log file. > >Has anyone come across this error before? I would appreciate any comments? > >Cheers >Mark > >- principal obtained from Axis transport - >EMA...@ma..., >CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >- principal obtained from Axis transport - >EMA...@ma..., >CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >- state {pending} reached >WseSourceProcessor: No destinations to route the event >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- principal obtained from Axis transport - >EMA...@ma..., >CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >- principal obtained from Axis transport - >EMA...@ma..., >CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- state {staging-in} reached >WseSourceProcessor: No destinations to route the event >- Proxy Credentials received : >/C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >- basic authentication scheme selected >- staging (copy) file >http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 > >-> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 >- basic authentication scheme selected >- total byte write 2508 >- datPlain12 staged >- state {staged-in} reached >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- executing groovy script >org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >- executed groovy script >org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- RSL &( arguments = "-f" "datPlain12" )( directory = >"551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( >stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType >= "mpi" ) >- Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs >- Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >WseSourceProcessor: No destinations to route the event >- globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ >- state {active} reached >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- state {staging-out} reached >WseSourceProcessor: No destinations to route the event >- staging file >gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> >webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt >[Fatal Error] :-1:-1: Premature end of file. >- total byte write 4353 >[Fatal Error] :-1:-1: Premature end of file. >- stdout.txt staged >- staging file >gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> >webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt >[Fatal Error] :-1:-1: Premature end of file. >- total byte write 194 >[Fatal Error] :-1:-1: Premature end of file. >- stderr.txt staged >- staging file >gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> >webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out >[Fatal Error] :-1:-1: Premature end of file. >- total byte write 32075 >[Fatal Error] :-1:-1: Premature end of file. >- _th-details.out staged >- state {staged-out} reached >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) >- state {done} reached >- done 1174414390889 1174414391097 1174414406236 1174414430046 >1174414449984 1174414470047 1174414482532 1174414482572 >WseSourceProcessor: No destinations to route the event >- Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw >a JobExecutionException: >org.quartz.JobExecutionException > at >org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) > at org.quartz.core.JobRunShell.run(JobRunShell.java:191) > at >org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) > > > > > -- ----------------------------------------------------------------- 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 ----------------------------------------------------------------- |
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From: Mark HB <m.h...@ma...> - 2007-03-22 08:32:25
|
Dear GRIDSam list, I am attempting to run an application on the NGS using AHE/GRIDSam bundled with the OMII-stack. I get the following error when trying to run the job: GridSAM state is: failed Time: 2007-03-22T08:23:48.172Z Description: cannot initialise working directory: Could not connect to FTP server on"gsiftp://grid-compute.leeds.ac.uk/ - User globus credential is required but not specified in the context". I can assure you that I have both a GRIDSam proxy certificate and proxy user certificate running. The GRAM log file found on the NGS machine can be found here: http://igrid-ext.cryst.bbk.ac.uk/gram_job_mgr_9570.log The main point in this log is "GRAM_SCRIPT_ERROR = 26" ABelow you will find the output produced in the catalina.log file. Has anyone come across this error before? I would appreciate any comments? Cheers Mark - principal obtained from Axis transport - EMA...@ma..., CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK - principal obtained from Axis transport - EMA...@ma..., CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK - state {pending} reached WseSourceProcessor: No destinations to route the event WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fec threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7feb threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - principal obtained from Axis transport - EMA...@ma..., CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK - principal obtained from Axis transport - EMA...@ma..., CN=igrid.cryst.bbk.ac.uk, L=EISD, OU=UCL, O=eScience, C=UK WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fea threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - state {staging-in} reached WseSourceProcessor: No destinations to route the event - Proxy Credentials received : /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown - basic authentication scheme selected - staging (copy) file http://test:to...@ig...:18080/filestage/551218202107278041688/datPlain12 -> gsiftp://grid-data.man.ac.uk/551218202107278041688/datPlain12 - basic authentication scheme selected - total byte write 2508 - datPlain12 staged - state {staged-in} reached WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe9 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - executing groovy script org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy - executed groovy script org/icenigrid/gridsam/core/plugin/connector/globus/rsl.groovy WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe8 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - RSL &( arguments = "-f" "datPlain12" )( directory = "551218202107278041688" )( executable = "/home/ngs0386/bin/cimmsim" )( stderr = "stderr.txt" )( stdout = "stdout.txt" )( count = "1" )( jobType = "mpi" ) - Submitting globus job to grid-data.man.ac.uk/jobmanager-pbs - Globus job submitted https://grid-data.man.ac.uk:64304/25112/1174414409/ WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe7 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) WseSourceProcessor: No destinations to route the event - globus job is active - https://grid-data.man.ac.uk:64304/25112/1174414409/ - state {active} reached WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe6 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - state {staging-out} reached WseSourceProcessor: No destinations to route the event - staging file gsiftp://grid-data.man.ac.uk/551218202107278041688/stdout.txt -> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stdout.txt [Fatal Error] :-1:-1: Premature end of file. - total byte write 4353 [Fatal Error] :-1:-1: Premature end of file. - stdout.txt staged - staging file gsiftp://grid-data.man.ac.uk/551218202107278041688/stderr.txt -> webdav://test:to...@ig...:18080/filestage/551218202107278041688/stderr.txt [Fatal Error] :-1:-1: Premature end of file. - total byte write 194 [Fatal Error] :-1:-1: Premature end of file. - stderr.txt staged - staging file gsiftp://grid-data.man.ac.uk/551218202107278041688/_th-details.out -> webdav://test:to...@ig...:18080/filestage/551218202107278041688/_th-details.out [Fatal Error] :-1:-1: Premature end of file. - total byte write 32075 [Fatal Error] :-1:-1: Premature end of file. - _th-details.out staged - state {staged-out} reached WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe5 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) - state {done} reached - done 1174414390889 1174414391097 1174414406236 1174414430046 1174414449984 1174414470047 1174414482532 1174414482572 WseSourceProcessor: No destinations to route the event - Job ff80808211705e810111708d76680005.-6a0625b2:111705f74ad:-7fe4 threw a JobExecutionException: org.quartz.JobExecutionException at org.icenigrid.gridsam.core.plugin.manager.DefaultJobManagerContext$StageTask.execute(DefaultJobManagerContext.java:525) at org.quartz.core.JobRunShell.run(JobRunShell.java:191) at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516) -- --------------------------------------------------------------------------- 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: Vesselin N. <ve...@do...> - 2007-03-20 18:50:47
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Hartmut Kaiser wrote: > >Vesselin Novov wrote: > > > >>The basic-execution-service.wsdl is a definition of a GridSAM >>interface compliant with the OGSA Basic Execution Service >>Working Group early version standard. This interface >>definition has changed substantially since. An implementation >>of a more recent version(but still not the latest) was added >>to the GridSAM CVS code base around November/December'06 - >>the new WS definition is in bes-factory.wsdl. >>As it is an outdated file, you'd probably not want to deal >>with it at all. >> >> > >Thanks for your response! >Could you give me a pointer to the CVS repository to look at? Does it >support anon access? > > It's on the project's web site: "http://gridsam.sourceforge.net/2.0.0/source-repository.html" Keep in mind the code in the CVS has been recently changed to accommodate the new security updates of OMII Container 3.3.1, but has not been fully tested yet. > > >>As to the exact cause of the exception - it could just be >>your wsdl conversion tooling. >> >> > >Yeah, I figured that. > > > >>If I remember correctly, some developers had a similar >>problem with the newer BES WS wsdl file in November while in >>preparation for our interoperability demo at SuperComputing'06. >>You may be able to find some discussions about it here: >>"http://www.ogf.org/pipermail/ogsa-hpcp-wg/" >> >> > >Thanks! Will try to find it there. > >Regards Hartmut > > > > >>regards >>Vesso >> >>Hartmut Kaiser wrote: >> >> >> >>>Hi all, >>> >>>I'm new to GridSAM and new to this list. We're currently >>> >>> >>developing a >> >> >>>GridSAM adaptor for our SAGA C++ reference implementation >>>(http://saga.cct.lsu.edu). As it's in C++ we need to generate C++ >>>wrappers for the GridSAM webservice. I tried to do so using the Axis >>>C++ wsdl2ws tool and succeeded for the gridsam.wsdl file. >>> >>>The same thing failed for the basic-execution-service.wsdl, though: >>> >>>org.apache.axis.wsdl.wsdl2ws.WrapperFault: unregistered type >>>{http://www.w3.org/2001/XMLSchema}anyType referred >>> at >>>org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.addDocumentStyleInputMes >>> >>> >>sageToMeth >> >> >>>odInf >>>o(Unknown Source) >>> at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.setMethodInfo(Unknown >>>Source) >>> at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.getServiceInfo(Unknown >>>Source) >>> at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.generateWrappers(Unknown >>>Source) >>> at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.main(Unknown Source) >>> >>>Any idea what's going wrong? >>> >>>Thanks and regards >>>Hartmut >>> >>> >>> >>>------------------------------------------------------------- >>> >>> >>---------- >> >> >>>-- 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=sourceforg >>> >>> >e&CID=DEVD > > >>>EV _______________________________________________ >>>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 >> >> >> > > >------------------------------------------------------------------------- >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: Hartmut K. <hk...@cc...> - 2007-03-20 18:16:36
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Vesselin Novov wrote: > The basic-execution-service.wsdl is a definition of a GridSAM > interface compliant with the OGSA Basic Execution Service > Working Group early version standard. This interface > definition has changed substantially since. An implementation > of a more recent version(but still not the latest) was added > to the GridSAM CVS code base around November/December'06 - > the new WS definition is in bes-factory.wsdl. > As it is an outdated file, you'd probably not want to deal > with it at all. Thanks for your response! Could you give me a pointer to the CVS repository to look at? Does it support anon access? > As to the exact cause of the exception - it could just be > your wsdl conversion tooling. Yeah, I figured that. > If I remember correctly, some developers had a similar > problem with the newer BES WS wsdl file in November while in > preparation for our interoperability demo at SuperComputing'06. > You may be able to find some discussions about it here: > "http://www.ogf.org/pipermail/ogsa-hpcp-wg/" Thanks! Will try to find it there. Regards Hartmut > > regards > Vesso > > Hartmut Kaiser wrote: > > >Hi all, > > > >I'm new to GridSAM and new to this list. We're currently > developing a > >GridSAM adaptor for our SAGA C++ reference implementation > >(http://saga.cct.lsu.edu). As it's in C++ we need to generate C++ > >wrappers for the GridSAM webservice. I tried to do so using the Axis > >C++ wsdl2ws tool and succeeded for the gridsam.wsdl file. > > > >The same thing failed for the basic-execution-service.wsdl, though: > > > >org.apache.axis.wsdl.wsdl2ws.WrapperFault: unregistered type > >{http://www.w3.org/2001/XMLSchema}anyType referred > > at > >org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.addDocumentStyleInputMes > sageToMeth > >odInf > >o(Unknown Source) > > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.setMethodInfo(Unknown > >Source) > > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.getServiceInfo(Unknown > >Source) > > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.generateWrappers(Unknown > >Source) > > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.main(Unknown Source) > > > >Any idea what's going wrong? > > > >Thanks and regards > >Hartmut > > > > > > > >------------------------------------------------------------- > ---------- > >-- 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=sourceforg e&CID=DEVD > >EV _______________________________________________ > >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: Vesselin N. <ve...@do...> - 2007-03-20 17:43:50
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Hi Hartmut, The basic-execution-service.wsdl is a definition of a GridSAM interface compliant with the OGSA Basic Execution Service Working Group early version standard. This interface definition has changed substantially since. An implementation of a more recent version(but still not the latest) was added to the GridSAM CVS code base around November/December'06 - the new WS definition is in bes-factory.wsdl. As it is an outdated file, you'd probably not want to deal with it at all. As to the exact cause of the exception - it could just be your wsdl conversion tooling. If I remember correctly, some developers had a similar problem with the newer BES WS wsdl file in November while in preparation for our interoperability demo at SuperComputing'06. You may be able to find some discussions about it here: "http://www.ogf.org/pipermail/ogsa-hpcp-wg/" regards Vesso Hartmut Kaiser wrote: >Hi all, > >I'm new to GridSAM and new to this list. We're currently developing a >GridSAM adaptor for our SAGA C++ reference implementation >(http://saga.cct.lsu.edu). As it's in C++ we need to generate C++ wrappers >for the GridSAM webservice. I tried to do so using the Axis C++ wsdl2ws tool >and succeeded for the gridsam.wsdl file. > >The same thing failed for the basic-execution-service.wsdl, though: > >org.apache.axis.wsdl.wsdl2ws.WrapperFault: unregistered type >{http://www.w3.org/2001/XMLSchema}anyType referred > at >org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.addDocumentStyleInputMessageToMethodInf >o(Unknown Source) > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.setMethodInfo(Unknown >Source) > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.getServiceInfo(Unknown >Source) > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.generateWrappers(Unknown >Source) > at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.main(Unknown Source) > >Any idea what's going wrong? > >Thanks and regards >Hartmut > > > >------------------------------------------------------------------------- >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: Hartmut K. <har...@gm...> - 2007-03-19 22:32:34
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Hi all, I'm new to GridSAM and new to this list. We're currently developing a GridSAM adaptor for our SAGA C++ reference implementation (http://saga.cct.lsu.edu). As it's in C++ we need to generate C++ wrappers for the GridSAM webservice. I tried to do so using the Axis C++ wsdl2ws tool and succeeded for the gridsam.wsdl file. The same thing failed for the basic-execution-service.wsdl, though: org.apache.axis.wsdl.wsdl2ws.WrapperFault: unregistered type {http://www.w3.org/2001/XMLSchema}anyType referred at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.addDocumentStyleInputMessageToMethodInf o(Unknown Source) at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.setMethodInfo(Unknown Source) at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.getServiceInfo(Unknown Source) at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.generateWrappers(Unknown Source) at org.apache.axis.wsdl.wsdl2ws.WSDL2Ws.main(Unknown Source) Any idea what's going wrong? Thanks and regards Hartmut |
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From: Stefan Z. <ste...@uc...> - 2007-02-22 10:02:35
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Hi Carlos, Could this be related to your globus machine setup? It looks like you are trying to use the GRAM fork jobmanager to start an MPI job. You could try submitting the rsl from the gram log using globusrun and see what happens. Cheers, Stefan. Carlos Alexandre Queiroz wrote: > Hi, > > After I've applied the Stefan's patch (thx stefan) I can submit jobs to > GT, however, GT is not processing the jobs, I always get this message: > job-failure-code: 26 > > the files are been staged on GT machine with no problem. > > Does anyone knows what is the problem ? I've attached the globus and > gridsam logs. > > thx, > > cax > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > 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 |
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From: Carlos A. Q. <cqu...@vp...> - 2007-02-22 01:43:43
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Hi, After I've applied the Stefan's patch (thx stefan) I can submit jobs to GT, however, GT is not processing the jobs, I always get this message: job-failure-code: 26 the files are been staged on GT machine with no problem. Does anyone knows what is the problem ? I've attached the globus and gridsam logs. thx, cax |
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From: Stefan Z. <ste...@uc...> - 2007-02-16 11:22:52
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Hi Mark, Glad to hear it. The ordering of elements in the MPIApplication block wasn't an issue in previous versions of GridSAM, so I guess this is due to a change in the way that JSDL is processed in GridSAM 2.x Stefan. Mark HB wrote: > 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 >>> >>> >> > > -- 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 |
|
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 --------------------------------------------------------------------------- |
|
From: Stefan Z. <ste...@uc...> - 2007-02-16 11:09:01
|
Hi, In the previous Util.pm I put the CPUCount element after the posix block, but from the error you got Mark, it could be that GridSAM is looking for CPUCount directly after wallTimeLimit? I've updated Util.pm to put CPUCount directly after wallTimeLimit at the end of the MPIApplication block (it's at the same url). Could you try giving this a go? Also, could you send the JSDL generated? Cheers, Stefan. Gordon Stewart wrote: > Well, the error has changed a little, but I'm not sure whether it's for > the better or worse... > > The GGF give an example MPI JSDL file for GridSAM > (http://www.ggf.org/GGF17/materials/253/gridsam-jsdl-mpi-sample.pdf): > > ... > <JobDescription> > <Application > xmlns:posix="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix"> > <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> > <posix:Executable>/bin/some-parallel-app</posix:Executable> > <posix:Argument>hello world</posix:Argument> > <posix:Environment name="ABC">DEF</posix:Environment> > <mpi:ProcessorCount>10</mpi:ProcessorCount> > <xyz:OtherExtension xmlns:xyz="urn:xyz">My > Extension</xyz:OtherExtension> > </mpi:MPIApplication> > </Application> > </JobDescription> > ... > > Assuming that the generated JSDL now has this form, I'm not really sure > what could be causing these errors. It now seems to be complaining > about the existence of the POSIX elements within the MPIApplication > element, but they are clearly allowed. Perhaps you could post the new > JSDL to see if that provides any further inspiration? > > Gordon > > -----Original Message----- > From: gri...@li... > [mailto:gri...@li...] On Behalf Of Mark > HB > Sent: 16 February 2007 09:28 > To: Stefan Zasada > Cc: cax...@gm...; gri...@li... > Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job > > > Dear Stefan, > > Unfortunately it doesn't seem to fix it for me. > I did this: > 1) Copied new Util.pm to OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE > 2) restarted OMII server > 3) ran the ahe_destroy....... & ahe_create.... scripts (just in case) > 4) Run the ahe-client as before, but got the error as before > > Error: > Description: Invalid JSDL v1.0 job description: [error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' > here in element MPIApplication@urn:gridsam:mpi, error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' > here in element MPIApplication@urn:gridsam:mpi, error: > cvc-complex-type.2.4a: Expected element 'ProcessorCount@urn:gridsam:mpi' > > instead of 'Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here > in element MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: > > Expected element 'ProcessorCount@urn:gridsam:mpi' instead of > 'Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here in element > MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4a: Expected > element 'ProcessorCount@urn:gridsam:mpi' instead of > 'WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix' here > in element MPIApplication@urn:gridsam:mpi] > > > Stefan Zasada wrote: > Dear Mark and Carlos, > > I've modified Util.pm to put the <mpi:ProcessorCount> > element after the JSDL posix stuff. Get it from: > > http://ccs.chem.ucl.ac.uk/~stefan/Util.pm > > Replace the Util.pm in your AHE distribution with it and let me know >> if > it works. > > Cheers, > > Stefan. > > Gordon Stewart wrote: > >>>> There's a file called Util.pm.mpi in the >>>> $OMII/jakarta-tomcat-5.0.25/webapps/ahe/src/AHE directory of the OMII >>>> 3.2.0 installation (and also in the ahe.war file within the >> installation >>>> bundle) that, at a brief glance, appears to contain the code which >>>> builds the JSDL. >>>> >>>> I'm not sure what changes you would have to make in order to modify >> the >>>> order of elements. >>>> >>>> Gordon >>>> >>>> >>>> -----Original Message----- >>>> From: Carlos Alexandre Queiroz [mailto:cax...@gm...] >>>> Sent: 16 February 2007 08:57 >>>> To: Gordon Stewart >>>> Cc: Mark HB >>>> Subject: Re: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>> >>>> Humm, it is a good guess, however, AHE-Server is generating this >>>> jsdl, anyone knows where we have to change it in order to >>>> generate a different jsdl file ?? >>>> >>>> >>>> thx, >>>> >>>> cax >>>> >>>> >>>> On 16/02/2007, at 7:49 PM, Gordon Stewart wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Looking at the error message, it would appear to be the JSDL which >>>>> is at >>>>> fault. I've had errors in the past where the order of elements >>>>> differs >>>>> from what the parser is expecting. According to the GridSAM >>>>> documentation for the MPIApplication element at >>>>> http://gridsam.sourceforge.net/2.0.0/gridsam-client/jsdl.html, the >>>>> definition is: >>>>> >>>> >>>>> <jsdl:Application> >>>>> .. >>>>> <mpi:MPIApplication xmlns:mpi="urn:gridsam:mpi"> >>>>> <jsdl-posix:*/>* >>>>> <mpi:ProcessorCount>xsd:positiveInteger</mpi:ProcessorCount> >>>>> </mpi:MPIApplication> >>>>> .. >>>>> </jsdl:Application> >>>>> >>>> >>>>> The POSIX application type (the jsdl-posix: element above) is >>>>> defined in >>>>> the XML schema as a sequence, which requires the child elements to >>>>> appear in the order specified. My guess (and it's only a guess as >>>>> I've >>>>> never used the MPI extensions) would be that this is the same with >>>>> MPIApplication, and that it is objecting to the ProcessorCount >> element >>>>> appearing before the POSIX stuff; relocating this after the >>>>> WallTimeLimit element may help. >>>>> >>>> >>>>> Gordon >>>>> >>>> >>>>> -----Original Message----- >>>>> From: gri...@li... >>>>> [mailto:gri...@li...] On Behalf Of > >>>>> Mark >>>>> HB >>>>> Sent: 16 February 2007 07:11 >>>>> To: gri...@li... >>>>> Subject: [gridsam-discuss] GRIDSam/AHE Invalid JSDL v1.0 job >>>>> >>>>> Hey, >>>>> Sincere apologies if this has sent twice! >>>>> >>>>> I am using AHE bundled with OMII server and have created a gridsam >>>>> instance to point at the Manchester node of the NGS (thanks list for >>>>> helping sort that out). >>>>> This GRIDSam instance was installed by following the instructions >>>>> found >>>>> at: >>>>> omii-server-3.2.0/managed_programme/AHE-1.0.2/dist/server/docs/ >>>>> index.htm >>>>> l >>>>> >>>>> However when I try to run a job, it all goes wrong. >>>>> Please find below the error I get, my jobmanger.xml and then the >> JSDL >>>>> message itself. >>>>> Can anyone help? >>>>> >>>>> Cheers >>>>> Mark >>>>> >>>>> ############## ERROR ############## >>>>> >>>>> 12:37:20 INFO (StartCall.java:182) - AHE Job Owner: >>>>> /C=UK/O=eScience/OU=Imperial/L=LeSC/CN=mark halling-brown >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job ID: >>>>> urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:176) - GridSAM Job >>>>> ID:urn:gridsam:ff80808210c53a780110c5681f5f000a >>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: pending >>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description:job >> is >>>>> being scheduled >>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>> 2007-02-15T12:37:19.840Z >>>>> 12:37:20 INFO (StartCall.java:185) - GridSAM Job submission time: >>>>> 2007-02-15T12:37:19.840Z >>>>> 12:37:20 INFO (StartCall.java:197) - GridSAM Job State: failed >>>>> 12:37:20 INFO (StartCall.java:179) - GridSAM State Description: >>>>> Invalid JSDL v1.0 job description: [error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Executable@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Argument@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Output@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> Error@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in element >>>>> MPIApplication@urn:gridsam:mpi, error: cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> WorkingDirectory@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>> element MPIApplication@urn:gridsam:mpi, error: >> cvc-complex-type.2.4b: >>>>> Element not allowed: >>>>> WallTimeLimit@http://schemas.ggf.org/jsdl/2005/11/jsdl-posix in >>>>> element >>>>> MPIApplication@urn:gridsam:mpi] >>>>> >>>>> ################ JOBMANAGER.XML ################ >>>>> <?xml version="1.0" encoding="UTF-8"?> >>>>> <module id="jobmanager.globus" version="1.0.0"> >>>>> <!-- dependent modules --> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/common.xml"/> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/embedded.xml"/> >>>>> <sub-module >>>>> descriptor="org/icenigrid/gridsam/resource/config/globus.xml"/> >>>>> <sub-module descriptor="database.xml"/> >>>>> <sub-module descriptor="authorisation.xml"/> >>>>> <!-- override the factory defaults here --> >>>>> <contribution configuration-id="hivemind.ApplicationDefaults"> >>>>> <!-- The job manager location --> >>>>> <default symbol="globus.JobManager" value="grid-data.man.ac.uk"/> >>>>> >>>>> <!-- The root file system for staging files >>>>> --> >>>>> <default symbol="globus.RootFileSystemURI" >>>>> value="gsiftp://grid-data.man.ac.uk"/> >>>>> <!-- How often the status of the job is polled >>>>> --> >>>>> <default symbol="globus.MonitoringPeriod" value="20000"/> >>>>> <!-- the default location of the classad generation script >>>>> WEB-INF/classes/rsl.groovy --> <default >>>>> symbol="globus.ScriptResource" value="rsl.groovy"/> >>>>> </contribution> >>>>> </module> >>>>> >>>>> #################### JSDL ######################## >>>>> <JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl"> >>>>> <JobDescription> >>>>> <JobIdentification> >>>>> <JobName>NAMD_NGS_MAN</JobName> >>>>> <Description>THIS IS FOR NAMD ON THE >> NGS</Description> >>>>> <JobAnnotation>NAMD Annotation</JobAnnotation> >>>>> <JobProject>AHE Project</JobProject> >>>>> </JobIdentification> >>>>> <Application> >>>>> <mpi:MPIApplication >>>>> xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl-posix" >>>>> xmlns:mpi="urn:gridsam:mpi"> >>>>> <mpi:ProcessorCount>1</mpi:ProcessorCount> >>>>> <Executable>/home/ngs0386/bin/cimmsim</Executable> >>>>> <Argument>datPlain12</Argument> >>>>> <Output>stdout.txt</Output> >>>>> <Error>stderr.txt</Error> >>>>> <WorkingDirectory>195914151107445079635</WorkingDirectory> >>>>> <WallTimeLimit>720</WallTimeLimit> >>>>> </mpi:MPIApplication> >>>>> </Application> >>>>> >>>>> <DataStaging> >>>>> <FileName>datPlain12</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Source><URI>http://test:to...@ig...:18080/ >>>>> filestage/19 >>>>> 5914151107445079635/datPlain12</URI></Source> >>>>> </DataStaging><DataStaging><FileName>stdout.txt</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/stdout.txt</URI></Target> >>>>> </DataStaging> >>>>> <DataStaging> >>>>> <FileName>stderr.txt</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/stderr.txt</URI></Target> >>>>> >>>> >>>>> </DataStaging> >>>>> <DataStaging> >>>>> <FileName>_th-details.out</FileName> >>>>> <CreationFlag>overwrite</CreationFlag> >>>>> <DeleteOnTermination>false</DeleteOnTermination> >>>>> >>>>> <Target><URI>webdav://test:to...@ig...:18080/ >>>>> filestage/ >>>>> 195914151107445079635/_th-details.out</URI></Target> >>>>> </DataStaging> >>>>> </JobDescription> >>>>> <myproxy:MyProxy >>>>> >> xmlns:myproxy="urn:gridsam:myproxy"><myproxy:ProxyServer>myproxy.grid- >>>>> >>>>> su >>>>> pport.ac.uk</myproxy:ProxyServer> >>>>> <myproxy:ProxyServerDN>/C=UK/O=eScience/OU=CLRC/L=DL/CN=host/ >>>>> myproxy.gri >>>>> d-support.ac.uk/E=a...@dl...</myproxy:ProxyServerDN> >>>>> <myproxy:ProxyServerPort>7512</myproxy:ProxyServerPort> >>>>> <myproxy:ProxyServerUserName>ghall04</myproxy:ProxyServerUserName> >>>>> <myproxy:ProxyServerPassPhrase>MYPSWORDHERE</ >>>>> myproxy:ProxyServerPassPhra >>>>> se> >>>>> <myproxy:ProxyServerLifetime>7512</myproxy:ProxyServerLifetime></ >>>>> myproxy >>>>> :MyProxy> >>>>> </JobDefinition> >>>>> >>>> >>>>> -- >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> --- >>>>> Mark Halling-Brown | Tel: +44-20-7631-6839 >>>>> Research Associate | >>>>> Room 359 | Fax: +44-20-7631-6803 >>>>> School of Crystallography | >>>>> Birkbeck College | Email: >>>>> Malet Street | >> gh...@ma... >>>>> London WC1E 7HX | ma...@gm... >>>>> UK | >>>>> http://people.cryst.bbk.ac.uk/~ghall04 >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> --- >>>>> >>>> >> ---------------------------------------------------------------------- >>>>> >>>>> -- >>>>> - >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>> share >>>>> your >>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>> http://www.techsay.com/default.php? >>>>> page=join.php&p=sourceforge&CID=DEVDE >>>>> V >>>>> _______________________________________________ >>>>> GridSAM-Discuss mailing list >>>>> Gri...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>> >>>>> >> ---------------------------------------------------------------------- >>>>> >>>>> --- >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the chance to >>>>> share your >>>>> opinions on IT & business topics through brief surveys-and earn cash >>>>> http://www.techsay.com/default.php? >>>>> page=join.php&p=sourceforge&CID=DEVDEV >>>>> _______________________________________________ >>>>> GridSAM-Discuss mailing list >>>>> Gri...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gridsam-discuss >>>>> >>>> cax >>>> ----------------------------- >>>> Think outside the box >>>> >>>> >>>> >>>> >>>> >>>> >>>> > - >> ------------------------------------------------------------------------ >> - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to >> share your > opinions on IT & business topics through brief surveys-and earn cash > >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE >> V > _______________________________________________ > GridSAM-Discuss mailing list > Gri...@li... > https://lists.sourceforge.net/lists/listinfo/gridsam-discuss > -- Stefan Zasada <ste...@uc...> Centre for Computational Science Chemistry Department, University College London, 20 Gordon Street, London, WC1H 0AJ, UK. Tel: +44 (0)20 7679 5300 |
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