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Re: [gridsam-discuss] Log file
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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 - 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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 --------------------------------------------------------------------------- |
