Re: [gridsam-discuss] Log file

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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)