[Swift-user] PADS

[Mihael Hategan]

Can you set debug=true in etc/provider-pbs.properties and capture a
submit script?

Mihael

On Sun, 2010-10-03 at 19:26 -0500, Jonathan Monette wrote:
> I am still not certain why I cannot compile Swift on the head node of 
> PADS but I ran across this error in my runs.Worker task failed: Error 
> submitting block task
> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException: 
> Cannot submit job: Could not submit job (qsub reported an exit code of 1).
> Error: /home/jonmon/.globus/scripts/PBS807550213750625026.submitUnknown 
> parameters, or invalid PBS script locationPlease contact 
> pads-support at ci.uchicago.eduQsub options: usage: qsub [-a date_time] [-A 
> account_string] [-b secs]      [-c [ none | { enabled | periodic | 
> shutdown |      depth=<int> | dir=<path> | interval=<minutes>}... ]      
> [-C directive_prefix] [-d path] [-D path]      [-e path] [-h] [-I] [-j 
> oe] [-k {oe}] [-l resource_list] [-m n|{abe}]      [-M user_list] [-N 
> jobname] [-o path] [-p priority] [-P proxy_user] [-q queue]       [-r 
> y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list] [-w] 
> path      [-W otherattributes=value...] [-v variable_list] [-V ] [-x] 
> [-X] [-z] [script]Additional site options:     [-h | --help] display 
> usageDetailed information available at:    
> http://www.ci.uchicago.edu/wiki/bin/view/PADS
> 
>      at 
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:63)
>      at 
> org.globus.cog.abstraction.impl.common.AbstractTaskHandler.submit(AbstractTaskHandler.java:45)
>      at 
> org.globus.cog.abstraction.impl.common.task.ExecutionTaskHandler.submit(ExecutionTaskHandler.java:56)
>      at 
> org.globus.cog.abstraction.coaster.service.job.manager.BlockTaskSubmitter.run(BlockTaskSubmitter.java:66)
> Caused by: 
> org.globus.cog.abstraction.impl.scheduler.common.ProcessException: Could 
> not submit job (qsub reported an exit code of 1).
> Error: /home/jonmon/.globus/scripts/PBS807550213750625026.submitUnknown 
> parameters, or invalid PBS script locationPlease contact 
> pads-support at ci.uchicago.eduQsub options: usage: qsub [-a date_time] [-A 
> account_string] [-b secs]      [-c [ none | { enabled | periodic | 
> shutdown |      depth=<int> | dir=<path> | interval=<minutes>}... ]      
> [-C directive_prefix] [-d path] [-D path]      [-e path] [-h] [-I] [-j 
> oe] [-k {oe}] [-l resource_list] [-m n|{abe}]      [-M user_list] [-N 
> jobname] [-o path] [-p priority] [-P proxy_user] [-q queue]       [-r 
> y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list] [-w] 
> path      [-W otherattributes=value...] [-v variable_list] [-V ] [-x] 
> [-X] [-z] [script]Additional site options:     [-h | --help] display 
> usageDetailed information available at:    
> http://www.ci.uchicago.edu/wiki/bin/view/PADS
> 
>      at 
> org.globus.cog.abstraction.impl.scheduler.common.AbstractExecutor.start(AbstractExecutor.java:102)
>      at 
> org.globus.cog.abstraction.impl.scheduler.common.AbstractJobSubmissionTaskHandler.submit(AbstractJobSubmissionTaskHandler.java:53)
>      ... 3 more
> 
> I got a bunch of failed to shutdown block and then got this error.  
> Attached is the stdout from that run.  I also noticed that inside my run 
> directories several PBS*.submit* files are in there.  In the 
> PBS*.submit.e* files they seem to be complaining that they can't find a 
> certain file.  This is the error that they are reporting:
> zsh: no such file or directory: 
> /var/spool/torque/mom_priv/jobs/505703.svc.pads.ci.uchicago.edu.SC
> 
> Does this new information help deduce what the problem is with PADS?  Is 
> this a system problem or has a new bug appeared in Swift?
> 
> On 10/03/2010 02:17 PM, Mihael Hategan wrote:
> > Ok. I don't think that's related to my commits.
> >
> > On Sun, 2010-10-03 at 13:44 -0500, Jonathan Monette wrote:
> >> Here is the compile error:
> >> generateVersion:
> >>
> >> antlr:
> >>        [java] ANTLR Parser Generator   Version 2.7.5 (20050128)
> >> 1989-2005 jGuru.com
> >>        [java] resources/swiftscript.g:1028: warning:nondeterminism upon
> >>        [java] resources/swiftscript.g:1028:     k==1:LBRACK
> >>        [java] resources/swiftscript.g:1028:
> >> k==2:ID,STRING_LITERAL,LBRACK,LPAREN,AT,PLUS,MINUS,STAR,NOT,INT_LITERAL,FLOAT_LITERAL,"true","false"
> >>        [java] resources/swiftscript.g:1028:     between alt 1 and exit
> >> branch of block
> >>
> >> compileSchema:
> >>        [java] IO Error java.io.FileNotFoundException:
> >> /tmp/xbean5901864127478979310.d/classes/schemaorg_apache_xmlbeans/src/swiftscript.xsd
> >> (No such file or directory)
> >>        [java] Time to build schema type system: 0.559 seconds
> >>        [java] Exception in thread "main"
> >> org.apache.xmlbeans.SchemaTypeLoaderException:
> >> /tmp/xbean5901864127478979310.d/classes/schemaorg_apache_xmlbeans/system/s4846B13C10E24B6C12C8DCBE3348DA75/procedure8537type.xsb
> >> (No such file or directory)
> >> (schemaorg_apache_xmlbeans.system.s4846B13C10E24B6C12C8DCBE3348DA75.procedure8537type)
> >> - code 9
> >>        [java]     at
> >> org.apache.xmlbeans.impl.schema.SchemaTypeSystemImpl$XsbReader.getSaverStream(SchemaTypeSystemImpl.java:2214)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.schema.SchemaTypeSystemImpl$XsbReader.writeRealHeader(SchemaTypeSystemImpl.java:1589)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.schema.SchemaTypeSystemImpl.saveType(SchemaTypeSystemImpl.java:1440)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.schema.SchemaTypeSystemImpl.saveTypesRecursively(SchemaTypeSystemImpl.java:1316)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.schema.SchemaTypeSystemImpl.save(SchemaTypeSystemImpl.java:1291)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.tool.SchemaCompiler.compile(SchemaCompiler.java:1098)
> >>        [java]     at
> >> org.apache.xmlbeans.impl.tool.SchemaCompiler.main(SchemaCompiler.java:368)
> >>
> >> BUILD FAILED
> >> /autonfs/home/jonmon/Library/Swift/trunk/cog/modules/swift/build.xml:247: Java
> >> returned: 1
> >>
> >> and here is the run error I receive once I compile on a different machine:
> >> Failed to transfer wrapper log from
> >> unrectified-20101003-1339-voon0t62/info/l on pads
> >> Execution failed:
> >>       Failed to transfer wrapper log from
> >> unrectified-20101003-1339-voon0t62/info/8 on pads
> >> Exception in mProject:
> >> Arguments: [-X, raw_dir/2mass-atlas-000713s-j0760245.fits,
> >> proj_dir/proj_2mass-atlas-000713s-j0760245.fits, header.hdr]
> >> Host: pads
> >> Directory: unrectified-20101003-1339-voon0t62/jobs/l/mProject-lvknimzj
> >> stderr.txt:
> >>
> >> stdout.txt:
> >>
> >> ----
> >>
> >> Caused by:
> >>       Task failed:
> >> org.globus.cog.abstraction.impl.scheduler.common.ProcessException:
> >> Exitcode file
> >> (/home/jonmon/.globus/scripts/PBS6388672747278247642.submit.exitcode)
> >> not found 5 queue polls after the job was reported done
> >>       at
> >> org.globus.cog.abstraction.impl.scheduler.common.Job.close(Job.java:66)
> >>       at
> >> org.globus.cog.abstraction.impl.scheduler.common.Job.setState(Job.java:177)
> >>       at
> >> org.globus.cog.abstraction.impl.scheduler.pbs.QueuePoller.processStdout(QueuePoller.java:126)
> >>       at
> >> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.pollQueue(AbstractQueuePoller.java:169)
> >>       at
> >> org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller.run(AbstractQueuePoller.java:82)
> >>       at java.lang.Thread.run(Thread.java:619)
> >>
> >> The run directory with the files needed to execute and log files is in
> >> ~jonmon/Workspace/Swift/Montage/katz_slides_test/run.0001
> >>
> >> On 10/3/10 1:30 PM, Mihael Hategan wrote:
> >>> On Sun, 2010-10-03 at 13:27 -0500, Jonathan Monette wrote:
> >>>> Hello,
> >>>>        Anyone having a problem using Swift on PADS?  I updated Swift and
> >>>> cog to the most recent from trunk and now I cannot compile Swift on
> >>>> PADS.
> >>> I made some recent commits which might be the cause. But I need specific
> >>> errors.
> >>>
> >>> Mihael
> >>>
> >>>>     I have to use bridled or another ci machine that shares the
> >>>> filesystem and compile there.  I then come back to PADS to execute my
> >>>> swift script and get all sorts of errors.  Is anyone experiencing
> >>>> similar problems when using PADS?
> >>>>
> >> -- 
> >> Jon
> >>
> >> Computers are incredibly fast, accurate, and stupid. Human beings are incredibly slow, inaccurate, and brilliant. Together they are powerful beyond imagination.
> >> - Albert Einstein
> >>
> >
> 
> -- 
> Jon
> 
> Computers are incredibly fast, accurate, and stupid. Human beings are incredibly slow, inaccurate, and brilliant. Together they are powerful beyond imagination.
> - Albert Einstein
>