[Swift-user] PADS
Michael Wilde
wilde at mcs.anl.gov
Sun Oct 3 20:08:22 CDT 2010
I was able to run a pbs job on pads using swift trunk just now.
Can you also post you sites.xml file, Jon?
Mine was:
<config>
<pool handle="pbs">
<execution provider="pbs" url="none"/>
<profile namespace="globus" key="queue">fast</profile>
<profile namespace="globus" key="maxwalltime">00:05:00</profile>
<filesystem provider="local"/>
<workdirectory >/home/wilde/swiftwork</workdirectory>
</pool>
</config>
- Mike
----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:
> 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
> >
>
>
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--
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory
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