[Swift-user] PADS

Jonathan Monette jon.monette at gmail.com
Sun Oct 3 19:26:47 CDT 2010


  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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