[Swift-user] PADS
Jonathan Monette
jon.monette at gmail.com
Sun Oct 3 20:45:57 CDT 2010
I am running jobs using coasters. Here is my sites file.
<config>
<pool handle="localhost">
<execution provider="local" />
<filesystem provider="local" />
<profile key="jobThrottle" namespace="karajan">.05</profile>
<workdirectory>/gpfs/pads/swift/jonmon/Swift/work/localhost</workdirectory>
</pool>
<pool handle="pads">
<execution jobmanager="local:pbs" provider="coaster" />
<filesystem provider="local" />
<profile key="maxtime" namespace="globus">3600</profile>
<profile key="internalhostname" namespace="globus">192.5.86.6</profile>
<profile key="workersPerNode" namespace="globus">1</profile>
<profile key="slots" namespace="globus">10</profile>
<profile key="nodeGranularity" namespace="globus">1</profile>
<profile key="maxNodes" namespace="globus">1</profile>
<profile key="queue" namespace="globus">fast</profile>
<profile key="jobThrottle" namespace="karajan">1</profile>
<profile key="initialScore" namespace="karajan">10000</profile>
<workdirectory>/gpfs/pads/swift/jonmon/Swift/work/pads</workdirectory>
</pool>
</config>
This is a PBS submit.o file
----------------------------------------
Begin PBS Prologue Sun Oct 3 19:15:42 CDT 2010
Job ID: 505699.svc.pads.ci.uchicago.edu
Username: jonmon
Group: ci-users
Nodes: c06.pads.ci.uchicago.edu
End PBS Prologue Sun Oct 3 19:15:42 CDT 2010
----------------------------------------
----------------------------------------
Begin PBS Epilogue Sun Oct 3 19:15:43 CDT 2010
Job ID: 505699.svc.pads.ci.uchicago.edu
Username: jonmon
Group: ci-users
Job Name: PBS1275966776980450327.submit
Session: 30684
Limits: ncpus=1,neednodes=1,nodes=1,size=1,walltime=00:18:00
Resources: cput=00:00:00,mem=0kb,vmem=0kb,walltime=00:00:01
Nodes: c06.pads.ci.uchicago.edu
End PBS Epilogue Sun Oct 3 19:15:43 CDT 2010
----------------------------------------
This is using the most recent trunk of Swift and cog. I did not change
any of the Swift code merely updated the library and re-compiled.
On 10/03/2010 08:08 PM, Michael Wilde wrote:
> 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
>>>
>>
>> _______________________________________________
>> Swift-user mailing list
>> Swift-user at ci.uchicago.edu
>> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
--
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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