[Swift-devel] Coaster error in RaptorLoops run
Wenjun Wu
wwj at ci.uchicago.edu
Mon Apr 26 16:01:06 CDT 2010
Sure. My config files are under the folder:
/gpfs/pads/oops/scienceportal/swift-svn/etc
the logs can be found at
/gpfs/pads/oops/scienceportal/scriptadmin/oops-raptorloop/test/RaptorLoops-20100426-1314-tna3q0a6.log
Wenjun
> Wenjun, can you post more details on the problem you describe below, to the swift-devel list (cc'ed here) pointing Mihael to a directory with all your logs and config files?
>
> Thanks,
>
> Mike
>
> ----- "wenjun wu"<wwjag at mcs.anl.gov> wrote:
>
>
>> Hi Mike,
>> Now I can run raptorloop locally but when I launch the jobs to
>> PADS
>> through coaster:ssh:pbs, I keep getting the following exceptions
>> after the swift finishes the most steps.
>>
>> 2010-04-26 13:27:25,408-0500 INFO AbstractStreamKarajanChannel
>> 01173289853: Channel shut down
>> java.lang.Throwable
>> at
>> org.globus.cog.karajan.workflow.service.channels.AbstractTCPChannel.close(AbstractTCPChannel.java:97)
>> at
>> org.globus.cog.karajan.workflow.service.channels.MetaChannel.close(MetaChannel.java:87)
>> at
>> org.globus.cog.abstraction.impl.execution.coaster.ServiceManager.statusChanged(ServiceManager.java:232)
>> at
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.notifyListeners(TaskImpl.java:236)
>> at
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:224)
>> at
>> org.globus.cog.abstraction.impl.common.task.TaskImpl.setStatus(TaskImpl.java:253)
>>
>> at
>> org.globus.cog.abstraction.impl.ssh.execution.JobSubmissionTaskHandler.SSHTaskStatusChanged(JobSubmissionTaskHandler.java:193)
>> at
>> org.globus.cog.abstraction.impl.ssh.SSHRunner.notifyListeners(SSHRunner.java:84)
>> at
>> org.globus.cog.abstraction.impl.ssh.SSHRunner.run(SSHRunner.java:43)
>>
>> at java.lang.Thread.run(Thread.java:595)
>> 2010-04-26 13:27:25,408-0500 INFO ChannelManager Handling channel
>> exception
>> java.io.IOException: Stream closed. at
>> java.net.PlainSocketImpl.available(PlainSocketImpl.java:428)
>> at
>> java.net.SocketInputStream.available(SocketInputStream.java:217)
>> at
>> org.globus.gsi.gssapi.net.GssInputStream.available(GssInputStream.java:107)
>>
>> at
>> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel.step(AbstractStreamKarajanChannel.java:113)
>> at
>> org.globus.cog.karajan.workflow.service.channels.AbstractStreamKarajanChannel$Multiplexer.run(AbstractStreamKarajanChannel.java:365)
>>
>> Progress: Finished successfully:7
>> Progress: Active:1 Finished successfully:7
>> Progress: Active:1 Finished successfully:7
>> Progress: Active:1 Finished successfully:7
>> Progress: Checking status:1 Finished successfully:7
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>> Progress: Finished successfully:8
>>
>> Wenjun
>>
>>> was: Re: notes from todays meeting
>>>
>>> Hi Aashish,
>>>
>>> Wenjun and Tom are integrated the latest OOPS scripts into the
>>>
>> portal for Web execution.
>>
>>> Wenjun is getting errors, as below. I suspect he's missing some
>>>
>> parameters or has incorrect parameters or inputs.
>>
>>> Can you send to Wenjun the latest parameters (ie shell calling
>>>
>> examples) to run Loops, RaptorLoops, and RaptorLoops with prep stage?
>>
>>> Best thing to do is quickly update README with the lastest shell
>>>
>> invocation lines and check it in; then Wenjun can verify that the
>> latest documented invocation instructions work for other people (which
>> will be useful for the OOPS group too!)
>>
>>> I cant get to this till late today or early this weekend, so any
>>>
>> help you can offer will be great.
>>
>>> Thanks!
>>>
>>> - Mike
>>>
>>> ----- "wenjun wu"<wwjag at mcs.anl.gov> wrote:
>>>
>>>
>>>
>>>> Hi Mike,
>>>> I run the raptorloop.sh and got the following error. Any clue?
>>>> Wenjun
>>>>
>>>> [wwj at login1 wwjtest]$ run.raptorloops.sh -target T1af7 -prepTar
>>>> T1af7.prep.tar.gz -templatesPerJob 800
>>>> Running in
>>>>
>>>>
>> /gpfs/pads/oops/scienceportal/oops-svn/oops/protlib2-0422/wwjtest/run.raptorloops.9229
>>
>>>> Running RaptorLoops with settings: target=T1af7 seqFile=
>>>> prepTar=T1af7.prep.tar.gz templatesPerJob=800 templateList=
>>>>
>> nModels=
>>
>>>> nSim=4 execsite=localhost maxSlots=16 resume= rlog=
>>>> Running from host with compute-node reachable address of
>>>>
>> 172.5.86.5
>>
>>>> protlib2 home is
>>>> /gpfs/pads/oops/scienceportal/oops-svn/oops/protlib2-0422
>>>> cp: warning: source file
>>>>
>>>>
>> `/gpfs/pads/oops/scienceportal/oops-svn/oops/protlib2-0422/swift/RaptorOut.map'
>>
>>>> specified more than once
>>>> cp: warning: source file
>>>>
>>>>
>> `/gpfs/pads/oops/scienceportal/oops-svn/oops/protlib2-0422/swift/TemplateList.map'
>>
>>>> specified more than once
>>>> cp: missing destination file operand after `.'
>>>> Try `cp --help' for more information.
>>>> basename: missing operand
>>>> Try `basename --help' for more information.
>>>> Variable nModels defined in scope 7122710 shadows variable of same
>>>> name
>>>> in scope 4890830
>>>> Variable tseg defined in scope 26460367 shadows variable of same
>>>>
>> name
>>
>>>> in
>>>> scope 4890830
>>>> Variable preparedInput defined in scope 26460367 shadows variable
>>>>
>> of
>>
>>>> same name in scope 4890830
>>>> Variable nModels defined in scope 26460367 shadows variable of
>>>>
>> same
>>
>>>> name
>>>> in scope 4890830
>>>> Variable targetId defined in scope 12182618 shadows variable of
>>>>
>> same
>>
>>>> name in scope 4890830
>>>> Variable modelIn defined in scope 12182618 shadows variable of
>>>>
>> same
>>
>>>> name
>>>> in scope 4890830
>>>> Variable targetId defined in scope 21925102 shadows variable of
>>>>
>> same
>>
>>>> name in scope 4890830
>>>> Variable models defined in scope 21925102 shadows variable of same
>>>> name
>>>> in scope 4890830
>>>> Swift svn swift-r3246 cog-r2721
>>>>
>>>> RunID: 20100422-1609-aqv1y329
>>>> Progress:
>>>> Execution failed:
>>>> java.lang.NumberFormatException: For input string: ""
>>>>
>>>>
>>>>
>>>>> Wenjun,
>>>>>
>>>>> The first two we need are psim.loops.swift and RaptorLoops.swift,
>>>>>
>>>>>
>>>> and their corresponding runs scripts.
>>>>
>>>>
>>>>> We run them from the corresponding .sh sripts in scripts/run
>>>>>
>>>>> I'll get back to you on this tonight with more details...after I
>>>>>
>>>>>
>>>> look for my 3rd script which is RaptorLoops with an addiitonal
>>>> pre-process step that takes a raw fasta file as input. I may need
>>>>
>> to
>>
>>>> check that in from my workspace.
>>>>
>>>>
>>>>> - Mike
>>>>>
>>>>>
>>>>> ----- "wenjun wu"<wwjag at mcs.anl.gov> wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Hi Mike:
>>>>>> I installed the latest version of protlib from SVN. I'd
>>>>>>
>> like
>>
>>>>>>
>>>>>>
>>>> to
>>>>
>>>>
>>>>>> clarify which swift scripts are needed into the portal.
>>>>>>
>>>>>> These are the swift scripts in the latest protlib2:
>>>>>>
>>>>>> rw-r--r-- 1 wwj ci-users 737 Apr 22 11:48 SwiftLib.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 3237 Apr 22 11:48 psim.itfixex2.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 2127 Apr 22 11:48 psim.itfixex1.swift
>>>>>> -rwxr-xr-x 1 wwj ci-users 509 Apr 22 11:48 psim.basicex1.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 2616 Apr 22 11:48 BoostThreader.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 1477 Apr 22 11:48 LoopLib.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 1193 Apr 22 11:48
>>>>>>
>>>>>>
>>>> BoostThreaderLib.swift
>>>>
>>>>
>>>>>> -rw-r--r-- 1 wwj ci-users 8869 Apr 22 11:48 oops.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 1525 Apr 22 11:48 psim.sweepex1.swift
>>>>>> -rwxr-xr-x 1 wwj ci-users 2188 Apr 22 11:48 psim.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 2933 Apr 22 11:48 psim.loops.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 6820 Apr 22 11:48
>>>>>> RaptorLoops.hanging.swift
>>>>>> -rw-r--r-- 1 wwj ci-users 2943 Apr 22 11:48 RaptorLoops.swift
>>>>>>
>>>>>> I guess the right swift scripts should be: psim.loops,
>>>>>>
>>>>>>
>>>> BoostThreader
>>>>
>>>>
>>>>>> and RaptorLoop.
>>>>>> I need to create packages for both Raptor-BoostThreader and
>>>>>> RaptorLoop
>>>>>> by grouping swift scripts and mapper scripts.
>>>>>>
>>>>>>
>>>>>> Wenjun
>>>>>>
>>>>>>
>>>>>>
>>>>>>> DataPort 2010.0421
>>>>>>>
>>>>>>> Coaster proxy issue: can Mihael automate this?
>>>>>>>
>>>>>>> Coaster proxy issue - use long proxy for now.
>>>>>>>
>>>>>>> Swift run status reporter?
>>>>>>>
>>>>>>> Adding new scripts and forms
>>>>>>> - how to shape the args? Like the email form?
>>>>>>>
>>>>>>> Need automation just for caps requests, then manual for Aashish
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> tests, then portal for Carl, Tobin et al
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Email notification
>>>>>>>
>>>>>>> Control over which swift the portal is running
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>
>
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