[Swift-devel] Re: test v0.1rc1
Veronika V. Nefedova
nefedova at mcs.anl.gov
Tue Feb 27 15:27:41 CST 2007
Workflow with 16 molecules finished on TG just swiftly (-;
At 03:03 PM 2/27/2007, Veronika V. Nefedova wrote:
>I have just 16 molecules (at present) for testing - I am running all of
>them now. Will let you know how did it go. I've already asked Yuqing to
>send my way all 350 molecules (;
>
>Nika
>
>At 02:54 PM 2/27/2007, Mihael Hategan wrote:
>>On Tue, 2007-02-27 at 14:54 -0600, Veronika V. Nefedova wrote:
>> > It worked! Thank you very much for tracking it down, Mihael.
>> >
>> > Anyway -- a complete MolDyn workflow just finished its first run on
>> > Teragrid (for 3 molecules only).
>>
>>Groovy. Can it be pumped up?
>>
>> >
>> > (-;
>> >
>> > Nika
>> >
>> > At 02:19 PM 2/27/2007, Veronika V. Nefedova wrote:
>> >
>> > >Thanks, Mihael!
>> > >I'll try it now
>> > >
>> > >Nika
>> > >
>> > >At 02:04 PM 2/27/2007, Mihael Hategan wrote:
>> > >>Try it now. The latest nightly build should contain the fix.
>> > >>
>> > >>The problem was an inner class having synchronized methods and me
>> > >>idiotically assuming that they will use the outer class' instance
>> > >>monitor.
>> > >>
>> > >>Mihael
>> > >>
>> > >>On Mon, 2007-02-26 at 22:17 -0600, Veronika V. Nefedova wrote:
>> > >> > If you give me your vds_home location - I can try to run the
>> workflow and
>> > >> > see if its working...
>> > >> >
>> > >> > NIka
>> > >> > At 09:57 PM 2/26/2007, Mihael Hategan wrote:
>> > >> > >Hmm. I made a change to the code that did not seem to be the
>> cause, but
>> > >> > >some other, smaller issue and enabled some more debugging in
>> log4j. With
>> > >> > >this, I've been running the workflow in a loop on wiggum for two
>> hours
>> > >> > >now, and got nothing yet. I don't know what to make of it.
>> > >> > >
>> > >> > >I'll keep running and eventually revert the changes to see if
>> they are
>> > >> > >the source.
>> > >> > >
>> > >> > >Mihael
>> > >> > >
>> > >> > >On Mon, 2007-02-26 at 14:47 -0600, Mihael Hategan wrote:
>> > >> > > > On Mon, 2007-02-26 at 14:46 -0600, Veronika V. Nefedova wrote:
>> > >> > > > > An additional info: This failure happened on TG with 070219
>> when
>> > >> I was
>> > >> > > > > running 2 molecules at the same time (i.e. two executables at
>> > >> the same
>> > >> > > > > time). When I tried to run just one, it failed with the same
>> > >> > > exitcode, but
>> > >> > > > > didn't have that handle exception:
>> > >> > > >
>> > >> > > > Right. This seems like a different problem, and I'm not sure
>> if it's
>> > >> > > > Swift or some problem with TP or the application. That needs
>> to be
>> > >> > > > investigated.
>> > >> > > >
>> > >> > > > >
>> > >> > > > > 2007-02-26 14:34:41,986 DEBUG vdl:execute2 Application
>> > >> exception: Job
>> > >> > > chrm
>> > >> > > > > failed with an exit code of 174
>> > >> > > > > sys:throw @ vdl-int.k, line: 108
>> > >> > > > > vdl:checkexitcode @ vdl-int.k, line: 367
>> > >> > > > > vdl:execute2 @ execute-default.k, line: 22
>> > >> > > > > vdl:execute @ swift-MolDyn.kml, line: 69
>> > >> > > > > charmm @ swift-MolDyn.kml, line: 279
>> > >> > > > > vdl:mains @ swift-MolDyn.kml, line: 261
>> > >> > > > > <here it re-tries it>
>> > >> > > > >
>> > >> > > > > Again, the failure with 070219 happens only on TG, on localhost
>> > >> (wiggum)
>> > >> > > > > its working just fine.
>> > >> > > > >
>> > >> > > > > Nika
>> > >> > > > >
>> > >> > > > >
>> > >> > > > > At 02:38 PM 2/26/2007, Mihael Hategan wrote:
>> > >> > > > > >That's fine. Just wanted to be clear that we're talking about
>> > >> the same
>> > >> > > > > >error. It's good that it also occurs in 070219, because there
>> > >> are no
>> > >> > > > > >recent changes I could remember that could trigger it. It's
>> > >> also good to
>> > >> > > > > >know that it may or may not occur, because I know
>> approximately
>> > >> what
>> > >> > > > > >class of problem we're dealing with.
>> > >> > > > > >
>> > >> > > > > >Mihael
>> > >> > > > > >
>> > >> > > > > >On Mon, 2007-02-26 at 14:37 -0600, Veronika V. Nefedova wrote:
>> > >> > > > > > > Yes, I didn't paste it -- its all in the log. If you'd like
>> > >> I can
>> > >> > > send you
>> > >> > > > > > > the log as an attachment...
>> > >> > > > > > >
>> > >> > > > > > > Nika
>> > >> > > > > > >
>> > >> > > > > > > At 02:33 PM 2/26/2007, Mihael Hategan wrote:
>> > >> > > > > > > >Wait, because I'm missing something. Wasn't the error
>> > >> supposed to be
>> > >> > > > > > > >"TaskHandler can only handle unsubmitted tasks"?
>> > >> > > > > > > >
>> > >> > > > > > > >On Mon, 2007-02-26 at 14:26 -0600, Veronika V.
>> Nefedova wrote:
>> > >> > > > > > > > > And now its getting interesting!
>> > >> > > > > > > > >
>> > >> > > > > > > > > I have now the same failure (as below) with 070219 as I
>> > >> had on
>> > >> > > > > > localhost
>> > >> > > > > > > > > with v0.1rc1 *BUT* when running on TG. Failed at
>> the same
>> > >> > > point (while
>> > >> > > > > > > > > trying to run the last app in the workflow), with
>> the same
>> > >> > > exceptions.
>> > >> > > > > > > > > Strange that 070219 worked on localhost (and still
>> working).
>> > >> > > > > > > > >
>> > >> > > > > > > > > The log is on wiggum:
>> > >> > > > > > > > /sandbox/ydeng/alamines/swift-MolDyn-690y7r1skc8z0.log
>> > >> > > > > > > > >
>> > >> > > > > > > > > 2007-02-26 14:10:16,543 INFO vdl:execute2 Running job
>> > >> > > > > > chrm-rmnoet7i chrm
>> > >> > > > > > > > > with arguments [system:solv_m001, title:solv,
>> stitle:m001,
>> > >> > > > > > > > > rtffile:parm03_gaff_all.rtf,
>> > >> paramfile:parm03_gaffnb_all.prm,
>> > >> > > > > > > > > gaff:m001_am1, nwater:400, ligcrd:lyz, rforce:0,
>> > >> iseed:3131887,
>> > >> > > > > > rwater:15,
>> > >> > > > > > > > > nstep:100, minstep:100, skipstep:100,
>> startstep:10000] in
>> > >> > > > > > > > > swift-MolDyn-690y7r1skc8z0/chrm-rmnoet7i on TG-NCSA
>> > >> > > > > > > > > 2007-02-26 14:11:18,586 DEBUG vdl:execute2 Application
>> > >> > > exception:
>> > >> > > > > > Job chrm
>> > >> > > > > > > > > failed with an exit code of 174
>> > >> > > > > > > > > <snip>
>> > >> > > > > > > > > All input files are staged in...
>> > >> > > > > > > > >
>> > >> > > > > > > > >
>> > >> > > > > > > > > Nika
>> > >> > > > > > > > >
>> > >> > > > > > > > > At 02:17 PM 2/26/2007, Veronika V. Nefedova wrote:
>> > >> > > > > > > > > >You can try to run my application, or look in the
>> logs. I
>> > >> > > ran it
>> > >> > > > > > all on
>> > >> > > > > > > > > >wiggum. The log is:
>> > >> > > > > > > > > >/sandbox/ydeng/alamines/swift-MolDyn-8q6ygr7cy15c2.log
>> > >> > > > > > > > > >
>> > >> > > > > > > > > >the dtm file I am running is
>> > >> > > /sandbox/ydeng/alamines/swift-MolDyn.dtm
>> > >> > > > > > > > > >
>> > >> > > > > > > > > >Nika
>> > >> > > > > > > > > >
>> > >> > > > > > > > > >At 01:39 PM 2/26/2007, Mihael Hategan wrote:
>> > >> > > > > > > > > >>That doesn't sound good. How do I reproduce this?
>> > >> > > > > > > > > >>
>> > >> > > > > > > > > >>Mihael
>> > >> > > > > > > > > >>
>> > >> > > > > > > > > >>On Mon, 2007-02-26 at 13:21 -0600, Veronika V.
>> > >> Nefedova wrote:
>> > >> > > > > > > > > >> > The one Ben asked us all to test:
>> > >> > > > > > > > > >> >
>> > >> > > > > > > > > >> > >http://www.ci.uchicago.edu/swift/tests/vdsk-0.
>> 1 rc1.
>> > >> t ar.gz
>> > >> > > > > > > > > >> >
>> > >> > > > > > > > > >> > At 01:15 PM 2/26/2007, Mihael Hategan wrote:
>> > >> > > > > > > > > >> > >On Mon, 2007-02-26 at 13:05 -0600, Veronika V.
>> > >> Nefedova
>> > >> > > wrote:
>> > >> > > > > > > > > >> > > > When I tried to run my working workflow
>> with a new
>> > >> > > version, it
>> > >> > > > > > > > > >> gave me an
>> > >> > > > > > > > > >> > > > exception:
>> > >> > > > > > > > > >> > >
>> > >> > > > > > > > > >> > >Which new version?
>> > >> > > > > > > > > >> > >
>> > >> > > > > > > > > >> > >Mihael
>> > >> > > > > > > > > >> > >
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > Warning: Task handler throws exception but
>> does not
>> > >> > > set status
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > >
>> > >> > >
>> org.globus.cog.abstraction.impl.common.task.TaskSubmissionException:
>> > >> > > > > > > > > >> > > > TaskHandler can only handle unsubmitted tasks
>> > >> > > > > > > > > >> > > > at
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > >
>> > >> > > > > > > > > >>
>> > >> > > > > > > >
>> > >> > > > > >
>> > >> > >
>> > >>
>> org.globus.cog.abstraction.impl.common.task.CachingFileOperationTaskHandler.submit(CachingFileOperationTaskHandler.java:20)
>> > >> > > > > > > > > >> > > > at
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > >
>> > >> > > > > > > > > >>
>> > >> > > > > > > >
>> > >> > > > > >
>> > >> > >
>> > >>
>> org.globus.cog.karajan.scheduler.submitQueue.NonBlockingSubmit.run(NonBlockingSubmit.java:78)
>> > >> > > > > > > > > >> > > > at
>> java.lang.Thread.run(Thread.java:534)
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > [349] wiggum /sandbox/ydeng/alamines > \\
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > I do not have this happening with 070219
>> built.
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > Nika
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > At 06:12 AM 2/26/2007, Ben Clifford wrote:
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > > >On Mon, 26 Feb 2007, Ben Clifford wrote:
>> > >> > > > > > > > > >> > > > >
>> > >> > > > > > > > > >> > > > > >
>> > >> > > > > > > > > >> > > > > > v0.1rc1 was built at the end of last week.
>> > >> > > please spend
>> > >> > > > > > > > some time
>> > >> > > > > > > > > >> > > testing
>> > >> > > > > > > > > >> > > > >
>> > >> > > > > > > > > >> > > > >here's the URL for download:
>> > >> > > > > > > > > >> > > > >
>> > >> > > > > > > > > >> > > > >http://www.ci.uchicago.edu/swift/tests/vds
>> k -0.1
>> > >> r c1.t
>> > >> > > ar.gz
>> > >> > > > > > > > > >> > > > >
>> > >> > > > > > > > > >> > > > >--
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> > > >
>> _______________________________________________
>> > >> > > > > > > > > >> > > > Swift-devel mailing list
>> > >> > > > > > > > > >> > > > Swift-devel at ci.uchicago.edu
>> > >> > > > > > > > > >> > > >
>> > >> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>> > >> > > > > > > > > >> > > >
>> > >> > > > > > > > > >> >
>> > >> > > > > > > > > >> >
>> > >> > > > > > > > > >
>> > >> > > > > > > > > >
>> > >> > > > > > > > > >_______________________________________________
>> > >> > > > > > > > > >Swift-devel mailing list
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>> > >> > > > > > > > > >http://mail.ci.uchicago.edu/mailman/listinfo/swift-
>> d evel
>> > >> > > > > > > > >
>> > >> > > > > > > > >
>> > >> > > > > > >
>> > >> > > > > > >
>> > >> > > > >
>> > >> > > > >
>> > >> > > >
>> > >> > > > _______________________________________________
>> > >> > > > Swift-devel mailing list
>> > >> > > > Swift-devel at ci.uchicago.edu
>> > >> > > > http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>> > >> > > >
>> > >> >
>> > >> >
>> > >
>> > >
>> > >_______________________________________________
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