[Swift-devel] Re: test v0.1rc1
Veronika V. Nefedova
nefedova at mcs.anl.gov
Tue Feb 27 15:03:47 CST 2007
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/vdsk
> -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
> > >> > > > > > > > > >Swift-devel at ci.uchicago.edu
> > >> > > > > > > > > >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
> > >> > > >
> > >> >
> > >> >
> > >
> > >
> > >_______________________________________________
> > >Swift-devel mailing list
> > >Swift-devel at ci.uchicago.edu
> > >http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> >
> >
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