[Swift-devel] Re: test v0.1rc1
Mike Wilde
wilde at mcs.anl.gov
Tue Feb 27 15:33:38 CST 2007
Awesome! Nice work Nika and everyone!!!
Just how "swift" was it?
:) Mike
^ thanks, I needed that!
Veronika V. Nefedova wrote, On 2/27/2007 3:27 PM:
> 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
>>> > >> > > > > > > > > >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
>>> >
>>> >
>>
>>
>> _______________________________________________
>> 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
>
>
--
Mike Wilde
Computation Institute, University of Chicago
Math & Computer Science Division
Argonne National Laboratory
Argonne, IL 60439 USA
tel 630-252-7497 fax 630-252-1997
More information about the Swift-devel
mailing list