[Swift-devel] swift 0.93 deadlock

David Kelly davidk at ci.uchicago.edu
Thu Sep 15 16:34:02 CDT 2011 

I was able to get it running on PADS with trunk. I ran into the same issue.

http://www.ci.uchicago.edu/~davidk/swat3/jstack.log
http://www.ci.uchicago.edu/~davidk/swat3/cce_ua-20110915-1617-sd4svyo2.log

David

----- Original Message -----
> From: "David Kelly" <davidk at ci.uchicago.edu>
> To: "Michael Wilde" <wilde at mcs.anl.gov>
> Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>, "Papia Rizwan" <papia.rizwan at gmail.com>
> Sent: Thursday, September 15, 2011 2:39:47 PM
> Subject: Re: [Swift-devel] swift 0.93 deadlock
> The sites.xml in /homes/papia/SwiftSCE2 seems to be using passive
> persistent coasters. Is there a way to use automatic coasters on the
> MCS workstations? I'll try copying this over to PADS and running there
> to see if I can reproduce it.
> 
> David
> 
> ----- Original Message -----
> > From: "Michael Wilde" <wilde at mcs.anl.gov>
> > To: "David Kelly" <davidk at ci.uchicago.edu>
> > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>, "Papia
> > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > <hategan at mcs.anl.gov>
> > Sent: Thursday, September 15, 2011 2:18:17 PM
> > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > Can you make SWAT run under trunk, as Papia is testing using
> > standard
> > auto coasters, and doesnt need any of the missing coaster-service
> > options.
> >
> > - Mike
> >
> >
> > ----- Original Message -----
> > > From: "David Kelly" <davidk at ci.uchicago.edu>
> > > To: "Michael Wilde" <wilde at mcs.anl.gov>
> > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>, "Papia
> > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > <hategan at mcs.anl.gov>
> > > Sent: Thursday, September 15, 2011 2:15:36 PM
> > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > I got past the compilation errors by renaming the all functions
> > > with
> > > capitalization, but ran into an issue with coaster-service. Last
> > > week
> > > I noticed coaster-service was missing options for dynamic ports. I
> > > found today that it is also missing -passive. I'll try to track
> > > down
> > > where this changed and restore the previous version.
> > >
> > > David
> > >
> > > ----- Original Message -----
> > > > From: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > To: "David Kelly" <davidk at ci.uchicago.edu>
> > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>, "Papia
> > > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > > <hategan at mcs.anl.gov>
> > > > Sent: Thursday, September 15, 2011 12:37:13 PM
> > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > Excellent, thanks - thats good. I also just verified that Papia
> > > > is
> > > > not
> > > > using the overAllocation tags in the sites file, so this problem
> > > > is
> > > > clearly a Java deadlock and has nothing to do with the
> > > > scheduling
> > > > problem that the (now fixed) overAllocation problem was
> > > > causing..
> > > >
> > > > My understanding is that this SWAT script is failing under trunk
> > > > because of the recent token case handling issue (I think the
> > > > camel-case one). Can you work with Papia to see if either that
> > > > issue
> > > > is now fixed, or if her script can be changed to avoid that, so
> > > > that
> > > > you can both test the SWAT script with trunk, to see if the
> > > > deadlock
> > > > still occurs?
> > > >
> > > > Thanks,
> > > >
> > > > - MIke
> > > >
> > > >
> > > > ----- Original Message -----
> > > > > From: "David Kelly" <davidk at ci.uchicago.edu>
> > > > > To: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>, "Papia
> > > > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > > > <hategan at mcs.anl.gov>
> > > > > Sent: Thursday, September 15, 2011 12:29:03 PM
> > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > I narrowed down the problem a bit. Last night I ran jstack on
> > > > > the
> > > > > wrong java process which is why it didn't report a deadlock.
> > > > >
> > > > > Papia and I are seeing the same issue.
> > > > >
> > > > > My jstack: http://www.ci.uchicago.edu/~davidk/swat2/jstack.log
> > > > > Papia's jstack:
> > > > > http://www.ci.uchicago.edu/~davidk/swat2/papia-jstack.log
> > > > >
> > > > > It happens in the same place:
> > > > >
> > > > > org.griphyn.vdl.karajan.lib.cache.File.lock(File.java:100)
> > > > > org.griphyn.vdl.karajan.lib.cache.LRUFileCache.addAndLockEntry(LRUFileCache.java:24)
> > > > >
> > > > > Filed as bug #559
> > > > >
> > > > > David
> > > > >
> > > > > ----- Original Message -----
> > > > > > From: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > > > To: "David Kelly" <davidk at ci.uchicago.edu>
> > > > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>,
> > > > > > "Papia
> > > > > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > > > > <hategan at mcs.anl.gov>
> > > > > > Sent: Thursday, September 15, 2011 11:46:59 AM
> > > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > > David, it sounds like more analysis is needed here. If the
> > > > > > SWAT
> > > > > > runs
> > > > > > are not showing a deadlock (but your runs are) then likely
> > > > > > we
> > > > > > have
> > > > > > two
> > > > > > different problems here.
> > > > > >
> > > > > > Another case we saw in 0.93 with scripts failing to progress
> > > > > > is
> > > > > > due
> > > > > > to
> > > > > > the overAllocation parameter problem that Mihael fixed
> > > > > > yesterday.
> > > > > > The
> > > > > > symptom there is that Swift starts a coaster with a time
> > > > > > slot
> > > > > > too
> > > > > > small for the apps in the script, and no apps wind up
> > > > > > running.
> > > > > > I
> > > > > > think
> > > > > > that situation in general merits a separate ticket, and may
> > > > > > have
> > > > > > been
> > > > > > discussed on swift-devel (but quite a while ago).
> > > > > >
> > > > > > Can you determine if indeed Papia's SWAT runs are hanging
> > > > > > for
> > > > > > a
> > > > > > reason
> > > > > > other than a Java deadlock?
> > > > > >
> > > > > > - Mike
> > > > > >
> > > > > >
> > > > > > ----- Original Message -----
> > > > > > > From: "David Kelly" <davidk at ci.uchicago.edu>
> > > > > > > To: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>,
> > > > > > > "Papia
> > > > > > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > > > > > <hategan at mcs.anl.gov>
> > > > > > > Sent: Thursday, September 15, 2011 8:03:09 AM
> > > > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > > > The jstack log corresponds to the most recent log file -
> > > > > > > http://www.ci.uchicago.edu/~davidk/swat/cce_ua-20110914-1934-frd3thja.log.
> > > > > > > jstack does not report any deadlocks, but I thought it
> > > > > > > might
> > > > > > > be
> > > > > > > useful
> > > > > > > so I included it. Swift was not making any progress for
> > > > > > > about
> > > > > > > 5
> > > > > > > hours
> > > > > > > before I sent the logs. I am running the latest 0.93
> > > > > > > branch.
> > > > > > > I
> > > > > > > will
> > > > > > > try again today.
> > > > > > >
> > > > > > > David
> > > > > > >
> > > > > > > ----- Original Message -----
> > > > > > > > From: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > > > > > To: "David Kelly" <davidk at ci.uchicago.edu>
> > > > > > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>,
> > > > > > > > "Papia
> > > > > > > > Rizwan" <papia.rizwan at gmail.com>, "Mihael Hategan"
> > > > > > > > <hategan at mcs.anl.gov>
> > > > > > > > Sent: Thursday, September 15, 2011 5:54:11 AM
> > > > > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > > > > David, which of the many Swift logs in that /swat dir
> > > > > > > > does
> > > > > > > > the
> > > > > > > > jstack.log pertain to? How many of these runs
> > > > > > > > deadlocked?
> > > > > > > >
> > > > > > > > And, did you verify that you (and Papia) are running on
> > > > > > > > the
> > > > > > > > latest
> > > > > > > > rev
> > > > > > > > of the 0.93 branch?
> > > > > > > >
> > > > > > > > - Mike
> > > > > > > >
> > > > > > > > ----- Original Message -----
> > > > > > > > > From: "David Kelly" <davidk at ci.uchicago.edu>
> > > > > > > > > To: "Mihael Hategan" <hategan at mcs.anl.gov>
> > > > > > > > > Cc: "swift-devel Devel" <swift-devel at ci.uchicago.edu>,
> > > > > > > > > "Papia
> > > > > > > > > Rizwan" <papia.rizwan at gmail.com>, "Michael Wilde"
> > > > > > > > > <wilde at mcs.anl.gov>
> > > > > > > > > Sent: Wednesday, September 14, 2011 11:04:41 PM
> > > > > > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > > > > > I was able to reproduce the problem with persistent
> > > > > > > > > coasters
> > > > > > > > > on
> > > > > > > > > the
> > > > > > > > > MCS servers.
> > > > > > > > >
> > > > > > > > > The jstack output is at
> > > > > > > > > http://www.ci.uchicago.edu/~davidk/swat/jstack.log
> > > > > > > > >
> > > > > > > > > The full collection of logs are at
> > > > > > > > > http://www.ci.uchicago.edu/~davidk/swat.
> > > > > > > > >
> > > > > > > > > David
> > > > > > > > >
> > > > > > > > > ----- Original Message -----
> > > > > > > > > > From: "Mihael Hategan" <hategan at mcs.anl.gov>
> > > > > > > > > > To: "Michael Wilde" <wilde at mcs.anl.gov>
> > > > > > > > > > Cc: "swift-devel Devel"
> > > > > > > > > > <swift-devel at ci.uchicago.edu>,
> > > > > > > > > > "Papia
> > > > > > > > > > Rizwan" <papia.rizwan at gmail.com>
> > > > > > > > > > Sent: Wednesday, September 14, 2011 10:30:48 PM
> > > > > > > > > > Subject: Re: [Swift-devel] swift 0.93 deadlock
> > > > > > > > > > Could you also forward the attachments please?
> > > > > > > > > >
> > > > > > > > > > Mihael
> > > > > > > > > >
> > > > > > > > > > On Wed, 2011-09-14 at 14:46 -0500, Michael Wilde
> > > > > > > > > > wrote:
> > > > > > > > > > > I think I am seeing a similar deadlock on 0.93 in
> > > > > > > > > > > the
> > > > > > > > > > > ParVis
> > > > > > > > > > > script,
> > > > > > > > > > > and am trying to get a clean log and jstack to
> > > > > > > > > > > confirm.
> > > > > > > > > > >
> > > > > > > > > > > As far as I can tell, Papia is running the correct
> > > > > > > > > > > 0.93
> > > > > > > > > > > code,
> > > > > > > > > > > but
> > > > > > > > > > > please verify.
> > > > > > > > > > >
> > > > > > > > > > > David will try to replicate this problem as well.
> > > > > > > > > > >
> > > > > > > > > > > - Mike
> > > > > > > > > > >
> > > > > > > > > > > ----- Original Message -----
> > > > > > > > > > > > From: "Papia Rizwan" <papia.rizwan at gmail.com>
> > > > > > > > > > > > To: "swift-devel Devel"
> > > > > > > > > > > > <swift-devel at ci.uchicago.edu>,
> > > > > > > > > > > > "Michael
> > > > > > > > > > > > Wilde" <wilde at mcs.anl.gov>, "Michael P. Shields"
> > > > > > > > > > > > <mpshields at anl.gov>
> > > > > > > > > > > > Sent: Wednesday, September 14, 2011 1:56:13 PM
> > > > > > > > > > > > Subject: swift 0.93 deadlock
> > > > > > > > > > > > Attached are the jstack output and the log file.
> > > > > > > > > > > >
> > > > > > > > > > > > --
> > > > > > > > > > > > Papia Rizwan
> > > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > _______________________________________________
> > > > > > > > > > Swift-devel mailing list
> > > > > > > > > > Swift-devel at ci.uchicago.edu
> > > > > > > > > > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> > > > > > > >
> > > > > > > > --
> > > > > > > > Michael Wilde
> > > > > > > > Computation Institute, University of Chicago
> > > > > > > > Mathematics and Computer Science Division
> > > > > > > > Argonne National Laboratory
> > > > > >
> > > > > > --
> > > > > > Michael Wilde
> > > > > > Computation Institute, University of Chicago
> > > > > > Mathematics and Computer Science Division
> > > > > > Argonne National Laboratory
> > > >
> > > > --
> > > > Michael Wilde
> > > > Computation Institute, University of Chicago
> > > > Mathematics and Computer Science Division
> > > > Argonne National Laboratory
> >
> > --
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel

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