[Swift-devel] Re: Swift hanging in complex iterate script

Mihael Hategan hategan at mcs.anl.gov
Thu Sep 16 14:17:13 CDT 2010 

That's the one.

On Thu, 2010-09-16 at 13:13 -0600, Michael Wilde wrote:
> I see this suspicious deadlock in that jstack output:
> 
> Found one Java-level deadlock:
> =============================
> "pool-1-thread-4":
>   waiting to lock monitor 0x0000000052b88650 (object 0x00002aaab5542348, a org.griphyn.vdl.mapping.RootDataNode),
>   which is held by "pool-1-thread-2"
> "pool-1-thread-2":
>   waiting to lock monitor 0x0000000052b879d8 (object 0x00002aaab5542540, a org.griphyn.vdl.mapping.RootArrayDataNode),
>   which is held by "pool-1-thread-4"
> 
> Java stack information for the threads listed above:
> ===================================================
> ...
> 
> - Mike
> 
> ----- "Michael Wilde" <wilde at mcs.anl.gov> wrote:
> 
> > OK, thats in ~wilde/swiftrhang/jstack.out
> > 
> > The jvm is still running: pid 22435 on bridled. Let me know if you
> > need any other traces from it.
> > 
> > It hung around 12:05
> > 
> > - Mike
> > 
> > 
> > bri$ mp
> > UID        PID  PPID  PGID   SID  C STIME TTY          TIME CMD
> > wilde    19025 19023 19023 19023  0 11:49 ?        00:00:00 sshd:
> > wilde at pts/29
> > wilde    19026 19025 19026 19026  0 11:49 pts/29   00:00:00   -bash
> > wilde    19203 19026 19203 19026  0 11:49 pts/29   00:00:00    
> > /usr/bin/screen -x
> > wilde    15373 15371 15371 15371  0 06:58 ?        00:00:00 sshd:
> > wilde at pts/14
> > wilde    15374 15373 15374 15374  0 06:58 pts/14   00:00:00   -bash
> > wilde    18291 15374 18291 15374  0 11:47 pts/14   00:00:00    
> > /home/wilde/R/R-2.11.0/bin/exec/R
> > wilde    11315 15374 11315 15374  0 13:59 pts/14   00:00:00    
> > /usr/bin/screen -x
> > wilde    15183 15181 15181 15181  0 06:58 ?        00:00:00 sshd:
> > wilde at pts/11
> > wilde    15184 15183 15184 15184  0 06:58 pts/11   00:00:00   -bash
> > wilde    15835 15184 15835 15184  0 06:59 pts/11   00:00:00    
> > /usr/bin/screen
> > wilde    15836 15835 15836 15836  0 06:59 ?        00:00:00      
> > /usr/bin/SCREEN
> > wilde    15837 15836 15837 15837  0 06:59 pts/15   00:00:00        
> > bash
> > wilde    15839 15836 15839 15839  0 06:59 pts/16   00:00:00        
> > bash
> > wilde    15841 15836 15841 15841  0 06:59 pts/19   00:00:00        
> > bash
> > wilde    15843 15836 15843 15843  0 06:59 pts/20   00:00:00        
> > bash
> > wilde    15845 15836 15845 15845  0 06:59 pts/21   00:00:00        
> > bash
> > wilde    15847 15836 15847 15847  0 06:59 pts/22   00:00:00        
> > bash
> > wilde    14845 15847 14845 15847  0 10:05 pts/22   00:00:00          
> > emacs Swift/exec/start-swift-workers
> > wilde    22364 15847 22364 15847  0 11:59 pts/22   00:00:00          
> > /bin/bash Swift/exec/RunRServer.sh
> > wilde    22378 22364 22364 15847  0 11:59 pts/22   00:00:00           
> >  /bin/sh /home/wilde/swift/rev/trunk/bin/swift -config swift.pr
> > wilde    22435 22378 22364 15847  0 11:59 pts/22   00:00:29           
> >    java -Xmx256M -Djava.endorsed.dirs=/home/wilde/swift/rev/tru
> > wilde    12506 15847 12506 15847  0 14:03 pts/22   00:00:00          
> > ps -fjH -u wilde
> > wilde    22930     1 22364 15847  0 11:59 pts/22   00:00:05
> > /home/wilde/R/R-2.11.0/bin/exec/R --slave --no-restore
> > --file=./SwiftRServ
> > wilde    22926     1 22364 15847  0 11:59 pts/22   00:00:04
> > /home/wilde/R/R-2.11.0/bin/exec/R --slave --no-restore
> > --file=./SwiftRServ
> > wilde    22920     1 22364 15847  0 11:59 pts/22   00:00:04
> > /home/wilde/R/R-2.11.0/bin/exec/R --slave --no-restore
> > --file=./SwiftRServ
> > wilde    22760     1 22364 15847  0 11:59 pts/22   00:00:04
> > /home/wilde/R/R-2.11.0/bin/exec/R --slave --no-restore
> > --file=./SwiftRServ
> > bri$
> > 
> > 
> > ----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:
> > 
> > > I can't tell what's causing the problem, but it may generally be a
> > > good
> > > idea to do a jstack -l when you get a hang.
> > >
> > > Mihael
> > >
> > > On Thu, 2010-09-16 at 12:14 -0600, wilde at mcs.anl.gov wrote:
> > > > Mihael,
> > > >
> > > > I've developed a Swift script that loops using iterate, reading
> > > requests to process an R function from a named pipe (fifo), calling
> > R,
> > > and replying "done" on a response fifo.
> > > >
> > > > This has been working very well, but I just hit a case where the
> > > script hangs.
> > > >
> > > > I exercise it using a small battery of R tests; I was manually
> > > restarting the test battery (which does hundreds of R calls in 30
> > > seconds or so, when it hung in the middle of the test suite.
> > > >
> > > > As far as I can tell it hung after receiving a work request,
> > mapping
> > > the files for the work request, but never called the app() function
> > > that invokes R.
> > > >
> > > > The log is in ~wilde/rserver-20100916-1159-y94hftt0.log
> > > > (I will try to post the script and all related files, but looks
> > like
> > > bridled may have just gone down for patches)
> > > >
> > > > look for these trace lines in the log, which are issued at the
> > start
> > > of every R request:
> > > >
> > > > line 37342:
> > > >
> > > > 2010-09-16 12:03:24,212-0500 INFO  vdl:execute END_SUCCESS
> > > thread=0-1-86-4 tr=bash
> > > > 2010-09-16 12:03:24,213-0500 INFO  apply STARTCOMPOUND
> > > thread=0-1-87-2 name=apply
> > > > 2010-09-16 12:03:24,215-0500 WARN  trace SwiftScript trace:
> > rserver:
> > > got dir, /autonfs/home/wilde/SwiftR/SwiftR.run.233
> > > > 2010-09-16 12:03:24,215-0500 INFO  SetFieldValue Set: done=false
> > > >
> > > > The END_SUCCESS is the completion of the last app() in the prior
> > > iterate pass, which signals the response ("done") fifo using a shell
> > > script.
> > > >
> > > > The trace says its starting to process the next R request, #233
> > > (randomly assigned)
> > > >
> > > > after mapping 20 files (for 5 R datasets containing 2 R evaluation
> > > requests each)
> > > >
> > > > it just hangs, and all I see in the log after that point is
> > coaster
> > > heartbeats.
> > > >
> > > > The last request prior to this hanging request is in the log at
> > line
> > > 37137:
> > > >
> > > > 2010-09-16 12:03:24,060-0500 INFO  vdl:execute END_SUCCESS
> > > thread=0-1-85-4 tr=bash
> > > > 2010-09-16 12:03:24,062-0500 INFO  apply STARTCOMPOUND
> > > thread=0-1-86-2 name=apply
> > > > 2010-09-16 12:03:24,062-0500 WARN  trace SwiftScript trace:
> > rserver:
> > > got dir, /autonfs/home/wilde/SwiftR/SwiftR.run.174
> > > > 2010-09-16 12:03:24,062-0500 INFO  SetFieldValue Set: done=false
> > > >
> > > > R request #174 (and all prior ones) completed fine, and should
> > > illustrate the normal processing sequence.
> > > >
> > > > Any ideas on what to look for regarding the cause of the hang?
> > > >
> > > > I will try to reproduce it and try to get a karajan status trace
> > > using swift stdin.
> > > >
> > > > - Mike
> > > >
> > 
> > --
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
>

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