[Swift-devel] Re: Swift hanging in complex iterate script
wilde at mcs.anl.gov
wilde at mcs.anl.gov
Thu Sep 16 14:26:57 CDT 2010
~wilde/swiftrhang/rserver.swift
sites.xml, tc, and properties are in the same dir.
Launched swift from ~wilde/SwiftR/Swift/exec/RunRServer.sh:
swift -config swift.properties -tc.file tc -sites.file sites.xml $script \
>& swift.stdouterr
- Mike
----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:
> Can you point me to the swift script?
>
> Mihael
>
> On Thu, 2010-09-16 at 13:13 -0600, Michael Wilde wrote:
> > I see this suspicious deadlock in that jstack output:
> >
> > Found one Java-level deadlock:
> > =============================
> > "pool-1-thread-4":
> > waiting to lock monitor 0x0000000052b88650 (object
> 0x00002aaab5542348, a org.griphyn.vdl.mapping.RootDataNode),
> > which is held by "pool-1-thread-2"
> > "pool-1-thread-2":
> > waiting to lock monitor 0x0000000052b879d8 (object
> 0x00002aaab5542540, a org.griphyn.vdl.mapping.RootArrayDataNode),
> > which is held by "pool-1-thread-4"
> >
> > Java stack information for the threads listed above:
> > ===================================================
> > ...
> >
> > - Mike
> >
> > ----- "Michael Wilde" <wilde at mcs.anl.gov> wrote:
> >
> > > OK, thats in ~wilde/swiftrhang/jstack.out
> > >
> > > The jvm is still running: pid 22435 on bridled. Let me know if
> you
> > > need any other traces from it.
> > >
> > > It hung around 12:05
> > >
> > > - Mike
> > >
> > >
> > > bri$ 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
> >
--
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory
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