Date: Fri, 18 Sep 2009 11:45:42 +0100 From: Anton Shterenlikht <mexas@bristol.ac.uk> To: Mel Flynn <mel.flynn+fbsd.questions@mailing.thruhere.net> Cc: freebsd-ia64@freebsd.org Subject: Re: mpt timed out and Re: port math/gnuplot hangs and ignores "kill -9" Message-ID: <20090918104542.GD50951@mech-cluster241.men.bris.ac.uk> In-Reply-To: <200909171941.59489.mel.flynn%2Bfbsd.questions@mailing.thruhere.net> References: <20090914153728.GA60162@mech-cluster241.men.bris.ac.uk> <20090917134024.GA2350@mech-cluster241.men.bris.ac.uk> <20090917135743.GA1013@mech-cluster241.men.bris.ac.uk> <200909171941.59489.mel.flynn%2Bfbsd.questions@mailing.thruhere.net>
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On Thu, Sep 17, 2009 at 07:41:59PM +0200, Mel Flynn wrote: > On Thursday 17 September 2009 15:57:43 Anton Shterenlikht wrote: > > On Thu, Sep 17, 2009 at 02:40:24PM +0100, Anton Shterenlikht wrote: > > > On Thu, Sep 17, 2009 at 03:16:16PM +0200, Roland Smith wrote: > > > > On Thu, Sep 17, 2009 at 01:34:04PM +0100, Anton Shterenlikht wrote: > > > > > > It could be that the process is stuck in the 'D' state > > > > > > (uninterruptable wait). You can veryfiy that by running 'ps -u' and > > > > > > looking in the eight column when gnuplot is running. > > > > > > > > > > > > Does the window with the plot actually appear? > > > > > > > > > > > > Interactive use of gnuplot-4.2.6 is fine on amd64 7.2-RELEASE-p2. > > > > > > > > > > I reinstalled gnuplot-4.2.6 and (hopefully) all ports on which it > > > > > depends. I still get the same behaviour. > > > > > > > > > > top -PISu shows: > > > > > > > > > > last pid: 108; load averages: 0.88, 0.35, 0.19 up 2+02:23:38 > > > > > 13:27:52 109 processes: 4 running, 88 sleeping, 17 waiting > > > > > CPU 0: 0.0% user, 0.0% nice, 0.0% system, 0.0% interrupt, 100% > > > > > idle CPU 1: 0.0% user, 0.0% nice, 100% system, 0.0% interrupt, > > > > > 0.0% idle Mem: 105M Active, 2074M Inact, 363M Wired, 768K Cache, 827M > > > > > Buf, 5322M Free Swap: 19G Total, 19G Free > > > > > > > > > > PID UID THR PRI NICE SIZE RES STATE C TIME WCPU > > > > > COMMAND 11 0 2 171 ki31 0K 64K RUN 0 77.9H > > > > > 100.00% idle 99992 1001 2 48 0 98240K 55608K CPU1 1 > > > > > 0:00 100.00% gnuplot > > > > > > > > > > so gnuplot is using 100% and all in system state. > > > > > > > > > > and ps -u: > > > > > > > > > > USER PID %CPU %MEM VSZ RSS TT STAT STARTED TIME COMMAND > > > > > mexas 99992 98.1 0.7 98240 55608 5 R+ 1:25pm 0:00.72 gnuplot > > > > > > > > > > so the state is not "D". > > > > > > > > > > The window does appear (just using simple gnuplot> plot sin(x), and > > > > > the terminal is set to 'wxt', but nothing ever apears in the window. > > > > > > > > The wxt terminal is only available when gnuplot is compiled with the > > > > wxWidgets toolkit. Try using the plain x11 terminal, and see if that > > > > works better? > > > > > > yes, that works fine! Thank you! > > > > > > So the problem must be with wxgtk2-2.8.10_1 and wxgtk2-common-2.8.10_1 ? > > > > > > How can I kill the offending gnuplot process? > > > > On reboot I see this on the console: > > > > System shutdown time has arrived > > Stopping cron. > > Stopping sshd. > > Stopping ntpd. > > Stopping devd. > > Writing entropy file:mpt0: request 0xa0000000000d2140:52792 timed out for > > ccb 0x > > > > e000000019ece800 (req->ccb 0xe000000019ece800) > > mpt0: completing timedout/aborted req 0xa0000000000d2140:52792 > > mpt0: Timedout requests already complete. Interrupts may not be > > functioning. Sep 17 14:49:59 mech-cluster241 syslogd: exiting on signal 15 > > Sep 17 14:49:59 init: timeout expired for /bin/sh on /etc/rc.shutdown: > > Interrupt > > > > ed system call; going to single user mode > > Sep 17 14:50:19 init: some processes would not die; ps axl advised > > Waiting (max 60 seconds) for system process `vnlru' to stop...done > > Waiting (max 60 seconds) for system process `bufdaemon' to stop...done > > Waiting (max 60 seconds) for system process `syncer' to stop... > > Syncing disks, vnodes remaining...3 1 2 > > > > > > I'm a bit worried about mpt0 messages - this is the SCSI driver. > > Does this indicate a problem with mpt? > > Since gnuplot was spinning in kernel mode, all bets are off. This timeout is > most likely a side effect from that, unless you see this every reboot not just > with an unkillable gnuplot. > > If your system has the ability to run procstat -k, you might find out what > gnuplot is spinning on. You'll need at least a 7.x system, but I'm not sure if > kernelthreads are supported on ia64 and kernel needs to have STACK or DDB > options. Marcel, are kernel threads supported on ia64? My ia64 system is 9.0-current. I've DDB in the kernel. I've rebuilt gnuplot without wxWidgets toolkit, so I don't have this problem now, but for the future, does this look right: > procstat -k 51055 PID TID COMM TDNAME KSTACK 51055 100114 gnuplot initial thread > many thanks anton -- Anton Shterenlikht Room 2.6, Queen's Building Mech Eng Dept Bristol University University Walk, Bristol BS8 1TR, UK Tel: +44 (0)117 331 5944 Fax: +44 (0)117 929 4423
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