port math/gnuplot hangs and ignores "kill -9"

[Anton Shterenlikht]

on ia64 HEAD,  gnuplot-4.2.6, any plot command
hangs the program. top shows gnuplot is using 100% of CPU,
yeat CPU time is zero:

  PID    UID    THR PRI NICE   SIZE    RES STATE   C   TIME   WCPU COMMAND
60071   1001      2  48    0 98008K 51424K CPU1    1   0:00 100.00% gnuplot

kill -9 60071, either from my account, or from root,
has no effect, the process is still there.

I cannot find a way to terminate this hanged process without reboot.

This seems to be a regression.

Please advise

many thanks

--
Anton Shterenlikht
Room 2.6, Queen's Building
Mech Eng Dept
Bristol University
University Walk, Bristol BS8 1TR, UK
Tel: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."

[Anton Shterenlikht]

On Mon, Sep 14, 2009 at 04:37:28PM +0100, Anton Shterenlikht wrote:

> on ia64 HEAD,  gnuplot-4.2.6, any plot command
> hangs the program. top shows gnuplot is using 100% of CPU,
> yeat CPU time is zero:
>
>   PID    UID    THR PRI NICE   SIZE    RES STATE   C   TIME   WCPU COMMAND
> 60071   1001      2  48    0 98008K 51424K CPU1    1   0:00 100.00% gnuplot
>
> kill -9 60071, either from my account, or from root,
> has no effect, the process is still there.
>
> I cannot find a way to terminate this hanged process without reboot.
>
> This seems to be a regression.

running gnuplot in batch (non-interactive) mode seems fine, so
the problem seems to be with the screen terminal.

I'm mostly puzzled by the fact that I cannot kill the process..

--
Anton Shterenlikht
Room 2.6, Queen's Building
Mech Eng Dept
Bristol University
University Walk, Bristol BS8 1TR, UK
Tel: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."

[Roland Smith]

On Mon, Sep 14, 2009 at 04:42:41PM +0100, Anton Shterenlikht wrote:

> On Mon, Sep 14, 2009 at 04:37:28PM +0100, Anton Shterenlikht wrote:
> > on ia64 HEAD,  gnuplot-4.2.6, any plot command
> > hangs the program. top shows gnuplot is using 100% of CPU,
> > yeat CPU time is zero:
> >
> >   PID    UID    THR PRI NICE   SIZE    RES STATE   C   TIME   WCPU COMMAND
> > 60071   1001      2  48    0 98008K 51424K CPU1    1   0:00 100.00% gnuplot
> >
> > kill -9 60071, either from my account, or from root,
> > has no effect, the process is still there.
> >
> > I cannot find a way to terminate this hanged process without reboot.
> >
> > This seems to be a regression.
>
> running gnuplot in batch (non-interactive) mode seems fine, so
> the problem seems to be with the screen terminal.
>
> I'm mostly puzzled by the fact that I cannot kill the process..

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.

Roland
--
R.F.Smith                                   http://www.xs4all.nl/~rsmith/
[plain text _non-HTML_ PGP/GnuPG encrypted/signed email much appreciated]
pgp: 1A2B 477F 9970 BA3C 2914  B7CE 1277 EFB0 C321 A725 (KeyID: C321A725)

[Anton Shterenlikht]

On Mon, Sep 14, 2009 at 07:22:33PM +0200, Roland Smith wrote:

> On Mon, Sep 14, 2009 at 04:42:41PM +0100, Anton Shterenlikht wrote:
> > On Mon, Sep 14, 2009 at 04:37:28PM +0100, Anton Shterenlikht wrote:
> > > on ia64 HEAD,  gnuplot-4.2.6, any plot command
> > > hangs the program. top shows gnuplot is using 100% of CPU,
> > > yeat CPU time is zero:
> > >
> > >   PID    UID    THR PRI NICE   SIZE    RES STATE   C   TIME   WCPU COMMAND
> > > 60071   1001      2  48    0 98008K 51424K CPU1    1   0:00 100.00% gnuplot
> > >
> > > kill -9 60071, either from my account, or from root,
> > > has no effect, the process is still there.
> > >
> > > I cannot find a way to terminate this hanged process without reboot.
> > >
> > > This seems to be a regression.
> >
> > running gnuplot in batch (non-interactive) mode seems fine, so
> > the problem seems to be with the screen terminal.
> >
> > I'm mostly puzzled by the fact that I cannot kill the process..
>
> 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.

My guess is that the problem is not in gnuplot, but in the base OS.

Any advice on how to debug this problem further.

Once again, batch use of gnuplot is fine, it's just the screen
operations which are affected.

many thanks
anton

--
Anton Shterenlikht
Room 2.6, Queen's Building
Mech Eng Dept
Bristol University
University Walk, Bristol BS8 1TR, UK
Tel: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."

[Roland Smith]

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?

Roland
--
R.F.Smith                                   http://www.xs4all.nl/~rsmith/
[plain text _non-HTML_ PGP/GnuPG encrypted/signed email much appreciated]
pgp: 1A2B 477F 9970 BA3C 2914  B7CE 1277 EFB0 C321 A725 (KeyID: C321A725)

[Anton Shterenlikht]

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?

many thanks

--
Anton Shterenlikht
Room 2.6, Queen's Building
Mech Eng Dept
Bristol University
University Walk, Bristol BS8 1TR, UK
Tel: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."

[Roland Smith]

On Thu, Sep 17, 2009 at 02:40:24PM +0100, Anton Shterenlikht wrote:
> > > 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 ?

Looks that way. Since gnuplot works very well with plain X11, I've never
bothered building it with wxWidgets. Rebuild gnuplot without wxWidgets to
circumvent the problem.

> How can I kill the offending gnuplot process?

You can try 'kill -9'. If the process is stuck in the 'D' state after you've
tried that, you'll have to reboot. :-)

Roland
--
R.F.Smith                                   http://www.xs4all.nl/~rsmith/
[plain text _non-HTML_ PGP/GnuPG encrypted/signed email much appreciated]
pgp: 1A2B 477F 9970 BA3C 2914  B7CE 1277 EFB0 C321 A725 (KeyID: C321A725)

[Anton Shterenlikht]

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?

many thanks
anton

--
Anton Shterenlikht
Room 2.6, Queen's Building
Mech Eng Dept
Bristol University
University Walk, Bristol BS8 1TR, UK
Tel: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."

[Anton Shterenlikht]

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: [phone]
Fax: [phone]
_______________________________________________
freebsd-ia64@... mailing list
http://lists.freebsd.org/mailman/listinfo/freebsd-ia64
To unsubscribe, send any mail to "freebsd-ia64-unsubscribe@..."