How to find and clear zombie processes w/o rebooting?

06-26-2008, 01:33 AM

Using F8, I have found that Nautilus sometimes hangs and
runs at 100% CPU. Force killing Nautilus's drive windows
was the only way to recover. I am not sure that force killing
this drive window is related to the zombie that I founding using
top.

I also discovered that my swap was increased to 2GB of 4GB
and has stayed there ever since.

So before I accuse Nautilus as being the zombie process, how
do I locate it using ps or some other tool to find out what is
going on and to what process the zombie was?

In the same breadth, is there a way to clear zombie processes
without being forced to reboot the system which would certainly
remove the zombie process and clear the swap space?

Thanks!
Dan

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06-26-2008, 01:52 AM

On 25Jun2008 18:33, Daniel B. Thurman <dant@cdkkt.com> wrote:
> Using F8, I have found that Nautilus sometimes hangs and
> runs at 100% CPU. Force killing Nautilus's drive windows
> was the only way to recover. I am not sure that force killing
> this drive window is related to the zombie that I founding using
> top.
> I also discovered that my swap was increased to 2GB of 4GB
> and has stayed there ever since.

Zombies are just process slots of exit()ed processes awaiting collection.
They do not consume CPU time or swap space.

> So before I accuse Nautilus as being the zombie process, how
> do I locate it using ps or some other tool to find out what is
> going on and to what process the zombie was?

Zombies are in the Z state. They are exited programs whose parents have
not called wait() to collect the exit status.

> In the same breadth, is there a way to clear zombie processes
> without being forced to reboot the system which would certainly
> remove the zombie process and clear the swap space?

Removing zombies will do NOTHING about your swap space, since they are
not consuming it. (Of course a reboot will clear the swap, as it does
everything else.)

They only way to clear a zombies process slot (which is all a zombie
process actually is) is to find the zombie's parent process (using ps'
"f" (forest) option, for example, or just looking at the PPID column)
and either causing the parent to do a wait() for the zombie if possible,
or to kill the parent (which will cause the zombies to be inherited by
process 1, which will then wait() for it, cleaning it up).

Zombies are essentially untidy but harmless. They are not eating you
machine's brains (ram/swap/cpu).

Cheers,
--
Cameron Simpson <cs@zip.com.au> DoD#743
http://www.cskk.ezoshosting.com/cs/

Zombies don't get pumped. - Jake, in rec.climbing

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06-26-2008, 01:52 AM

On Wed, 2008-06-25 at 18:33 -0700, Daniel B. Thurman wrote:
> Using F8, I have found that Nautilus sometimes hangs and
> runs at 100% CPU. Force killing Nautilus's drive windows
> was the only way to recover. I am not sure that force killing
> this drive window is related to the zombie that I founding using
> top.
>
> I also discovered that my swap was increased to 2GB of 4GB
> and has stayed there ever since.
>
> So before I accuse Nautilus as being the zombie process, how
> do I locate it using ps or some other tool to find out what is
> going on and to what process the zombie was?
>
> In the same breadth, is there a way to clear zombie processes
> without being forced to reboot the system which would certainly
> remove the zombie process and clear the swap space?
----
you have to kill the parent - you can locate the parent process by
running 'ps auxwwf'

Craig

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06-26-2008, 02:01 AM

Title: Re: How to find and clear zombie processes w/o rebooting?

Cameron Simpson wrote:

On 25Jun2008 18:33, Daniel B. Thurman
<dant@cdkkt.com> wrote:

> Using F8, I have found that Nautilus sometimes
hangs and

> runs at 100% CPU.* Force killing Nautilus's drive
windows

> was the only way to recover.* I am not sure that
force killing

> this drive window is related to the zombie that I
founding using

> top.

> I also discovered that my swap was increased to
2GB of 4GB

> and has stayed there ever since.

Zombies are just process slots of exit()ed
processes awaiting collection.

They do not consume CPU time or swap space.

> So before I accuse Nautilus as being the
zombie process, how

> do I locate it using ps or some other tool to
find out what is

> going on and to what process the zombie was?

Zombies are in the Z state. They are exited
programs whose parents have

not called wait() to collect the exit status.

> In the same breadth, is there a way to clear
zombie processes

> without being forced to reboot the system which
would certainly

> remove the zombie process and clear the swap
space?

Removing zombies will do NOTHING about your swap
space, since they are

not consuming it. (Of course a reboot will clear the
swap, as it does

everything else.)

They only way to clear a zombies process slot
(which is all a zombie

process actually is) is to find the zombie's parent
process (using ps'

"f" (forest) option, for example, or just looking at
the PPID column)

and either causing the parent to do a wait() for the
zombie if possible,

or to kill the parent (which will cause the zombies to
be inherited by

process 1, which will then wait() for it, cleaning it
up).

Zombies are essentially untidy but harmless. They
are not eating you

machine's brains (ram/swap/cpu).

Cheers,

--

Cameron Simpson <cs@zip.com.au> DoD#743

http://www.cskk.ezoshosting.com/cs/

Zombies don't get pumped.****** - Jake, in
rec.climbing

I like your signature

I did a ps aux | grep Z :

USER****** PID %CPU %MEM*** VSZ** RSS TTY***** STAT START** TIME COMMAND

dant***** 3902* 0.0* 0.0***** 0**** 0 ?******* Z*** Jun24** 0:00
[Xsession] <defunct>

Um - ok.* Something "burped" with the Xsession.* Wonder what happened.

I noticed that my system became slightly sluggish and I have no clue
what is

causing it.* I do know that a reboot will bring the system into a
'snappy' state

and my script that converts ape to mp3 and splits mp3 with a provided
cue

file and it really rips.* But then over the last few days, it started
slowing down

quite noticeably.

Ah- I think I will just do it the BGM$ way: just hit "reset"

Thanks for the pointer,

Dan

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06-26-2008, 02:08 AM

Title: Re: How to find and clear zombie processes w/o rebooting?

Craig White wrote:

On Wed, 2008-06-25 at 18:33 -0700, Daniel B.
Thurman wrote:

> Using F8, I have found that Nautilus sometimes
hangs and

> runs at 100% CPU.* Force killing Nautilus's drive
windows

> was the only way to recover.* I am not sure that
force killing

> this drive window is related to the zombie that I
founding using

> top.

>

> I also discovered that my swap was increased to
2GB of 4GB

> and has stayed there ever since.

>

> So before I accuse Nautilus as being the zombie
process, how

> do I locate it using ps or some other tool to
find out what is

> going on and to what process the zombie was?

>

> In the same breadth, is there a way to clear
zombie processes

> without being forced to reboot the system which
would certainly

> remove the zombie process and clear the swap
space?

----

you have to kill the parent - you can locate the
parent process by

running 'ps auxwwf'

Craig

Interesting!*

Looks like the parent is related to gdm-binary?

Strange about my comment previously - hit 'reset'

Wonder what is going on with Xsession and why it died.

This is what I found:

===================

root***** 3704* 0.0* 0.1* 18416* 2096 ?******* Ss** Jun24** 0:00
/usr/sbin/gdm-binary -nodaemon

root***** 3797* 0.0* 0.0* 17896* 2064 ?******* S*** Jun24** 0:00* \_
/usr/sbin/gdm-binary -nodaemon

root***** 3801* 2.4* 2.2* 63512 47528 tty7**** Ss+* Jun24* 40:15*****
\_ /usr/bin/X :0 -br -audit 0 -auth /var/gdm/:0.Xauth -nolisten tcp vt7

dant***** 3854* 0.0* 0.1* 33768* 4104 ?******* Ssl* Jun24** 0:01*****
\_ /usr/bin/gnome-session

dant***** 3902* 0.0* 0.0***** 0**** 0 ?******* Z*** Jun24**
0:00********* \_ [Xsession] <defunct>

dant***** 3956* 0.0* 0.0** 6328** 252 ?******* Ss** Jun24**
0:00********* \_ /usr/bin/ssh-agent /usr/bin/dbus-launch
--exit-with-session /etc/X11/xinit/Xclients

dant***** 3976* 0.3* 0.1* 53684* 3188 ?******* Sl** Jun24**
5:01********* \_ /usr/bin/pulseaudio --log-target=syslog

dant***** 3982* 0.0* 0.0** 5216* 1300 ?******* S*** Jun24**
0:00********* |** \_ /usr/libexec/pulse/gconf-helper

dant***** 3986* 0.0* 0.5* 45136 10576 ?******* S*** Jun24**
0:36********* \_ metacity --sm-client-id
110a010008000120153982800000046910003

dant***** 3989* 0.0* 0.7* 75252 15236 ?******* S*** Jun24**
0:09********* \_ gnome-panel --sm-config-prefix /gnome-panel-imrZa5/
--sm-client-id 110a010008000120153982700000046910001 --screen 0

dant***** 4013* 0.7* 0.3* 65148* 7292 ?******* S*** Jun24*
12:56********* \_ gkrellm --sm-client-id
110a010008000120794573900000093780003

dant***** 4026* 0.0* 0.7 127592 14612 ?******* Sl** Jun24**
1:33********* \_ gnome-terminal --sm-config-prefix
/gnome-terminal-1dtJD1/ --sm-client-id
110a010008000120153989800000046910008 --screen 0
--window-with-profile-internal-id=Default --show-menubar
--role=gnome-terminal-5108--2081150439-1201539898 --active --geometry
80x24+135+141 --title dant@gold:~ --working-directory /home/dant --zoom
1 --window-with-profile-internal-id=Default --show-menubar
--role=gnome-terminal-5108-574728165-1201539901 --active --geometry
80x24+135+550 --title dant@gold:~ --working-directory /home/dant --zoom
1 --window-with-profile-internal-id=Default --show-menubar
--role=gnome-terminal-5108-1143529827-1201539901 --active --geometry
80x24+799+141 --title dant@gold:~ --working-directory /home/dant --zoom
1 --window-with-profile-internal-id=Default --show-menubar
--role=gnome-terminal-5108--1131700843-1201539902 --active --geometry
80x24+799+550 --title dant@gold:~ --working-directory /home/dant --zoom
1

dant***** 4191* 0.0* 0.0** 2616** 628 ?******* S*** Jun24**
0:00********* |** \_ gnome-pty-helper

dant***** 4192* 0.0* 0.0** 5616* 1056 pts/1*** Ss** Jun24**
0:00********* |** \_ bash

root***** 5533* 0.0* 0.0** 4716** 916 pts/1*** S*** Jun24**
0:00********* |** |** \_ su

root***** 5539* 0.0* 0.0** 5620* 1608 pts/1*** S*** Jun24**
0:00********* |** |****** \_ bash

root**** 23634* 0.0* 0.0** 4016** 828 pts/1*** S+** 18:34**
0:00********* |** |********** \_ man ps

root**** 23654* 0.0* 0.0** 4652* 1092 pts/1*** S+** 18:34**
0:00********* |** |************** \_ sh -c /usr/bin/bzip2 -c -d
/var/cache/man/cat1/ps.1.bz2 | /usr/bin/less -is

root**** 23656* 0.0* 0.0** 4372** 932 pts/1*** S+** 18:34**
0:00********* |** |****************** \_ /usr/bin/less -is

dant***** 4198* 0.0* 0.0** 5616* 2016 pts/2*** Ss** Jun24**
0:00********* |** \_ bash

root**** 23690* 0.0* 0.0** 4716* 1232 pts/2*** S*** 18:36**
0:00********* |** |** \_ su

root**** 23697* 0.0* 0.1** 5620* 2480 pts/2*** S*** 18:36**
0:00********* |** |****** \_ bash

root**** 24340* 1.0* 0.0** 4652** 980 pts/2*** R+** 19:02**
0:00********* |** |********** \_ ps auxwwf

dant***** 4203* 0.0* 0.0** 5616* 2036 pts/3*** Ss+* Jun24**
0:00********* |** \_ bash

dant***** 4215* 0.0* 0.0** 5616* 1056 pts/4*** Ss+* Jun24**
0:00********* |** \_ bash

dant***** 5267* 0.0* 0.0** 5608* 1056 pts/6*** Ss** Jun24**
0:00********* |** \_ bash

root***** 5329* 0.0* 0.0** 4716** 916 pts/6*** S*** Jun24**
0:00********* |** |** \_ su

root***** 5339* 0.0* 0.0** 5620* 1912 pts/6*** S+** Jun24**
0:00********* |** |****** \_ bash

dant**** 10269* 0.0* 0.0** 5616* 1056 pts/5*** Ss** Jun24**
0:00********* |** \_ bash

root**** 10328* 0.0* 0.0** 4716** 936 pts/5*** S*** Jun24**
0:00********* |****** \_ su

root**** 10335* 0.0* 0.0** 5912* 1728 pts/5*** S*** Jun24**
0:00********* |********** \_ bash

root**** 24065* 0.0* 0.0** 3824** 528 pts/5*** S+** 18:51**
0:00********* |************** \_ tail -f /var/log/messages

dant***** 4040 19.5 30.2 3125956 624924 ?***** Sl** Jun24
326:57********* \_ strigidaemon

dant***** 4044* 0.0* 0.1* 28888* 2504 ?******* SNl* Jun24**
0:00********* \_ pinot-dbus-daemon

dant***** 4185* 0.0* 0.0** 3796** 372 ?******* S*** Jun24**
0:00********* |** \_ /bin/cat

dant***** 4046* 0.0* 0.2* 69920* 5456 ?******* S*** Jun24**
0:16********* \_ mugshot --no-show-window

dant***** 4054* 0.0* 0.2* 20480* 4796 ?******* S*** Jun24**
0:00********* \_ tracker-applet

dant***** 4055* 0.0* 0.1* 39268* 3696 ?******* SNl* Jun24**
0:17********* \_ trackerd

dant***** 4061* 0.0* 0.0** 4148* 1792 ?******* S*** Jun24**
0:00********* \_ online-prefs-sync-daemon

dant***** 4064* 0.0* 0.4* 78908* 8976 ?******* S*** Jun24**
0:00********* \_ /usr/bin/python -tt /usr/bin/puplet

dant***** 4065* 0.0* 0.2* 28192* 4588 ?******* S*** Jun24**
0:00********* \_ python /usr/share/system-config-printer/applet.py

dant***** 4072* 0.0* 0.2* 99360* 4148 ?******* S*** Jun24**
0:00********* \_ nm-applet --sm-disable

dant***** 4078* 0.0* 0.1* 65020* 4012 ?******* S*** Jun24**
0:00********* \_ padevchooser

dant***** 4118* 0.0* 0.1* 17476* 3416 ?******* S*** Jun24**
0:00********* \_ /usr/bin/pam-panel-icon --sm-client-id
110a010008000120153983200000046910006

root***** 4136* 0.0* 0.0** 1956** 580 ?******* S*** Jun24**
0:04********* |** \_ /sbin/pam_timestamp_check -d root

dant**** 23276* 0.5* 2.0 142092 42544 ?******* S*** 18:18**
0:15********* \_ nautilus --sm-config-prefix /nautilus-vN3JUZ/
--sm-client-id 110a010008000120153982700000046910002 --screen 0

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