Debian Bug report logs - #562503
upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: tony mancill <tmancill@debian.org>

To: submit@bugs.debian.org

Subject: upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Thu, 24 Dec 2009 15:59:44 -0800

Package: man-db
Version: 2.5.6-4
Severity: important

After the most recent upgrade (pure sid system), man-db hangs and consumes
all available cpu.


$ sudo dpkg --configure -a
Setting up man-db (2.5.6-4) ...
Updating database of manual pages ...

(open another console to see what's going on)

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 4311 man       20   0 22972 1516  484 R  101  0.1  25:27.68 mandb

(wait at bit longer)

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 4311 man       20   0 22972 1516  484 R   99  0.1  30:21.86 mandb

and so on...

I can stop the installation with CTRL-C and see:

$ sudo dpkg --configure -a
Setting up man-db (2.5.6-4) ...
Updating database of manual pages ...
^Cdpkg: error processing man-db (--configure):
 subprocess installed post-installation script killed by signal (Interrupt)
Errors were encountered while processing:
 man-db

I then edited the postinst and removed the -q argument from the calls to
run_mandb and received the following output:

$ sudo dpkg --configure -a
Setting up man-db (2.5.6-4) ...
Updating database of manual pages ...
Processing manual pages under /usr/share/man...
Processing manual pages under /usr/share/man/zh_TW...
Processing manual pages under /usr/share/man/vi...
Processing manual pages under /usr/share/man/ko...
Processing manual pages under /usr/share/man/ru...
Processing manual pages under /usr/share/man/sv...
Processing manual pages under /usr/share/man/de...
Processing manual pages under /usr/share/man/it...
Processing manual pages under /usr/share/man/tr...
Processing manual pages under /usr/share/man/fr.UTF-8...
Processing manual pages under /usr/share/man/ja...
Updating index cache for path `/usr/share/man/ja/man5'. Wait...

(and here it hung again)


What other information would be helpful in tracking down this behavior?

Thank you,
Tony

-- System Information:
Debian Release: squeeze/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 2.6.31-1-amd64 (SMP w/2 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages man-db depends on:
ii  bsdmainutils            8.0.3            collection of more utilities from
ii  debconf [debconf-2.0]   1.5.28           Debian configuration management sy
ii  dpkg                    1.15.5.5         Debian package management system
ii  groff-base              1.20.1-6         GNU troff text-formatting system (
ii  libc6                   2.10.2-2         GNU C Library: Shared libraries
ii  libgdbm3                1.8.3-9          GNU dbm database routines (runtime
ii  zlib1g                  1:1.2.3.4.dfsg-1 compression library - runtime

man-db recommends no packages.

Versions of packages man-db suggests:
ii  groff                         1.20.1-6   GNU troff text-formatting system
ii  less                          436-1      pager program similar to more
ii  w3m [www-browser]             0.5.2-2.1  WWW browsable pager with excellent

-- debconf information:
  man-db/install-setuid: false
  man-db/auto-update: true

Message #10 received at 562503@bugs.debian.org (full text, mbox, reply):

From: tony mancill <tmancill@debian.org>

To: 562503@bugs.debian.org

Subject: it's not just that man-db is long-running

Date: Thu, 24 Dec 2009 21:24:34 -0800

I opted to try to let man-db run longer to configure itself, but to no
avail.  This is on a dual-core 2GHz Athlon:

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND

 4811 man       20   0 23100 1516  488 R  100  0.1 324:59.69 mandb

Message #15 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Frans Pop <elendil@planet.nl>

To: 562503@bugs.debian.org

Subject: #562503 upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 13:01:54 +0100

severity 562503 serious
thanks

I'm seeing the same issue in an amd64/sid pbuilder environment when mandb
gets installed as one of the build dependencies of cdebconf-entropy.

If I kill the mandb PID I get:
/usr/bin/mandb: /usr/lib/man-db/manconv -f UTF-8:EUC-JP -t UTF-8//IGNORE -q: Terminated

But that does not solve it as the same process restarts again.

Message #22 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Jurriaan <thunder7@xs4all.nl>

To: Debian Bug Tracking System <562503@bugs.debian.org>

Subject: Re: of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 13:07:30 +0100

Package: man-db
Version: 2.5.6-4
Severity: normal


Additional information:

running strace on the mandb process while it hangs, reveals an endles list of

read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0
read(9, "", 65535)                      = 0

lsof -p 6733 output:

COMMAND  PID USER   FD   TYPE DEVICE SIZE/OFF   NODE NAME
mandb   6733  man  cwd    DIR    8,1     4096 613478 /usr/share/man/ja
mandb   6733  man  rtd    DIR    8,1     4096      2 /
mandb   6733  man  txt    REG    8,1   177416 582133 /usr/bin/mandb
mandb   6733  man  mem    REG    8,1    99632 662899 /usr/lib/gconv/libJIS.so
mandb   6733  man  mem    REG    8,1    42572 496814 /lib/i686/cmov/libnss_files-2.10.2.so
mandb   6733  man  mem    REG    8,1    38504 496817 /lib/i686/cmov/libnss_nis-2.10.2.so
mandb   6733  man  mem    REG    8,1    79676 496834 /lib/i686/cmov/libnsl-2.10.2.so
mandb   6733  man  mem    REG    8,1    30496 496824 /lib/i686/cmov/libnss_compat-2.10.2.so
mandb   6733  man  mem    REG    8,1  1330784 679753 /usr/lib/locale/locale-archive
mandb   6733  man  mem    REG    8,1  1331684 496835 /lib/i686/cmov/libc-2.10.2.so
mandb   6733  man  mem    REG    8,1    79980 850568 /usr/lib/libz.so.1.2.3.4
mandb   6733  man  mem    REG    8,1    19788 639527 /usr/lib/libgdbm.so.3.0.0
mandb   6733  man  mem    REG    8,1    13624 662852 /usr/lib/gconv/EUC-JP.so
mandb   6733  man  mem    REG    8,1    26048 662909 /usr/lib/gconv/gconv-modules.cache
mandb   6733  man  mem    REG    8,1   117416 499033 /lib/ld-2.10.2.so
mandb   6733  man    0r  FIFO    0,6      0t0 207126 pipe
mandb   6733  man    1w  FIFO    0,6      0t0 207127 pipe
mandb   6733  man    2u   CHR  136,0      0t0      3 /dev/pts/0
mandb   6733  man    3w  FIFO    0,6      0t0 207076 pipe
mandb   6733  man    4r   DIR    8,1     4096 605321 /usr/share/man
mandb   6733  man    5r   DIR    8,1     4096 613478 /usr/share/man/ja
mandb   6733  man    6u   REG    8,1    18358 464335 /var/cache/man/ja/6726
mandb   6733  man    7r   DIR    8,1     4096 662343 /usr/share/man/ja/man5
mandb   6733  man    9r  FIFO    0,6      0t0 207128 pipe

Applying a big hammer to this problem and typing rm -rf /usr/share/man/ja from another terminal,
then applying control-C to the endless man-db process did, however, allow the dpkg --configure -a
process to continue. I think I will survive without Japanese man-pages until the next version :-)

Good luck,
Jurriaan

-- System Information:
Debian Release: squeeze/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: i386 (i686)

Kernel: Linux 2.6.32 (SMP w/2 CPU cores; PREEMPT)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages man-db depends on:
ii  bsdmainutils            8.0.3            collection of more utilities from 
ii  debconf [debconf-2.0]   1.5.28           Debian configuration management sy
ii  dpkg                    1.15.5.5         Debian package management system
ii  groff-base              1.20.1-6         GNU troff text-formatting system (
ii  libc6                   2.10.2-2         GNU C Library: Shared libraries
ii  libgdbm3                1.8.3-9          GNU dbm database routines (runtime
ii  zlib1g                  1:1.2.3.4.dfsg-1 compression library - runtime

man-db recommends no packages.

Versions of packages man-db suggests:
ii  elinks [www-browser]      0.12~pre5-1+b1 advanced text-mode WWW browser
ii  epiphany-browser [www-bro 2.29.3-1       Intuitive GNOME web browser
pn  groff                     <none>         (no description available)
ii  iceweasel [www-browser]   3.5.5-1        lightweight web browser based on M
ii  less                      436-1          pager program similar to more
ii  w3m [www-browser]         0.5.2-2.1      WWW browsable pager with excellent

-- debconf information:
  man-db/install-setuid: false
  man-db/auto-update: true

Message #27 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Kurt Roeckx <kurt@roeckx.be>

To: 562503@bugs.debian.org

Subject: Re: upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 14:34:30 +0100

On Thu, Dec 24, 2009 at 03:59:44PM -0800, tony mancill wrote:
> Package: man-db
> Version: 2.5.6-4
> Severity: important
> 
> $ sudo dpkg --configure -a
> Setting up man-db (2.5.6-4) ...
> Updating database of manual pages ...
> 
> (open another console to see what's going on)
> 
>   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
>  4311 man       20   0 22972 1516  484 R  101  0.1  25:27.68 mandb

Alot of the buildds are currently doing this, and in a completly
useless state now.  I see I have 1 of them doing this for 16 hours
now.


Kurt

Message #32 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Kurt Roeckx <kurt@roeckx.be>

To: 562503@bugs.debian.org

Subject: Re: upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 14:51:58 +0100

On Fri, Dec 25, 2009 at 02:34:30PM +0100, Kurt Roeckx wrote:
> On Thu, Dec 24, 2009 at 03:59:44PM -0800, tony mancill wrote:
> > Package: man-db
> > Version: 2.5.6-4
> > Severity: important
> > 
> > $ sudo dpkg --configure -a
> > Setting up man-db (2.5.6-4) ...
> > Updating database of manual pages ...
> > 
> > (open another console to see what's going on)
> > 
> >   PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
> >  4311 man       20   0 22972 1516  484 R  101  0.1  25:27.68 mandb
> 
> Alot of the buildds are currently doing this, and in a completly
> useless state now.  I see I have 1 of them doing this for 16 hours
> now.

This is probably caused by a change in zlib1g.  See
http://bugs.debian.org/562518
http://bugs.debian.org/301283


Kurt

Message #37 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Mark Brown <broonie@debian.org>

To: Lucas Nussbaum <lucas@lucas-nussbaum.net>, 562518@bugs.debian.org

Cc: 562503@bugs.debian.org

Subject: Re: Bug#562518: zlib1g 1:1.2.3.4.dfsg-1 hangs(?)

Date: Fri, 25 Dec 2009 15:05:13 +0000

On Fri, Dec 25, 2009 at 11:33:05AM +0100, Lucas Nussbaum wrote:

> If, in a clean minimal chroot, I install zlib1g from testing first, then
> install man-db, it works fine.

> My guess is that it is related to the fixing of #301283.

As far as I can tell zlib is performing correctly here, the man-db
process doing the decompression exits correctly having detected EOF and
closed the file, then exits.  The read() that's spinning with zero bytes
is certainly not a zlib one, it reads data in 16384 byte chunks but
that's a read of 65535 bytes (and the man-db debug output says the
process that's spinning is a manconv one.

That said, I can't immediately spot a problem in the man-db code and
reverting the explict reporting of EOF in zlib makes man-db stop falling
over so I'll upload a package just now.

Message #42 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Mark Brown <broonie@debian.org>

To: Lucas Nussbaum <lucas@lucas-nussbaum.net>, 562518@bugs.debian.org

Cc: 562503@bugs.debian.org

Subject: Re: Bug#562518: zlib1g 1:1.2.3.4.dfsg-1 hangs(?)

Date: Fri, 25 Dec 2009 19:12:25 +0000

On Fri, Dec 25, 2009 at 03:05:12PM +0000, Mark Brown wrote:

> As far as I can tell zlib is performing correctly here, the man-db
> process doing the decompression exits correctly having detected EOF and
> closed the file, then exits.  The read() that's spinning with zero bytes
> is certainly not a zlib one, it reads data in 16384 byte chunks but
> that's a read of 65535 bytes (and the man-db debug output says the
> process that's spinning is a manconv one.

> That said, I can't immediately spot a problem in the man-db code and
> reverting the explict reporting of EOF in zlib makes man-db stop falling
> over so I'll upload a package just now.

Having looked further there was a problem with zlib truncating output
which should now be fixed with the change I made, however this shouldn't
explain the spin in man-db so there may still be a latent bug there
that's worth looking into.

Message #47 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Frans Pop <elendil@planet.nl>

To: 562503@bugs.debian.org

Subject: Re: #562503 upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 20:16:26 +0100

On Friday 25 December 2009, Frans Pop wrote:
> I'm seeing the same issue in an amd64/sid pbuilder environment when
> mandb gets installed as one of the build dependencies of
> cdebconf-entropy.

To show the severity of the issue, this is from my sparc box during a 
regular upgrade (last one was 2 months ago):
 9630 man       20   0  5448 1960  680 R 98.8  0.2  54:11.05 mandb

And no idea how much longer it's going to take.

One problem is that there is absolutely no indication man-db is doing 
anything special. It just shows:
   Processing triggers for man-db ...

Users are very likely to conclude something is in an endless loop.

And even if it did show some king of progress, processes that take so much 
time IMO shouldn't be done from maintainer scripts. An upgrade should be 
completed within a reasonable time to avoid the risk of leaving random 
services of unrelated packages stopped for so long.

Message #52 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Mark Brown <broonie@debian.org>

To: Frans Pop <elendil@planet.nl>, 562503@bugs.debian.org

Subject: Re: Bug#562503: #562503 upgrade of man-db hangs during postinst, consumes 100% cpu for over 30 minutes

Date: Fri, 25 Dec 2009 19:22:29 +0000

On Fri, Dec 25, 2009 at 08:16:26PM +0100, Frans Pop wrote:

> To show the severity of the issue, this is from my sparc box during a 
> regular upgrade (last one was 2 months ago):
>  9630 man       20   0  5448 1960  680 R 98.8  0.2  54:11.05 mandb

> And no idea how much longer it's going to take.

It will spin for ever unless you kill man-db.  A fix has already been
accepted into the archive (it's triggered by a change in zlib, though
the spinning appears to be an issue in man-db).

> Users are very likely to conclude something is in an endless loop.

It is in an endless loop.

Message #59 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Stefano Zacchiroli <zack@debian.org>

To: Mark Brown <broonie@debian.org>

Cc: 562503@bugs.debian.org, 562518@bugs.debian.org

Subject: Re: Bug#562503: Bug#562518: zlib1g 1:1.2.3.4.dfsg-1 hangs(?)

Date: Tue, 29 Dec 2009 12:00:55 +0100

severity 562503 normal
severity 562518 grave
thanks 

[ wrong bug number in the previous post, I'm fixing up my own mess ]

On Fri, Dec 25, 2009 at 07:12:25PM +0000, Mark Brown wrote:
> > That said, I can't immediately spot a problem in the man-db code and
> > reverting the explict reporting of EOF in zlib makes man-db stop falling
> > over so I'll upload a package just now.
> 
> Having looked further there was a problem with zlib truncating output
> which should now be fixed with the change I made, however this shouldn't
> explain the spin in man-db so there may still be a latent bug there
> that's worth looking into.

Agreed, but this is anyhow no longer RC. I'm hence downgrading severity
to "normal", leaving up to the maintainer investigation or closure.

Thanks for your feedback,
Cheers.

-- 
Stefano Zacchiroli -o- PhD in Computer Science \ PostDoc @ Univ. Paris 7
zack@{upsilon.cc,pps.jussieu.fr,debian.org} -<>- http://upsilon.cc/zack/
Dietro un grande uomo c'è ..|  .  |. Et ne m'en veux pas si je te tutoie
sempre uno zaino ...........| ..: |.... Je dis tu à tous ceux que j'aime

Message #68 received at 562503@bugs.debian.org (full text, mbox, reply):

From: Colin Watson <cjwatson@debian.org>

To: Mark Brown <broonie@debian.org>, 562503@bugs.debian.org

Cc: Lucas Nussbaum <lucas@lucas-nussbaum.net>, 562518@bugs.debian.org, tony mancill <tmancill@debian.org>, Kurt Roeckx <kurt@roeckx.be>, Joern Heissler <debianbugs@joern.heissler.de>, Jurriaan <thunder7@xs4all.nl>, Frans Pop <elendil@planet.nl>, Stefano Zacchiroli <zack@debian.org>, Guillem Jover <guillem@debian.org>, 562535@bugs.debian.org

Subject: Re: Bug#562503: Bug#562518: zlib1g 1:1.2.3.4.dfsg-1 hangs(?)

Date: Fri, 1 Jan 2010 13:34:08 +0000

On Fri, Dec 25, 2009 at 03:05:13PM +0000, Mark Brown wrote:
> On Fri, Dec 25, 2009 at 11:33:05AM +0100, Lucas Nussbaum wrote:
> > If, in a clean minimal chroot, I install zlib1g from testing first, then
> > install man-db, it works fine.
> 
> > My guess is that it is related to the fixing of #301283.
> 
> As far as I can tell zlib is performing correctly here, the man-db
> process doing the decompression exits correctly having detected EOF and
> closed the file, then exits.  The read() that's spinning with zero bytes
> is certainly not a zlib one, it reads data in 16384 byte chunks but
> that's a read of 65535 bytes (and the man-db debug output says the
> process that's spinning is a manconv one.
> 
> That said, I can't immediately spot a problem in the man-db code and
> reverting the explict reporting of EOF in zlib makes man-db stop falling
> over so I'll upload a package just now.

Thanks to those who worked on tracking this down and mitigating it. I
was away over Christmas and so didn't see this report until today.

The core problem was zlib sometimes truncating output by reporting EOF
too early, which Mark fixed in 1:1.2.3.4.dfsg-3. This in turn exposed an
infinite loop bug in manconv when it sees an incomplete multibyte
character at the end of an input file. This only happened with multibyte
legacy encodings, hence why a number of people reported this happening
with Japanese pages.

I've uploaded a fix for this in man-db 2.5.6-5. Here are the upstream
changelog entries, for the record (I made a slight mistake in the first
attempt, caught during testing):

Fri Jan  1 13:26:21 GMT 2010  Colin Watson  <cjwatson@debian.org>

        * src/manconv.c (try_iconv): Only handle iconv errors when iconv
          returned -1.

Fri Jan  1 11:37:13 GMT 2010  Colin Watson  <cjwatson@debian.org>

        * src/manconv.c (try_iconv): Handle iconv errors when attempting to
          convert the last input encoding to UTF-8 (Debian bug #562503).
        * src/tests/manconv-3: Add test for this.
        * src/tests/Makefile.am (TESTS): Add manconv-3.

Mark, as far as I can see, you can drop the workaround in zlib
1:1.2.3.4.dfsg-2. The fix in 1:1.2.3.4.dfsg-3 is sufficient even without
the fix in man-db 2.5.6-5.

-- 
Colin Watson                                       [cjwatson@debian.org]

Message #73 received at 562503-close@bugs.debian.org (full text, mbox, reply):

From: Colin Watson <cjwatson@debian.org>

To: 562503-close@bugs.debian.org

Subject: Bug#562503: fixed in man-db 2.5.6-5

Date: Fri, 01 Jan 2010 13:47:25 +0000

Source: man-db
Source-Version: 2.5.6-5

We believe that the bug you reported is fixed in the latest version of
man-db, which is due to be installed in the Debian FTP archive:

man-db_2.5.6-5.diff.gz
  to main/m/man-db/man-db_2.5.6-5.diff.gz
man-db_2.5.6-5.dsc
  to main/m/man-db/man-db_2.5.6-5.dsc
man-db_2.5.6-5_i386.deb
  to main/m/man-db/man-db_2.5.6-5_i386.deb



A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 562503@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Colin Watson <cjwatson@debian.org> (supplier of updated man-db package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 1.8
Date: Fri, 01 Jan 2010 13:27:06 +0000
Source: man-db
Binary: man-db
Architecture: source i386
Version: 2.5.6-5
Distribution: unstable
Urgency: low
Maintainer: Colin Watson <cjwatson@debian.org>
Changed-By: Colin Watson <cjwatson@debian.org>
Description: 
 man-db     - on-line manual pager
Closes: 562503
Changes: 
 man-db (2.5.6-5) unstable; urgency=low
 .
   * Remove Ubuntu buildd hack now that the Ubuntu buildd chroots preseed
     man-db/auto-update=false (thanks, LaMont Jones).
   * Backport from trunk:
     - Handle iconv errors when attempting to convert the last input encoding
       to UTF-8 (closes: #562503).
   * Unless we're cross-compiling, get dh_installman to use the version of
     man we just built.
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