symbol lookup error: /usr/lib/libxml2.so.2: undefined symbol: gzopen64

[Matthias Hillenbrand]

Hello,

Since I have upgraded to SAGE 2.10.x I get the following error message
when starting the notebook:

gnome-www-browser: symbol lookup error: /usr/lib/libxml2.so.2:
undefined symbol: gzopen64

I get this error message on two different computers (one running
Ubuntu 7.10 the other Debian Testing, which I installed today) and
with any browser (e.g. Firefox as standard browser). If I open a
session of the browser before starting SAGE, the error won't occur.

I searched for this error message with google and it seems to occur,
if different versions of libz.so.1 are involved. Till now I found a
libz.so.1 in the SAGE dir /local/lib, which differs from the one
included in my Debian installation.

The Version of the installed libxml2 is 2.6.31.dfsg-1 and my system
has the following dependencies:

ldd /usr/lib/libxml2.so.2
linux-gate.so.1 => (0xffffe000)
libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb7def000)
libz.so.1 => /usr/lib/libz.so.1 (0xb7dda000)
libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7db4000)
libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7c67000)
/lib/ld-linux.so.2 (0x80000000)

ls -l /usr/lib/libz*
lrwxrwxrwx 1 root root 15 2008-02-16 12:56 /usr/lib/libz.so.1 ->
libz.so.1.2.3.3
-rw-r--r-- 1 root root 81012 2008-01-20 00:22 /usr/lib/libz.so.1.2.3.3

Thanks in advance!

Matthias

[mabshoff]

On Feb 16, 5:31 pm, Matthias Hillenbrand <mailanhi...@googlemail.com>
wrote:
> Hello,

Hi Matthias,

> Since I have upgraded to SAGE 2.10.x I get the following error message
> when starting the notebook:
>
> gnome-www-browser: symbol lookup error: /usr/lib/libxml2.so.2:
> undefined symbol: gzopen64

The issue you mentioned has happened in the past and been fixed by
resetting LD_LIBRARY_PATH to the original version when launching
applications from Sage that are not in $SAGE_LOCAL/bin. So the problem
should not happen, unless you have SAGE_LOCAL/lib in LD_LIBRARY_PATH
somehow.

> I get this error message on two different computers (one running
> Ubuntu 7.10 the other Debian Testing, which I installed today) and
> with any browser (e.g. Firefox as standard browser). If I open a
> session of the browser before starting SAGE, the error won't occur.
>
> I searched for this error message with google and it seems to occur,
> if different versions of libz.so.1 are involved. Till now I found a
> libz.so.1 in the SAGE dir /local/lib, which differs from the one
> included in my Debian installation.
>
> The Version of the installed libxml2 is 2.6.31.dfsg-1 and my system
> has the following dependencies:
>
> ldd /usr/lib/libxml2.so.2
> linux-gate.so.1 => (0xffffe000)
> libdl.so.2 => /lib/i686/cmov/libdl.so.2 (0xb7def000)
> libz.so.1 => /usr/lib/libz.so.1 (0xb7dda000)
> libm.so.6 => /lib/i686/cmov/libm.so.6 (0xb7db4000)
> libc.so.6 => /lib/i686/cmov/libc.so.6 (0xb7c67000)
> /lib/ld-linux.so.2 (0x80000000)
>
> ls -l /usr/lib/libz*
> lrwxrwxrwx 1 root root 15 2008-02-16 12:56 /usr/lib/libz.so.1 ->
> libz.so.1.2.3.3
> -rw-r--r-- 1 root root 81012 2008-01-20 00:22 /usr/lib/libz.so.1.2.3.3
>
> Thanks in advance!

Could you post the output from "env" from a clean session and also one
where the launch fails? Since there are potentially large a diff of
those two would also be good.

What was the last working version of Sage before you upgraded?

> Matthias

Cheers,

Michael

[Matthias Hillenbrand]

Hi Michael,

the last version I used before upgrading was 2.9.2.

here is the output of 'env' before and after starting the notebook.

------------------------------------------------------------------------------------------------------------

m@q172:~/sage$ ./sage
----------------------------------------------------------------------
| SAGE Version 2.10.1, Release Date: 2008-02-02 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------

sage: env

{'AR': 'ar',
'AS': 'as',
'CC': 'gcc',
'CHMOD': 'chmod',
'COLORTERM': 'gnome-terminal',
'CP': 'cp',
'CUR': '/home/m/sage',
'CXX': 'g++',
'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-
cDNaQsFOS3,guid=9ccba688d4c22fb58d776dc347b70962',
'DESKTOP_SESSION': 'gnome',
'DESKTOP_STARTUP_ID': '',
'DISPLAY': ':0.0',
'DOT_SAGE': '/home/m/.sage/',
'GDMSESSION': 'gnome',
'GDM_LANG': 'de_DE.UTF-8',
'GDM_XSERVER_LOCATION': 'local',
'GNOME_DESKTOP_SESSION_ID': 'Default',
'GNOME_KEYRING_SOCKET': '/tmp/keyring-IyT6bO/socket',
'GPDOCDIR': '/home/m/sage/local/share/pari/doc',
'GPHELP': '/home/m/sage/local/bin/gphelp',
'GP_DATA_DIR': '/home/m/sage/local/share/pari',
'GTK_MODULES': 'gnomebreakpad',
'GTK_RC_FILES': '/etc/gtk/gtkrc:/home/m/.gtkrc-1.2-gnome2',
'HOME': '/home/m',
'IPYTHONDIR': '/home/m/.sage//ipython',
'IPYTHONRC': 'ipythonrc',
'LANG': 'de_DE.UTF-8',
'LD': 'ld',
'LDFLAGS': '',
'LD_LIBRARY_PATH': '/home/m/sage/local/lib/openmpi:/home/m/sage/local/
lib/:',
'LIBRARY_PATH': '/home/m/sage/local/lib/',
'LN': 'ln',
'LOGNAME': 'm',
'MAKE': 'make',
'MATPLOTLIBRC': '/home/m/.sage//',
'MKDIR': 'mkdir',
'MV': 'mv',
'OLDPWD': '/home/m/sage',
'PATH': '/home/m/sage:/home/m/sage/local/bin:/usr/local/bin:/usr/bin:/
bin:/usr/games',
'PWD': '/home/m/sage/local/bin',
'PYTHONHOME': '/home/m/sage/local',
'PYTHONPATH': ':/home/m/sage/local/lib/python',
'RANLIB': 'ranlib',
'RM': 'rm',
'SAGE64': 'no',
'SAGE_DATA': '/home/m/sage/data',
'SAGE_LOCAL': '/home/m/sage/local',
'SAGE_ORIG_LD_LIBRARY_PATH': '',
'SAGE_PACKAGES': '/home/m/sage/spkg',
'SAGE_ROOT': '/home/m/sage',
'SAGE_SERVER': 'http://www.sagemath.org/',
'SAGE_STARTUP_COMMAND': '\nimport sage.misc.misc; print
sage.misc.misc.branch_current_hg_notice(sage.misc.misc.branch_current_hg());
from sage.misc.interpreter import preparser; preparser(True);import
sage.all_cmdline; sage.all_cmdline._init_cmdline(globals());from
sage.all import Integer, RealNumber;import os; os.chdir("/home/m/
sage");import sage.misc.interpreter;from sage.misc.interpreter import
attached_files;from sage.all_cmdline import
*;_=sage.misc.interpreter.load_startup_file("/home/m/.sage//
init.sage")',
'SAGE_STARTUP_FILE': '/home/m/.sage//init.sage',
'SESSION_MANAGER': 'local/q172:/tmp/.ICE-unix/3288',
'SHAREDFLAGS': '-fPIC',
'SHELL': '/bin/bash',
'SHLVL': '3',
'SSH_AGENT_PID': '3333',
'SSH_AUTH_SOCK': '/tmp/ssh-IkusNK3288/agent.3288',
'TERM': 'xterm',
'TOUCH': 'touch',
'UNAME': 'Linux',
'USER': 'm',
'USERNAME': 'm',
'WINDOWID': '48234571',
'WINDOWPATH': '7',
'XAUTHORITY': '/home/m/.Xauthority',
'XDG_DATA_DIRS': '/usr/local/share/:/usr/share/:/usr/share/gdm/',
'_': '/home/m/sage/local/bin/sage-ipython',
'__sage__': ''}
sage: notebook()
The notebook files are stored in: /home/m/.sage//sage_notebook
****************************************************
* *
* Open your web browser to https://localhost:8000 *
* *
****************************************************
There is an admin account. If you do not remember the password,
quit the notebook and type notebook(reset=True).
Removing stale pidfile /home/m/.sage/sage_notebook/twistd.pd
2008/02/16 18:52 +0200 [-] Log opened.
2008/02/16 18:52 +0200 [-] twistd 2.5.0 (/home/m/sage/local/bin/python
2.5.1) starting up
2008/02/16 18:52 +0200 [-] reactor class: <class
'twisted.internet.selectreactor.SelectReactor'>
2008/02/16 18:52 +0200 [-] Loading sage_notebook/twistedconf.tac...
2008/02/16 18:52 +0200 [-] Loaded.
2008/02/16 18:52 +0200 [-] twisted.web2.channel.http.HTTPFactory
starting on 8000
2008/02/16 18:52 +0200 [-] Starting factory
<twisted.web2.channel.http.HTTPFactory instance at 0x8540f6c>

gnome-www-browser: symbol lookup error: /usr/lib/libxml2.so.2:
undefined symbol: gzopen64

2008/02/16 18:53 +0200 [-] (Notebook cleanly saved. Press control-C
again to exit.)
True
sage: env

{'AR': 'ar',
'AS': 'as',
'CC': 'gcc',
'CHMOD': 'chmod',
'COLORTERM': 'gnome-terminal',
'CP': 'cp',
'CUR': '/home/m/sage',
'CXX': 'g++',
'DBUS_SESSION_BUS_ADDRESS': 'unix:abstract=/tmp/dbus-
cDNaQsFOS3,guid=9ccba688d4c22fb58d776dc347b70962',
'DESKTOP_SESSION': 'gnome',
'DESKTOP_STARTUP_ID': '',
'DISPLAY': ':0.0',
'DOT_SAGE': '/home/m/.sage/',
'GDMSESSION': 'gnome',
'GDM_LANG': 'de_DE.UTF-8',
'GDM_XSERVER_LOCATION': 'local',
'GNOME_DESKTOP_SESSION_ID': 'Default',
'GNOME_KEYRING_SOCKET': '/tmp/keyring-IyT6bO/socket',
'GPDOCDIR': '/home/m/sage/local/share/pari/doc',
'GPHELP': '/home/m/sage/local/bin/gphelp',
'GP_DATA_DIR': '/home/m/sage/local/share/pari',
'GTK_MODULES': 'gnomebreakpad',
'GTK_RC_FILES': '/etc/gtk/gtkrc:/home/m/.gtkrc-1.2-gnome2',
'HOME': '/home/m',
'IPYTHONDIR': '/home/m/.sage//ipython',
'IPYTHONRC': 'ipythonrc',
'LANG': 'de_DE.UTF-8',
'LD': 'ld',
'LDFLAGS': '',
'LD_LIBRARY_PATH': '/home/m/sage/local/lib/openmpi:/home/m/sage/local/
lib/:',
'LIBRARY_PATH': '/home/m/sage/local/lib/',
'LN': 'ln',
'LOGNAME': 'm',
'MAKE': 'make',
'MATPLOTLIBRC': '/home/m/.sage//',
'MKDIR': 'mkdir',
'MV': 'mv',
'OLDPWD': '/home/m/sage',
'PATH': '/home/m/sage:/home/m/sage/local/bin:/usr/local/bin:/usr/bin:/
bin:/usr/games',
'PWD': '/home/m/sage/local/bin',
'PYTHONHOME': '/home/m/sage/local',
'PYTHONPATH': ':/home/m/sage/local/lib/python',
'RANLIB': 'ranlib',
'RM': 'rm',
'SAGE64': 'no',
'SAGE_DATA': '/home/m/sage/data',
'SAGE_LOCAL': '/home/m/sage/local',
'SAGE_ORIG_LD_LIBRARY_PATH': '',
'SAGE_PACKAGES': '/home/m/sage/spkg',
'SAGE_ROOT': '/home/m/sage',
'SAGE_SERVER': 'http://www.sagemath.org/',
'SAGE_STARTUP_COMMAND': '\nimport sage.misc.misc; print
sage.misc.misc.branch_current_hg_notice(sage.misc.misc.branch_current_hg());
from sage.misc.interpreter import preparser; preparser(True);import
sage.all_cmdline; sage.all_cmdline._init_cmdline(globals());from
sage.all import Integer, RealNumber;import os; os.chdir("/home/m/
sage");import sage.misc.interpreter;from sage.misc.interpreter import
attached_files;from sage.all_cmdline import
*;_=sage.misc.interpreter.load_startup_file("/home/m/.sage//
init.sage")',
'SAGE_STARTUP_FILE': '/home/m/.sage//init.sage',
'SESSION_MANAGER': 'local/q172:/tmp/.ICE-unix/3288',
'SHAREDFLAGS': '-fPIC',
'SHELL': '/bin/bash',
'SHLVL': '3',
'SSH_AGENT_PID': '3333',
'SSH_AUTH_SOCK': '/tmp/ssh-IkusNK3288/agent.3288',
'TERM': 'xterm',
'TOUCH': 'touch',
'UNAME': 'Linux',
'USER': 'm',
'USERNAME': 'm',
'WINDOWID': '48234571',
'WINDOWPATH': '7',
'XAUTHORITY': '/home/m/.Xauthority',
'XDG_DATA_DIRS': '/usr/local/share/:/usr/share/:/usr/share/gdm/',
'_': '/home/m/sage/local/bin/sage-ipython',
'__sage__': ''}
sage:

-----------------------------------------------------------------------------------------------------------------

Cheers,

Matthias

[Matthias Hillenbrand]

There seems to be no difference between the output form 'env' before

[mabshoff]

On Feb 16, 6:06 pm, Matthias Hillenbrand <mailanhi...@googlemail.com>
wrote:

> There seems to be no difference between the output form 'env' before
> and after starting the notebook.

Hi Matthias,

Jason Grout has figured out what the problem is and will probably post
a patch in the next 24 hours or so that should make it into 2.10.2.

Cheers,

Michael

[Matthias Hillenbrand]

Hi Michael,

Thank you very much for your help. I am looking forward to the next
release of SAGE.

Matthias

[mabshoff]

On Feb 16, 10:38 pm, Matthias Hillenbrand <mailanhi...@googlemail.com>
wrote:
> Hi Michael,

Hi Matthias,

> Thank you very much for your help. I am looking forward to the next
> release of SAGE.

I didn't really do much, I just ended up writing a couple emails :).
We are tracking the issue at

http://trac.sagemath.org/sage_trac/ticket/2182

> Matthias

Cheers,

Michael

[Jason Grout]

Matthias,

I saw the problem too on my Ubuntu 7.10 computers too. Thanks for the
motivation to make the time to fix it :).

There are two patches up at the above URL that fix the problem for me
and should fix the problem for you. If you have experience applying
patches and doing development with mercurial, you could try the patches
and tell us if it fixes the problem for you (one patch is for
SAGE_ROOT/local/bin/sage-env and the other is for
SAGE_ROOT/devel/sage/sage/server/misc.py). If you don't have experience
with patches and development or don't want to somehow mess up your
current sage installation, I suggest doing your workaround (opening the
browser first, then starting the notebook) until 2.10.2. I think the
fixes will make it into 2.10.2.

Thanks,

Jason

[mabshoff]

<SNIP>

Hi,

> Matthias,
>
> I saw the problem too on my Ubuntu 7.10 computers too. Thanks for the
> motivation to make the time to fix it :).

I do remember complaining about the fact that the notebook is launched
with its own code instead of the new infrastructure. I never filed a
bug report, but I am sure I can find it in my IRC log.

> There are two patches up at the above URL that fix the problem for me
> and should fix the problem for you. If you have experience applying
> patches and doing development with mercurial, you could try the patches
> and tell us if it fixes the problem for you (one patch is for
> SAGE_ROOT/local/bin/sage-env and the other is for
> SAGE_ROOT/devel/sage/sage/server/misc.py). If you don't have experience
> with patches and development or don't want to somehow mess up your
> current sage installation, I suggest doing your workaround (opening the
> browser first, then starting the notebook) until 2.10.2. I think the
> fixes will make it into 2.10.2.

It has been merged and will be in Sage 2.10.2.alpha1, which should be
out "soon", i.e. by Sunday.

> Thanks,
>
> Jason

Cheers,

Michael

[Matthias Hillenbrand]

Hi Jason,

Today I installed the new version of SAGE and can confirm that the
problem is fixed.

Thanks,

Matthias