[GeoNode-users] segmentation fault on saving maps (was error on saving maps, again!)

Tue Jan 12 07:20:01 PST 2016

Hi Simone,

just tried to remove -purge proj-bin and proj-data (this operation removed also: gdal-bin libgdal1h liblwgeom-2.1.2 libmapserver1 libogdi3.2 libproj-dev libproj0 libspatialite5 mapserver-bin php5-mapscript postgis postgresql-9.3-postgis-2.1 python-gdal) and reinstall proj-bin and proj-data.
Unfortunately on saving maps I have the same segmentation fault, but slightly different in the final part:

sudo gdb apache2 -c /tmp/cores/core.apache2.20927.repoigg.1452611149
GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.2) 7.7.1
Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from apache2...Reading symbols from /usr/lib/debug//usr/sbin/apache2...done.
done.
[New LWP 20937]
[New LWP 20938]
[New LWP 20949]
[New LWP 20950]
[New LWP 20939]
[New LWP 20934]
[New LWP 20948]
[New LWP 20935]
[New LWP 20947]
[New LWP 20940]
[New LWP 20946]
[New LWP 20945]
[New LWP 20936]
[New LWP 20944]
[New LWP 20943]
[New LWP 20927]
[New LWP 20942]
[New LWP 20941]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/mysql.so" does not match "/usr/lib/php5/20121212/mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/mysql.so" does not match "/usr/lib/php5/20121212/mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/mysqli.so" does not match "/usr/lib/php5/20121212/mysqli.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/mysqli.so" does not match "/usr/lib/php5/20121212/mysqli.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/pdo_mysql.so" does not match "/usr/lib/php5/20121212/pdo_mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/pdo_mysql.so" does not match "/usr/lib/php5/20121212/pdo_mysql.so" (CRC mismatch).

Core was generated by `/usr/sbin/apache2 -k start'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  __GI___libc_free (mem=0x160) at malloc.c:2929
2929    malloc.c: No such file or directory.
Traceback (most recent call last):
  File "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19-gdb.py", line 63, in <module>
    from libstdcxx.v6.printers import register_libstdcxx_printers
ImportError: No module named 'libstdcxx'
(gdb)

Now it seems to be a memory problem....isn't it?
What can I do?

E.

From: simone.dalmasso at gmail.com
Date: Tue, 12 Jan 2016 16:00:05 +0100
Subject: Re: segmentation fault on saving maps (was error on saving maps, again!)
To: frippe12573 at hotmail.com
CC: xbartolone at gmail.com; geonode-users at lists.osgeo.org

Hi Eugenio,
the error could be this one
src/pj_gridcatalog.c: No such file or directory

which seems related to the PROJ.4/pyproj libraries. 
Not sure what is wrong but try to reinstall them. Is the best I can tell :)
good luck
2016-01-12 15:42 GMT+01:00 Eugenio Trumpy <frippe12573 at hotmail.com>:

Dear all,

I'm trying to go ahead  to solve my segmentation error on saving maps.
Just a brief summary: as wrote in the email here below (dated 04/12/2015)
I had a problem during the map saving.
Francesco suggested me to debug the apache coredump.
I got these lines during the gdb command run:

 sudo gdb apache2 -c /tmp/cores/core.apache2.20926.repoigg.1452608854
GNU gdb (Ubuntu 7.7.1-0ubuntu5~14.04.2) 7.7.1
Copyright (C) 2014 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from apache2...Reading symbols from /usr/lib/debug//usr/sbin/apache2...done.
done.
[New LWP 20955]
[New LWP 20963]
[New LWP 20961]
[New LWP 20958]
[New LWP 20965]
[New LWP 20957]
[New LWP 20964]
[New LWP 20956]
[New LWP 20962]
[New LWP 20959]
[New LWP 20926]
[New LWP 20966]
[New LWP 20960]
[New LWP 20951]
[New LWP 20954]
[New LWP 20953]
[New LWP 20952]
[New LWP 20933]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".

warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/mysql.so" does not match "/usr/lib/php5/20121212/mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/mysql.so" does not match "/usr/lib/php5/20121212/mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/mysqli.so" does not match "/usr/lib/php5/20121212/mysqli.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/mysqli.so" does not match "/usr/lib/php5/20121212/mysqli.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug//usr/lib/php5/20121212/pdo_mysql.so" does not match "/usr/lib/php5/20121212/pdo_mysql.so" (CRC mismatch).
warning: the debug information found in "/usr/lib/debug/usr/lib/php5/20121212/pdo_mysql.so" does not match "/usr/lib/php5/20121212/pdo_mysql.so" (CRC mismatch).

Core was generated by `/usr/sbin/apache2 -k start'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  pj_gc_apply_gridshift (defn=0x7f82098149e0, inverse=0, point_count=1, point_offset=1, x=0x7f820982e6a0, 
    y=0x7f8209908f90, z=0x7f8209908fb0) at src/pj_gridcatalog.c:145
145    src/pj_gridcatalog.c: No such file or directory.
Traceback (most recent call last):
  File "/usr/share/gdb/auto-load/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.19-gdb.py", line 63, in <module>
    from libstdcxx.v6.printers import register_libstdcxx_printers
ImportError: No module named 'libstdcxx'
(gdb)

Can those lines help to find out the problem, and of course solve it?

I got the same problem by using both geonode 2.4.dev20151119194919 and the last origin/master version.

Please let me know.

best
Eugenio 

Subject: Re: [GeoNode-users] error on saving maps, again!
From: xbartolone at gmail.com
Date: Sun, 6 Dec 2015 16:33:10 +0100
CC: simone.dalmasso at gmail.com; geonode-users at lists.osgeo.org
To: frippe12573 at hotmail.com

Eugenio,
a possible way to investigate more your problem is to attach httpd child process to gdb, cause it’s not reproducible. Follow instructions in this blog [1] and then look at the next crash.
Francesco
[1] http://sysadmin.carlusgg.com/?p=197
Il giorno 06/dic/2015, alle ore 10:58, Eugenio Trumpy <frippe12573 at hotmail.com> ha scritto:

Hi Francesco,

I'm trying  to use geonode 2.4.dev20151203130956.
I tried to save both an empty map and one containing a wms from an external geoserver. Same error.
I also tried to upload a new layer for using it on a new map, but that geonode version misses the category choose, so I got error also on upload a shp file.

Any idea on the reason of my problem?

Eugenio 

Subject: Re: [GeoNode-users] error on saving maps, again!
From: xbartolone at gmail.com
Date: Sat, 5 Dec 2015 18:03:21 +0100
CC: simone.dalmasso at gmail.com; geonode-users at lists.osgeo.org
To: frippe12573 at hotmail.com

Hi Eugenio,
what version are you running? Did your unsaved map contain remote any layer from remote service?
Francesco
Il giorno 04/dic/2015, alle ore 16:51, Eugenio Trumpy <frippe12573 at hotmail.com> ha scritto:

Dear Simone and all,

I'm very sad to announce you that I'm getting the same error I got 1 month ago.
I got an error on saving maps, and I retrieve the same error in apache error.log:

[Fri Dec 04 16:40:39.271057 2015] [core:notice] [pid 15782] AH00051: child pid 26334 exit signal Segmentation fault (11), possible coredump in /etc/apache2

same stuff on segmentation fault!

I can consider me very unlucky on this installation.
Actually It was 10 days up to yesterday that I did not use geonode, but I'm sure it was working fine.
Yesterday I had the problem raised on the geonode user mailing list, so today I decided to upgrade all geonode system.
The installation went fine, but I have the same problem on saving map.

I don't understand what happen. 
I solved this problem upgrading the server from 12.04 up to 14.04 version. This task was a bit time spending but all the applications
as well as geonode then worked fine. 
In the meanwhile no important activities I performed on the server, only a few OS update.

Can you help me again?

Eugenio 

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-- 
Simone 

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