Hi all,
I've been running through a recurrent problem since working on a 64 bits
Linux station under Ubuntu 20.04.3.
I can run and use Coot (version 0.9.6 through my CCP4 7.1 install) for a
few minutes before it crashes while going through a structure, loading a
pdb entry or a map, etc... It doesn't seem to be linked to a specific
action.
The kind of crash message I'm getting:
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
/opt/xtal/ccp4-7.1/bin/coot: line 272: 66298 Segmentation fault (core
dumped) $coot_bin "$@"
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 (0x00007ffdfdbd3000)
libguile.so.17 => /opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17
(0x00007f4c12699000)
libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10
(0x00007f4c12418000)
libcrypt.so.1 => /lib/x86_64-linux-gnu/libcrypt.so.1
(0x00007f4c123c8000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4c12279000)
libltdl.so.7 => /opt/xtal/ccp4-7.1/libexec/../lib/libltdl.so.7
(0x00007f4c1206f000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007f4c1204c000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4c11e58000)
/lib64/ld-linux-x86-64.so.2 (0x00007f4c1299d000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f4c11e52000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005,
2006, 2007, 2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
Gtk-Message: Failed to load module "canberra-gtk-module"
coot-exe: "/opt/xtal/ccp4-7.1/libexec/coot-bin"
/usr/bin/ls
-rwxrwxrwx 1 root root 9169416 Sep 14 10:32
/opt/xtal/ccp4-7.1/libexec/coot-bin
coot-version:
/opt/xtal/ccp4-7.1/libexec/coot-bin
Builder_info: CCP4, Oxfordshire
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool
Goocanvas GSL SQLite3 LibCurl
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP4, Oxfordshire
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.6 (revision-count 10625)
platform:
/usr/bin/uname
Linux jnomme-Precision-Tower-5810 5.11.0-38-generic #42~20.04.1-Ubuntu
SMP Tue Sep 28 20:41:07 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
core: #f
No core file found. No debugging
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Looking into the Mail Archive, it looks like the "Failed to load
canberra module" is commonly found in crash reports...
I have libcanberra-gtk-module, libcanberra-gtk3-module installed.
Does anyone have experienced the same problem and/or could suggest a
solution to fix this?
Thanks,
Julian
--
Dr Julian NOMME
Institut de Biologie Moléculaire et Cellulaire (IBMC-ARN-CNRS)
Biologie des ARNt et pathogénicité
2 allée Conrad Roentgen
F-67084 Strasbourg - France
tel +33 (0)388 417 122
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