Dear CCP4 members,
I am trying to install the
coot-Linux-x86_64-scientific-linux-7.6-gtk2-python on CentOS 7.9 with
Nvidia Quadro FX 4800 graphics card.
Coot crashes soon after launching the window. The log file is shown
below. Not sure what is missing. The only error I can see is
*./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin
"$@"".
*
The older version of coot (0.8.9.2) is working fine on the same machine.
Thanks for the help.
With regards
Karthik
IMTECH, Chandigarh
===========================================================================
xray6 <1:14pm> 8% pwd
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/bin
xray6 <1:14pm> 9% ./coot
(coot-bin:5365): GLib-GObject-WARNING **: 13:14:08.004:
g_object_set_is_valid_property: object class 'GtkSettings' has no
property named 'gtk-application-prefer-dark-theme'
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/home/programs/linux/ccp4-7.0/lib/data/monomers/
There are 153 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ALA.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASP.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ASN.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CYS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLN.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLY.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GLU.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PHE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HIS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/i/ILE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LYS.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/l/LEU.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MET.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/m/MSE.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PRO.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/a/ARG.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SER.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/THR.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/v/VAL.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TRP.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/t/TYR.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/p/PO4.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/s/SO4.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/g/GOL.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/c/CIT.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/e/EDO.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/a/A.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/c/C.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/g/G.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/u/U.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DA.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DC.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DG.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/d/DT.cif
There are 2 data in
/home/programs/linux/ccp4-7.0/lib/data/monomers/h/HOH.cif
There are 2 data in /home/programs/linux/ccp4-7.0/lib/data/monomers/n/NA.cif
Spacegroup: P 1
*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
INFO:: coot.py imported
INFO:: coot_python initialized
Running python script
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Afternoon Person with no name, Welcome to Coot version 0.9.5
(set-display-intro-string "Good Afternoon Person with no name, Welcome
to Coot version 0.9.5")
Coot Python Scripting GUI code found and loaded.
Coot Python Scripting GUI code found and loaded.
(use-graphics-interface-state)
Running python script /home/skarthik/.coot-preferences/0-coot-history.py
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-display-intro-string "Good Afternoon Person with no name, Welcome
to Coot version 0.8.9.2")
(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(set-display-intro-string "Good afternoon . Welcome to Coot 0.8.9.2")
(set-display-lists-for-maps 0)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Coot Scheme Scripting GUI code found and loaded.
Good afternoon . Welcome to Coot 0.9.5.
(set-display-intro-string "Good afternoon . Welcome to Coot 0.9.5")
(set-display-lists-for-maps 1)
*./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin "$@"*
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 => (0x00007ffdba7c2000)
libguile.so.17 =>
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libguile.so.17
(0x00002b22f95e8000)
libgmp.so.10 =>
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libgmp.so.10
(0x00002b22f98dd000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00002b22f9b52000)
libm.so.6 => /lib64/libm.so.6 (0x00002b22f9d89000)
libltdl.so.3 =>
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libltdl.so.3
(0x00002b22fa08b000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b22fa293000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b22fa497000)
libc.so.6 => /lib64/libc.so.6 (0x00002b22fa6b3000)
/lib64/ld-linux-x86-64.so.2 (0x00002b22f93c4000)
libfreebl3.so => /lib64/libfreebl3.so (0x00002b22faa81000)
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:
coot-exe:
"/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin"
/usr/bin/ls
coot-version:
/home/programs/linux/tmp/coot/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin
platform:
/usr/bin/uname
core: #f
No core file found. No debugging
xray6 <1:14pm> 10%
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