Dear Kay,
Thanks for the suggestions.
The model name for the computer is "Intel(R) Xeon(R) CPU E5440 @ 2.83GHz".
As suggested, I downloaded and installed the latest ccp4 (7.1) which
bundles with coot 0.9.5. The coot works just fine with the latest ccp4
bundle.
I used the graphic driver from Nvidia package. I will try to use NVidia
driver from ELRepo.
Time being I will use the one bundled with CCP4-7.1.
Once again thanks for the help.
With regards
Karthik
On 22-04-2021 02:18 pm, Kay Diederichs wrote:
Dear Karthikeyan Subramanian,
which processor does your computer have? Look at the output of e.g. "head -20
/proc/cpuinfo". What is "model name"?
To my understanding, the main problem is
*./coot: line 264: 5365 Illegal instruction (core dumped) $coot_bin
This means that the compiler, when producing the coot binary, used instructions that your
processor does not understand (in the /proc/cpuinfo output, some flags would be missing).
This happens on old AMD processors (unless such an old processor is also used when
compiling), and is the reason why CCP4 has its own distribution for these: go to
http://www.ccp4.ac.uk/download/#os=linux and scroll down to "Legacy systems".
If you indeed have an old AMD, just install CCP4 from there - CCP4 currently (at least
the non-legacy distribution) has coot 0.9.5 .
The other problem is
*** Cannot find the double-buffered visual.
*** Trying single-buffered visual.
which points to the graphics driver; it is not properly installed. Are you
using the NVidia driver from ElRepo? If not, you should try that.
hope this helps,
Kay
On Thu, 22 Apr 2021 13:27:39 +0530, Karthikeyan Subramanian
<[email protected]> wrote:
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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