Hello.
I'm attempting to run coot on CentOS 7 using
"coot-Linux-x86_64-scientific-linux-7.6-gtk2-python" binaries
I'm getting the splash screen, but then coot crashes. I appreciate any help!
Here is the output:
./coot
CLIBD_MON not set using COOT_REFMAC_LIB_DIR
(coot-bin:13947): GLib-GObject-WARNING **: 11:44:21.607:
g_object_set_is_valid_property: object class 'GtkSettings' has no property
named 'gtk-application-prefer-dark-theme'
There are 143 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/e/EDO.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/a/A.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/c/C.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/g/G.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/u/U.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/d/DA.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/d/DC.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/d/DG.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/d/DT.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/lib/data/monomers/h/HOH.cif
There are 2 data in
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/share/coot/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
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Root, Welcome to Coot version 0.9.5
(set-display-intro-string "Good Morning Root, 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)
(filter-fileselection-filenames-state)
(get-active-map-drag-flag)
(use-graphics-interface-state)
Coot Scheme Scripting GUI code found and loaded.
Good morning root. Welcome to Coot 0.9.5.
(set-display-intro-string "Good morning root. Welcome to Coot 0.9.5")
(set-display-lists-for-maps 1)
./coot: line 264: 13947 Illegal instruction (core dumped) $coot_bin "$@"
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 => (0x00007ffe800cd000)
libguile.so.17 =>
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libguile.so.17
(0x00007effc7f05000)
libgmp.so.10 =>
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libgmp.so.10
(0x00007effc7c90000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007effc7a59000)
libm.so.6 => /lib64/libm.so.6 (0x00007effc7757000)
libltdl.so.3 =>
/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/lib/libltdl.so.3
(0x00007effc754f000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007effc734b000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007effc712f000)
libc.so.6 => /lib64/libc.so.6 (0x00007effc6d61000)
/lib64/ld-linux-x86-64.so.2 (0x00007effc81fa000)
libfreebl3.so => /lib64/libfreebl3.so (0x00007effc6b5e000)
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:
"/root/Downloads/coot-Linux-x86_64-scientific-linux-7.6-gtk2-python/libexec/coot-bin"
/usr/bin/ls
coot-version:
/root/Downloads/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
[root@centos7 bin]#
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