Since updating to the 0.9.8 and 0.9.8.1 versions, I cannot get any
version of coot to work. I've tried on fresh installs of CentOS 7 and
of Rocky Linux 8 to no avail. It also says it can't find the core
dump file. Thanks to anyone that can help!
See output below.
[chris@athena ~]$ /usr/local/coot-0.9.8.1/bin/coot
There are 166 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/a/ALA.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/a/ASP.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/a/ASN.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/c/CYS.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/g/GLN.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/g/GLY.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/g/GLU.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/p/PHE.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/h/HIS.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/i/ILE.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/l/LYS.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/l/LEU.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/m/MET.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/m/MSE.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/p/PRO.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/a/ARG.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/s/SER.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/t/THR.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/v/VAL.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/t/TRP.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/t/TYR.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/p/PO4.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/s/SO4.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/g/GOL.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/c/CIT.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/e/EDO.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/a/A.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/c/C.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/g/G.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/u/U.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/d/DA.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/d/DC.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/d/DG.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/d/DT.cif
There are 2 data in
/usr/local/coot-0.9.8.1/share/coot/lib/data/monomers/h/HOH.cif
There are 2 data in
/usr/local/coot-0.9.8.1/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
/usr/local/coot-0.9.8.1/lib/python2.7/site-packages/coot/coot_load_modules.py
Good Morning Person with no name, Welcome to Coot version 0.9.8.1
(set-display-intro-string "Good Morning Person with no name, Welcome
to Coot version 0.9.8.1")
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 . Welcome to Coot 0.9.8.1.
(set-display-intro-string "Good morning . Welcome to Coot 0.9.8.1")
(set-display-lists-for-maps 1)
Stack trace (most recent call last):
#0 Object "/usr/local/coot-0.9.8.1/lib/libgmp.so.10", at
0x7fc7b828a2bb, in __gmpn_mul_1
Illegal instruction (Illegal operand [0x7fc7b828a2bb])
/usr/local/coot-0.9.8.1/bin/coot: line 264: 32629 Illegal instruction
(core dumped) $coot_bin "$@"
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 => (0x00007ffe59644000)
libguile.so.17 => /usr/local/coot-0.9.8.1/lib/libguile.so.17
(0x00007f85afde4000)
libgmp.so.10 => /usr/local/coot-0.9.8.1/lib/libgmp.so.10
(0x00007f85afb6c000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007f85af934000)
libm.so.6 => /lib64/libm.so.6 (0x00007f85af62c000)
libltdl.so.3 => /usr/local/coot-0.9.8.1/lib/libltdl.so.3
(0x00007f85af424000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f85af21c000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f85aeffc000)
libc.so.6 => /lib64/libc.so.6 (0x00007f85aec2c000)
/lib64/ld-linux-x86-64.so.2 (0x00007f85b00dc000)
libfreebl3.so => /lib64/libfreebl3.so (0x00007f85aea24000)
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: "/usr/local/coot-0.9.8.1/libexec/coot-bin"
/usr/bin/ls
-rwxr-xr-x 1 chris sbio 270082640 Mar 18 12:36
/usr/local/coot-0.9.8.1/libexec/coot-bin
coot-version:
/usr/local/coot-0.9.8.1/libexec/coot-bin
Builder_info: built by: Paul Emsley build-host: charybdis on: Fri 18
Mar 1626.47 GMT 2022
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool
Goocanvas GSL SQLite3 LibCurl
Binary type: Linux-x86_64-scientific-linux-7.6-python-gtk2
git commit: 58ccfeebc5f76e5e4373269c1fa510dec22e3a8d
Builder_info: built by: Paul Emsley build-host: charybdis on: Fri 18
Mar 1626.47 GMT 2022
[with python 2.7.18 embedded]
[with guile 1.8.8 embedded]
0.9.8.1 (revision-count 10823)
platform:
/usr/bin/uname
Linux athena 3.10.0-1160.62.1.el7.x86_64 #1 SMP Tue Apr 5 16:57:59 UTC
2022 x86_64 x86_64 x86_64 GNU/Linux
core: #f
No core file found. No debugging
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