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 <skarthi...@gmail.com> 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% > > ====================================================================================================================== > > >######################################################################## > >To unsubscribe from the CCP4BB list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing >list hosted by www.jiscmail.ac.uk, terms & conditions are available at >https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
