I would appreciate instruction for getting a downloaded coot binary to run. I got coot-0.9.7-binary-Linux-x86_64-centos-7-python-gtk2.tar.gz There is no README file in the top directory. I edited bin/coot to set #PYTHON=/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/include/python2.7 #PYTHON=/usr/bin/python2.7 PYTHON=/usr/lib64/python2.7
With or without those edits, it runs as far as bringing up the graphics screen, loading the standard residues, and saying hello- then crashes with: (set-display-lists-for-maps 1) Stack trace (most recent call last): #0 Object "/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libgmp.so.10", at 0x7f3097b3133b, in __gmpn_mul_1 Illegal instruction (Illegal operand [0x7f3097b3133b]) /sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/bin/coot: line 264: 10999 Illegal instruction (core dumped) $coot_bin "$@" (more below) The crash-catcher then fails : core: "core.10999" /usr/bin/gdb Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site setenv PYTHONHOME /usr/bin/python2.7 setenv PYTHONHOME /usr/lib64/python2.7 did not make any difference I hope the fix is obvious to someone more familiar with python! If I run gdb from the command line: $ gdb /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin core.10999 GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-120.el7 Reading symbols from /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin...done. [New LWP 10999] [New LWP 11007] [New LWP 11005] [New LWP 11008] [New LWP 11001] [New LWP 11002] [New LWP 11003] [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib64/libthread_db.so.1". Core was generated by `/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin'. Program terminated with signal 4, Illegal instruction. #0 0x00007f308e4d34fb in raise () from /lib64/libpthread.so.0 Missing separate debuginfos, use: debuginfo-install PackageKit-gtk3-module-1.1.10-2.el7.centos.x86_64 . . . followed by ~50 lines of debuginfo packages to be downloaded. More complete output: Stack trace (most recent call last): #0 Object "/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libgmp.so.10", at 0x7f3097b3133b, in __gmpn_mul_1 Illegal instruction (Illegal operand [0x7f3097b3133b]) /sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/bin/coot: line 264: 10999 Illegal instruction (core dumped) $coot_bin "$@" . ------ Coot crashed - trying to diagnose ----- ldd -r on guile gives: linux-vdso.so.1 => (0x00007ffc3c3f8000) libguile.so.17 => /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libguile.so.17 (0x00007f74666cd000) libgmp.so.10 => /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libgmp.so.10 (0x00007f7466458000) libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007f7466221000) libm.so.6 => /lib64/libm.so.6 (0x00007f7465f1f000) libltdl.so.3 => /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libltdl.so.3 (0x00007f7465d17000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f7465b13000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f74658f7000) libc.so.6 => /lib64/libc.so.6 (0x00007f7465529000) /lib64/ld-linux-x86-64.so.2 (0x00007f74669c2000) libfreebl3.so => /lib64/libfreebl3.so (0x00007f7465326000) 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: "/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin" /usr/bin/ls -rwxr-xr-x 1 berry strbiol 270085184 Feb 17 2022 /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin coot-version: /tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/libexec/coot-bin Builder_info: build-host: centos7.localdomain on: Fri 18 Feb 0038.14 GMT 2022 by paule Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas GSL SQLite3 LibCurl Binary type: Linux-x86_64-centos-7-python-gtk2 git commit: 622df3626966809ee069e29954e1c0842f5969e8 Builder_info: build-host: centos7.localdomain on: Fri 18 Feb 0038.14 GMT 2022 by paule [with python 2.7.18 embedded] [with guile 1.8.8 embedded] 0.9.7 (revision-count 10775) platform: /usr/bin/uname Linux oswego 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux core: "core.10999" /usr/bin/gdb Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] ImportError: No module named site ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
