Re: [COOT] Problem installing coot binary

2023-08-08 Thread Paul Emsley 

On 08/08/2023 06:49, Edward A. Berry wrote:
> I would appreciate instruction for getting a downloaded coot binary to
> run.


Fair enough.


The idea is that you untar the binary tar file and put
/somewhere/coot-something/bin in your PATH. That's it. You shouldn't
need to edit any coot files. Coot is compiled and distributed with its
own python, so setting PYTHON to the system one will upset it, because
the system python doesn't know about the coot module.


Keeping on top of making binaries is the majority of a full-time job
itself and I just have not been able to manage it. I can make binaries
for the computers I use that are connected to the internet - i.e. the
Scientific Linux build. Maybe one day things will change. But at the
moment it's just sad times. The options are, pick it up from CCP4 or
compile it yourself.


Regards,


Paul.



> 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)
>



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Re: [COOT] Problem installing coot binary

2023-08-07 Thread Edward A. Berry 
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):
#0Object 
"/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 
Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
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  0x7f308e4d34fb 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):
#0Object 
"/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 =>  (0x7ffc3c3f8000)
  libguile.so.17 => 
/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libguile.so.17 
(0x7f74666cd000)
  libgmp.so.10 => 
/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libgmp.so.10 
(0x7f7466458000)
  libcrypt.so.1 => /lib64/libcrypt.so.1 (0x7f7466221000)
  libm.so.6 => /lib64/libm.so.6 (0x7f7465f1f000)
  libltdl.so.3 => 
/tb2/sw/lnx/coot-Linux-x86_64-centos-7-gtk2-python/lib/libltdl.so.3 
(0x7f7465d17000)
  libdl.so.2 => /lib64/libdl.so.2 (0x7f7465b13000)
  libpthread.so.0 => /lib64/libpthread.so.0 (0x7f74658f7000)
  libc.so.6 => /lib64/libc.so.6 (0x7f7465529000)
  /lib64/ld-linux-x86-64.so.2 (0x7f74669c2000)
  libfreebl3.so => /lib64/libfreebl3.so (0x7f7465326000)
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 
Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
ImportError: No module named site





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