Bugzilla Bug 32085

PyMol 0.92 has just been released on http://pymol.sf.net/. 
 
Please find attached the file "pymol-0.92.ebuild". The only change from the 
existing "app-sci/pymol-0.90.ebuild" is the removal of the line "epatch 
${FILESDIR}/setup.py-gentoo.patch", since this patch is no longer necessary. 
 
With this ebuild, PyMol 0.92 compiles fine, at least on my Pentium-4 system. 

Reproducible: Always
Steps to Reproduce:
1.
2.
3.

Created an attachment (id=19843) [details]
ebuild for PyMol 0.92

It has just been announced on pymol-users that some problems have been found
in PyMol 0.92 and that a 0.93 bugfix version will be released ASAP.

Created an attachment (id=20180) [details]
ebuild for PyMol 0.93

I have attached pymol-0.93.ebuild for the app-sci category. It is exactly
the same a pymol-0.92.ebuild except for its name and builds fine on a Pentium-4
system.

The 0.93 ebuild also works fine for me on an Athlon XP system

Could you please test pymol-0.95 that will be in portage later today? Thanks.

The 0.95 ebuild in the Portage tree installs correctly. When running PyMOL
0.95, I sometimes get a seqmentation fault during raytracing, but I also get
that on non-Gentoo systems, so it's probably a PyMOL problem.

Maybe this is a gcc related problem, see
http://sourceforge.net/tracker/index.php?func=detail&aid=806361&group_id=4546&atid=104546

I've been looking at the raytracing crash over the weekend. It doesn't happen
when I compile PyMOL 0.95 "manually" (using python setup.py install), but it
does occur when I use Portage with CFLAGS="-march=pentium4 -O2 -pipe
-funroll-loops".

After some elimination, it seems that the problem is caused by the "-fgcse"
optimization flag enabled by "-O2". When I set CFLAGS (in /etc/make.conf) to
"... -O2 -fno-gcse ...", the resulting PyMOL build doesn't crash.

I was under the impression that compiler optimizations were not supposed to
cause crashes :-), so it's probably a gcc bug. Anybody know how to report
things like this?

Can you give some instructions on how to produce this crash? Maybe one could
track it down to some specific gcc versions.... Maybe it is a gcc bug, maybe it
just shows a bug in PyMol code, I think it's too early to tell.

Re-opening, changing subject.

I created a small test script "crash.pml" which loads a small PDB file
("mgl.pdb"), creates a stick representation and starts the raytracing. I'll
attach both files to the report. You can start PyMOL in non-GUI mode with
"pymol -qc crash.pml". If the build is OK, it should print the time it took to
make the image, otherwise it will segfault.

Created an attachment (id=30587) [details]
Structure file for PyMOL test script

Created an attachment (id=30588) [details]
PyMOL script to test raytracer crash

Minimal script to trigger raytracer segfault

I have been testing 0.97 for a few days and it seems that this new version
solves the ray-tracing bug. Aggressive optimizations no longer seem to make
pymol segfault when raytracing. I you still have problems with the current
version, please comment. Otherwise, I'll mark this bug as WONTFIX in a couple
of weeks, and try to mark 0.97 stable as soon as possible. 

Yup, 0.97 seems fine, even with "-fgcse" enabled. I'm still curious about the 
cause of the problem, but I don't really hav the time to delve into the 
necessary depths now :-). Thanks for the 0.97 ebuild!

I guess we'll never know if it was a gcc, PyMOL or X driver problem... But at
least it works, now ;-)

It was the gcc. I have emerged 0.97 with gcc 3.3.2. I was having the same
problem... then I upgraded the gcc to 3.3.3 and all is fine now..