John, Thanks for following up.
Officially speaking, PyMOL 1.0 is incompatible with Python 2.5, and we do not yet support 64 bits executables on any platform, though that should change with PyMOL 1.1: (certain on Linux, likely on Windows [if Python 2.5.2 is released], and it remains a target on Leopard). However, I finally managed to reproduce this problem with the pymol/branches/b10/pymol source on a Core 2 Duo machine with stock Fedora 8 x86_64 (running under VMWare). There is indeed a serious problem with PyMOL 1.0 source code under 64-bit Linux when building against Python 2.5. However, the current pymol/trunk/pymol source builds and runs fine, so it appears that we have solved this problem in the subsequent months of development. Given all of the accumulated changes between 1.0 and 1.1, finding the fix may not be a trivial task. Anyway, building the open-source code from trunk is an immediate solution for running PyMOL Python 2.5 in 64-bit mode under Linux. Cheers, Warren > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of JJ > Sent: Monday, February 11, 2008 1:18 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] strange pymol crash > > Hello. > I have just installed version 1.0r2 from svn on a brand new > AMD Fedora 8 64-bit machine and it installed without error. > However, when I try to run pymol I get the same startup error > that I had received some time ago on a different machine (the > earlier problem seemed to fix itself for some reason): > > python: Modules/gcmodule.c:276: visit_decref: > Assertion `gc->gc.gc_refs != 0' failed. > /usr/local/bin/pymol: line 2: 2916 Aborted > /usr/bin/python > /usr/lib64/python2.5/site-packages/pymol/__init__.py > $* > > I appreciate your reply on that earlier issue, Warren, but > I'm afraid I do not understand what steps I can take for a > workaround. Are you suggesting below that I change the gcc > instructions in some file? Any clarification would be > appreciated. Has any other workarounds been identified? > > Thanks, > > John > ------------------ > <<< > Re: [PyMOL] strange pymol crash > From: DeLano Scientific <del...@de...> - 2007-12-22 > 20:35 > John, > > This is a bug we haven't yet been able to figure out yet. > However, Jack Howarth has provided the following workaround: > > [with] the compile flags... > > -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions > -fstack-protector > --param=ssp-buffer-size=4 -m64 -mtune=generic > > Out of those it turns out that "-fstack-protector > --param=ssp-buffer-size=4" > triggers the run-time failures. These same flags don't cause > a problem on > x86 (-m32) builds. You might want to look into this to see if > the stack protection code is picking up on a real flaw in > pymol at -m64. > > I hope this helps! > > Cheers, > Warren >>> > > > > ______________________________________________________________ > ______________________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > > -------------------------------------------------------------- > ----------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
