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 > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of JJ > Sent: Saturday, December 22, 2007 4:18 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] strange pymol crash > > Hello: > I have a strange crash problem with pymol. I've had the 64 > bit version 1.0r2 installed on two Fedora 8 machines for > several weeks and up until yesterday or so everything was > working just fine. Now pymol will not start on either > machine. Here is the error: > > python: Modules/gcmodule.c:276: visit_decref: > Assertion `gc->gc.gc_refs != 0' failed. > /usr/local/bin/pymol: line 2: 3127 Aborted > /usr/bin/python > /usr/lib64/python2.5/site-packages/pymol/__init__.py > $* > > I tried rebuilding the NVIDIA driver for one machine, but > that did not fix the problem. I also uninstalled and > reinstalled pymol, but it didn't help either. > Perhaps I did something to both machines to cause pymol to > crash, but I don't know what that was. As far as I know, no > Fedora updates were made before the crashes. I did try > installing updates for one machine, but that did not help. I > get the same error if I try to use "import pymol" in an > interactive python shell. Any ideas on how to fix it? > > John > > > > > > > ______________________________________________________________ > ______________________ > 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 2005. > 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
