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
I hope this helps!
> -----Original Message-----
> From: pymol-users-bounces@...
> [mailto:pymol-users-bounces@...] On Behalf Of JJ
> Sent: Saturday, December 22, 2007 4:18 AM
> To: pymol-users@...
> Subject: [PyMOL] strange pymol crash
> 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
> 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?
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