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 >>>
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