VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 24 2012 - 10:09:45 CST

Michael,
  Thanks for the gdb traceback. Are you running a 32-bit or 64-bit
version of VMD?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 24, 2012 at 03:55:23PM +0000, Michael Doig wrote:
> On 24/01/12 14:46, Axel Kohlmeyer wrote:
> >>>Please try again with the latest VMD beta version.
> >>>
> >>>Axel
> >>>
> >>>
> >>I tried the new beta version of VMD and get the same result. I tried it
> >>with
> >>both the bundled version of topotools (not sure which version), and the
> >>newest version from your website (topotools-1.2-20120114), but it
> >>continues
> >>to segfault, at the writelammpsdata stage.
> >ok. that means that you are not stumbling over the bug
> >that was fixed in the beta.
> >
> >any segfault has to either come from a bug inside of VMD
> >or you running out of stack/address space.
> >
> >can you please try one more thing to help identifying
> >the real cause. please launch VMD like this
> >
> >vmd -debug
> >
> >then at the (gdb) prompt type "run"
> >
> >and then proceed as usual until you get the segfault.
> >this should drop you back into the debugger.
> >then type "where"
> >
> >and report back the output.
> >
> >thanks,
> > axel.
> >
> I have run with the debugger as you suggested and this the output.
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00000000004f8bd1 in atomparser_node::~atomparser_node() ()
>
>
> #0 0x00000000004f8bd1 in atomparser_node::~atomparser_node() ()
> #1 0x00000000004f8be7 in atomparser_node::~atomparser_node() ()
> #2 0x00000000004f8bd1 in atomparser_node::~atomparser_node() ()
> ...
> ...
> ...
> #327223 0x00000000004f8be7 in atomparser_node::~atomparser_node() ()
> #327224 0x00000000004f8be7 in atomparser_node::~atomparser_node() ()
> #327225 0x00000000004f8be7 in atomparser_node::~atomparser_node() ()
> #327226 0x00000000005ee8af in ParseTree::~ParseTree() ()
> #327227 0x000000000050aebd in AtomSel::~AtomSel() ()
> #327228 0x000000000068f8c2 in ?? ()
> #327229 0x00000000008f3102 in Tcl_DeleteCommandFromToken ()
> #327230 0x00000000008f45da in TclRenameCommand ()
> #327231 0x00000000008f55c7 in ?? ()
> #327232 0x0000000000937886 in ?? ()
> #327233 0x0000000000972f77 in TclObjInterpProcCore ()
> #327234 0x00000000008f55c7 in ?? ()
> #327235 0x00000000008f680d in ?? ()
> #327236 0x000000000097f955 in ?? ()
> #327237 0x0000000000980f43 in TclCallVarTraces ()
> #327238 0x0000000000986cf1 in ?? ()
> #327239 0x0000000000989cac in ?? ()
> #327240 0x0000000000989e30 in ?? ()
> #327241 0x00000000008f55c7 in ?? ()
> #327242 0x00000000008f680d in ?? ()
> #327243 0x00000000008f740d in Tcl_Eval ()
> #327244 0x00000000008f7497 in Tcl_VarEvalVA ()
> #327245 0x00000000008f753d in Tcl_VarEval ()
> #327246 0x000000000068e066 in ?? ()
> #327247 0x000000000068be7b in ?? ()
> #327248 0x00000000008f55c7 in ?? ()
> #327249 0x0000000000937886 in ?? ()
> #327250 0x0000000000972f77 in TclObjInterpProcCore ()
> #327251 0x00000000008f55c7 in ?? ()
> #327252 0x0000000000937886 in ?? ()
> #327253 0x0000000000972f77 in TclObjInterpProcCore ()
> #327254 0x00000000008f55c7 in ?? ()
> #327255 0x0000000000937886 in ?? ()
> #327256 0x0000000000972f77 in TclObjInterpProcCore ()
> #327257 0x00000000008f55c7 in ?? ()
> #327258 0x00000000008f5788 in Tcl_EvalObjv ()
> #327259 0x000000000094499e in ?? ()
> #327260 0x00000000008f55c7 in ?? ()
> #327261 0x0000000000937886 in ?? ()
> #327262 0x000000000093d7a4 in ?? ()
> #327263 0x00000000008f7153 in TclEvalObjEx ()
> #327264 0x00000000009431ec in Tcl_RecordAndEvalObj ()
> #327265 0x00000000006a2bf0 in TclTextInterp::doEvent() ()
> #327266 0x000000000064bfb1 in UIText::check_event() ()
> #327267 0x000000000052af12 in CommandQueue::check_events() ()
> #327268 0x000000000065cbd5 in VMDApp::VMDupdate(int) ()
> #327269 0x0000000000686869 in main ()
>
>
> >>
> >>>>Thanks,
> >>>>Michael
> >>>>
> >>>>--
> >>>>The University of Edinburgh is a charitable body, registered in
> >>>>Scotland, with registration number SC005336.
> >>>>
> >>
> >>--
> >>The University of Edinburgh is a charitable body, registered in
> >>Scotland, with registration number SC005336.
> >>
> >
> >
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336. 

-- 
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