From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 24 2012 - 10:15:38 CST

Would it be possible for you to package up all of the files you're
working with and provide a script that runs topotools and
causes the crash you observe? If you can do that, and either post it
somewhere that I can download it, or send it to me (if it is small)
I will have a close look at what is going on there and see if I can
track down the source of that problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 24, 2012 at 04:13:24PM +0000, Michael Doig wrote:
> On 24/01/12 16:09, John Stone wrote:
> >Michael,
> > Thanks for the gdb traceback. Are you running a 32-bit or 64-bit
> >version of VMD?
> >
>
> I'm running the 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.
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078