VMD-L Mailing List

From: Michael Doig (m.doig_at_sms.ed.ac.uk)
Date: Tue Jan 24 2012 - 09:55:23 CST

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.