VMD-L Mailing List

From: Michael Doig (m.doig_at_sms.ed.ac.uk)
Date: Tue Jan 24 2012 - 10:13:24 CST

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.