[vtkusers] vtkGraph::AddVertex segfault

[Caleb Johnston]

Sorry, I wanted to clarify that I was mistaken about that GDB output. As you
might expect, those internal error statements are output at the start.

The program does still crash in release mode, and from what I can tell it
happens at the same point.

Caleb


On Thu, May 13, 2010 at 4:07 PM, Aashish Chaudhary <
aashish.chaudhary at kitware.com> wrote:

>
> On Thu, May 13, 2010 at 3:59 PM, Caleb Johnston <cjj37 at cornell.edu> wrote:
>
>> I only get a SIGSEGV signal from the OS. However, I do get some other
>> strange behavior that I don't fully understand. I have included it below.
>>
>> When I start the program in the debugger, I get this:
>> ** (<unknown>:15767): CRITICAL **: atk_object_set_name: assertion `name !=
>> NULL' failed
>>
>> I believe this is gtk / gnome issue. I used to see this when I was using
> Ubuntu 9.04 not anymore with 10.04
>
>
>> And when the seg fault happens, I see this:
>> (Internal error: pc 0x3b4adb in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3b4ada in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3b4ada in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3b4ada in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3b4a80 in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3c25a7 in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3c25a6 in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3c25a6 in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3c25a6 in read in psymtab, but not in symtab.)
>> (Internal error: pc 0x3c2390 in read in psymtab, but not in symtab.)
>>
>> I just did a quick google search .. looks like this is more or less gdb
> issue
>
>>
>> On windows, I just get error code 3 at the same point. The only reason I
>> tried to perform the Update call is because I thought it might alleviate
>> this problem. But it didn't. If its of use, here is some more system info:
>>
>> Linux: Ubuntu 9.10
>> Windows: XP SP3
>>
>> Linux runs in VMware Fusion but i get the same problem in windows without
>> the VM. And the Windows machine has over 3GB of Ram, so I doubt that its out
>> of memory in this case.
>>
>> Does your program crash in release mode (release build) ?
>
>
>>  thanks,
>> Caleb
>>
>>
>> On Thu, May 13, 2010 at 3:45 PM, Aashish Chaudhary <
>> aashish.chaudhary at kitware.com> wrote:
>>
>>> normally a push on vector should not result in crash. Something else is
>>> wrong somewhere.
>>>
>>> Also are you getting std::bad_alloc exception?
>>>
>>>
>>> On Thu, May 13, 2010 at 3:41 PM, Caleb Johnston <cjj37 at cornell.edu>wrote:
>>>
>>>> If I comment out the code, it does not crash. But I also have to end the
>>>> whole control flow at that point because everything after it depends upon
>>>> that data. But there is no crash.
>>>>
>>>> Caleb
>>>>
>>>>
>>>> On Thu, May 13, 2010 at 3:25 PM, Aashish Chaudhary <
>>>> aashish.chaudhary at kitware.com> wrote:
>>>>
>>>>> Can you try this..
>>>>>
>>>>> Can you comment the code where you are loading volume data? And see if
>>>>> you can replicate the crash?
>>>>>
>>>>>
>>>>> On Thu, May 13, 2010 at 3:17 PM, Caleb Johnston <cjj37 at cornell.edu>wrote:
>>>>>
>>>>>> The code is not that compilable without Qt, VTK, ITK, and Cmake
>>>>>> installed. It is publicly hosted at SourceForge:
>>>>>> http://sourceforge.net/projects/glassbrain/
>>>>>>
>>>>>> And the stack trace shows the problem arrises from the AddVertex call.
>>>>>>
>>>>>>
>>>>>> On Thu, May 13, 2010 at 2:25 PM, David Doria <
>>>>>> daviddoria+vtk at gmail.com <daviddoria%2Bvtk at gmail.com>> wrote:
>>>>>>
>>>>>>> On Thu, May 13, 2010 at 2:16 PM, Caleb Johnston <cjj37 at cornell.edu>
>>>>>>> wrote:
>>>>>>> > I'm getting a segfault when calling
>>>>>>> vtkMutableUndirectedGraph::AddVertex.
>>>>>>> > However, it does not always occur at the same vertex. Sometimes it
>>>>>>> is after
>>>>>>> > the 2nd vertex. Sometimes it won't happen at all (though rarely).
>>>>>>> I'm only
>>>>>>> > adding about 120 vertices. And the program is not consuming large
>>>>>>> amounts of
>>>>>>> > data so I don't understand why this is happening. Also, this only
>>>>>>> happens in
>>>>>>> > Linux and Windows but not MacOS X. Below, I have included my
>>>>>>> algorithm for
>>>>>>> > adding vertices.
>>>>>>> > thanks,
>>>>>>> > Caleb
>>>>>>> > ...
>>>>>>> > int len = 0;
>>>>>>> > double X,Y,Z,Count;
>>>>>>> > for(i=0, j=0; j<numberOfLabels; i+=3, j++){
>>>>>>> >    X = (double)coords[i];
>>>>>>> >    Y = (double)coords[i+1];
>>>>>>> >    Z = (double)coords[i+2];
>>>>>>> >    Count = (double)centroids[j];
>>>>>>> >    if(Count>0.0){
>>>>>>> >       X = X / Count;
>>>>>>> >       Y = Y / Count;
>>>>>>> >       Z = Z / Count;
>>>>>>> >       len++;
>>>>>>> >       graph->AddVertex();  // crashes here.
>>>>>>> >       graph->Update();
>>>>>>> >       points->InsertNextPoint(X, Y, Z);
>>>>>>> >    }
>>>>>>> > }
>>>>>>> > ...
>>>>>>>
>>>>>>> I've used this in Linux plenty of times with no problems. If you post
>>>>>>> some compilable code I can see if it works on my machine. My initial
>>>>>>> bet is that something is going wrong around there, like accessing out
>>>>>>> of bounds elements in coords or centroids.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> David
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Please keep messages on-topic and check the VTK FAQ at:
>>>>>> http://www.vtk.org/Wiki/VTK_FAQ
>>>>>>
>>>>>> Follow this link to subscribe/unsubscribe:
>>>>>> http://www.vtk.org/mailman/listinfo/vtkusers
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> | Aashish Chaudhary
>>>>> | R&D Engineer
>>>>> | Kitware Inc.
>>>>> | www.kitware.com
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> | Aashish Chaudhary
>>> | R&D Engineer
>>> | Kitware Inc.
>>> | www.kitware.com
>>>
>>
>>
>
>
> --
> | Aashish Chaudhary
> | R&D Engineer
> | Kitware Inc.
> | www.kitware.com
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.vtk.org/pipermail/vtkusers/attachments/20100513/a59ab431/attachment.htm>