[vtkusers] vtkGraph::AddVertex segfault

[Caleb Johnston]

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

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.)


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.

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
>>>>>
>>>>
>>>>
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>>>
>>>
>>> --
>>> | Aashish Chaudhary
>>> | R&D Engineer
>>> | Kitware Inc.
>>> | www.kitware.com
>>>
>>
>>
>
>
> --
> | Aashish Chaudhary
> | R&D Engineer
> | Kitware Inc.
> | www.kitware.com
>
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