[vtkusers] Potential bug in graph pedigreeId handling / AbstractArray::LookupValue

Wed Aug 27 20:19:35 EDT 2014

Ah interesting. Note that I plan to remove DataChanged() in the future. It
is a serious performance bottleneck when multiple threads are setting
different parts of an array because it causes all threads to write to the
same memory location where that flag is stored. The right way of doing this
is to call Modified() after doing a set of changes to notify whatever may
depend on an array.

Best,
-berk

On Wed, Aug 27, 2014 at 5:30 PM, Jeff Baumes <jeff.baumes at kitware.com>
wrote:

> It is unclear what changed exactly, but the current behavior is that for
> numeric arrays, setting data with SetValue() (which is what AddVertex
> ultimately does to the pedigree ID array), does not in fact invoke
> DataChanged() on the array which would signal the lookup to rebuild on the
> next LookupValue() call (which is what FindVertex() performs). This was
> done for performance reasons, and perhaps this change was made between 5.8
> and 5.10.
>
> If you call pedigreeIds->DataChanged() just before the call to
> FindVertex(), the issue should be resolved.
>
>
> On Wed, Aug 27, 2014 at 9:28 AM, Adrian Friebel <
> friebel at izbi.uni-leipzig.de> wrote:
>
>> Hey,
>> so far I compiled my software against vtk 5.8. Recently I tried to
>> compile it against 5.10.1 and noticed unexpected behaviour while adding
>> vertices to a graph while passing pedigree ids.
>> Below a minimal example and its output:
>>
>> #include <stdio.h>
>> #include <iostream>
>>
>> #include <vtkDataSetAttributes.h>
>> #include <vtkMutableUndirectedGraph.h>
>> #include <vtkSmartPointer.h>
>> #include <vtkUnsignedLongArray.h>
>>
>> int  main(int argc, char **argv)
>> {
>>     vtkSmartPointer<vtkMutableUndirectedGraph> graph = vtkSmartPointer<
>> vtkMutableUndirectedGraph>::New();
>>
>>     vtkSmartPointer<vtkUnsignedLongArray> pedigreeIds = vtkSmartPointer<
>> vtkUnsignedLongArray>::New();
>>     pedigreeIds->Initialize();
>>     pedigreeIds->SetName("Pedigree IDs");
>>
>>     graph->GetVertexData()->SetPedigreeIds(pedigreeIds);
>>
>>     for(unsigned int i=0; i<10; ++i) {
>>         vtkIdType v = graph->AddVertex(i*100);
>>         std::cout << "i = " << i << ": v = " << v <<
>>                 ", graph->GetVertex[..]->GetVariantValue( " << v << ") =
>> " << graph->GetVertexData()->GetPedigreeIds()->GetVariantValue(v) <<
>>                 ", graph->FindVertex(" << i << "*100) = " <<
>> graph->FindVertex(i*100) << std::endl;
>>     }
>>     return 0;
>> }
>>
>> VTK-5.8:
>> i = 0: v = 0, graph->GetVertex[..]->GetVariantValue( 0) = 0,
>> graph->FindVertex(0*100) = 0
>> i = 1: v = 1, graph->GetVertex[..]->GetVariantValue( 1) = 100,
>> graph->FindVertex(1*100) = 1
>> i = 2: v = 2, graph->GetVertex[..]->GetVariantValue( 2) = 200,
>> graph->FindVertex(2*100) = 2
>> i = 3: v = 3, graph->GetVertex[..]->GetVariantValue( 3) = 300,
>> graph->FindVertex(3*100) = 3
>> i = 4: v = 4, graph->GetVertex[..]->GetVariantValue( 4) = 400,
>> graph->FindVertex(4*100) = 4
>> i = 5: v = 5, graph->GetVertex[..]->GetVariantValue( 5) = 500,
>> graph->FindVertex(5*100) = 5
>> i = 6: v = 6, graph->GetVertex[..]->GetVariantValue( 6) = 600,
>> graph->FindVertex(6*100) = 6
>> i = 7: v = 7, graph->GetVertex[..]->GetVariantValue( 7) = 700,
>> graph->FindVertex(7*100) = 7
>> i = 8: v = 8, graph->GetVertex[..]->GetVariantValue( 8) = 800,
>> graph->FindVertex(8*100) = 8
>> i = 9: v = 9, graph->GetVertex[..]->GetVariantValue( 9) = 900,
>> graph->FindVertex(9*100) = 9
>>
>> VTK-5.10.1:
>> i = 0: v = 0, graph->GetVertex[..]->GetVariantValue( 0) = 0,
>> graph->FindVertex(0*100) = 0
>> i = 1: v = 1, graph->GetVertex[..]->GetVariantValue( 1) = 100,
>> graph->FindVertex(1*100) = 1
>> i = 2: v = 2, graph->GetVertex[..]->GetVariantValue( 2) = 200,
>> graph->FindVertex(2*100) = -1
>> i = 3: v = 3, graph->GetVertex[..]->GetVariantValue( 3) = 300,
>> graph->FindVertex(3*100) = 3
>> i = 4: v = 4, graph->GetVertex[..]->GetVariantValue( 4) = 400,
>> graph->FindVertex(4*100) = -1
>> i = 5: v = 5, graph->GetVertex[..]->GetVariantValue( 5) = 500,
>> graph->FindVertex(5*100) = -1
>> i = 6: v = 6, graph->GetVertex[..]->GetVariantValue( 6) = 600,
>> graph->FindVertex(6*100) = -1
>> i = 7: v = 7, graph->GetVertex[..]->GetVariantValue( 7) = 700,
>> graph->FindVertex(7*100) = 7
>> i = 8: v = 8, graph->GetVertex[..]->GetVariantValue( 8) = 800,
>> graph->FindVertex(8*100) = -1
>> i = 9: v = 9, graph->GetVertex[..]->GetVariantValue( 9) = 900,
>> graph->FindVertex(9*100) = -1
>>
>>
>> It seems that there is something wrong with the
>> AbstractArray::LookupValue in 5.10.1, since the array entries value->pedId
>> are made.
>> I am aware that 6.1 was released some time ago. Maybe the issue was
>> solved already, but since I couldn't find any reports on this I thought I
>> might inform you guys.
>> Or am I just missing some newly introduced update call?
>>
>> Best,
>> Adrian.
>>
>> --
>> Dipl.-Inform. Adrian Friebel
>> Research Group for Multicellular Systems Biology
>> Interdisciplinary Centre for BioInformatics
>> University of Leipzig
>> Haertelstrasse 16-18
>> 04107 Leipzig
>> Germany
>> Tel.: +49 341 97-16627
>> email:  adrian.friebel at uni-leipzig.de
>>
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