[Paraview] Ridiculously slow D3 (a bug in vtkMergeCells)

[Zhanping Liu]

Got it and thanks.
-Zhanping

2009/10/1 Takuya OSHIMA <oshima at eng.niigata-u.ac.jp>

> Guys, thanks for all the responses, the tracker entry and applying the
> patch.
>
> I'm afraid I'm not sure if I can provide a good test dataset since the
> bug does not affect small cases (the point insertion should take
> O(n^2) of time where n is the number of points, when the hasing is not
> working) and relies on indeterminate values (there's always a
> possibility that the problem doesn't reproduce), which is why I did
> all the tracking down by myself. But I'll see if I can do something.
>
> Takuya
>
> Takuya OSHIMA, Ph.D.
> Faculty of Engineering, Niigata University
> 8050 Ikarashi-Ninocho, Nishi-ku, Niigata, 950-2181, JAPAN
>
> From: Zhanping Liu <zhanping.liu at kitware.com>
> Subject: Re: [Paraview] Ridiculously slow D3 (a bug in vtkMergeCells)
> Date: Wed, 30 Sep 2009 12:39:15 -0400
>
> > *
>  > Takuya:
> >
> >     The problem was reflected on Mantis (issue #009626) and the suggested
> fix
> > was applied. If you have any test (and shareable datasets), please feel
> free
> > to submit it via Mantis.
> >
> >     Thanks for the report and the fix.
> >
> >     -Zhanping
> >    --
> > Zhanping Liu, PhD
> > Kitware, Inc.
> > 28 Corporate Drive
> > Clifton Park, NY 12065-8662
> > Phone: 518-371-3971 x 138
> > http://www.zhanpingliu.org
> > On Wed, Sep 30, 2009 at 3:51 AM, Takuya OSHIMA <
> oshima at eng.niigata-u.ac.jp>
> > wrote:
> >
> >     Hi,
> >
> >     I have had a problem of ridiculously slow D3 of PV 3.6.1/3.7-cvs
> under
> >     some conditions. Most of the time the problem occurs when I have more
> >     pvserver processes than the number of data pieces, in which case D3
> >     takes two orders of magnitude more time than usual, despite that the
> >     resulting repartitioned dataset looks fine.
> >
> >     Attaching a performance analyzer (Apple's Shark) to the pvserver
> >     processes revealed that, in one of the pvserver processes
> >     vtkMergePoints::InsertUniquePoint() took up virtually all of the
> >     processor time, as attached sharkOutput.jpg.
> >
> >     It further turned out that this is because the instance of
> >     vtkMergePoints is given indeterminate bounds by its caller
> >     vtkMergeCells::MapPointsToIdsUsingLocator() and hence hashing based
> on
> >     relative point coordinates in the bounds is not working. Here is a
> >     proposed fix to the problem (the comment
> "points0->GetNumberOfPoints()
> >     is equal to..." was taken from about 50 lines below the patched lines
> >     in the same function. I believe it explains everything.).
> >
> >     Index: vtkMergeCells.cxx
> >     ===================================================================
> >     RCS file:
> /cvsroot/ParaView3/ParaView3/VTK/Graphics/vtkMergeCells.cxx,v
> >     retrieving revision 1.9
> >     diff -u -r1.9 vtkMergeCells.cxx
> >     --- vtkMergeCells.cxx   23 Jan 2009 03:25:07 -0000      1.9
> >     +++ vtkMergeCells.cxx   30 Sep 2009 06:47:09 -0000
> >     @@ -723,7 +723,12 @@
> >         if (npoints0 > 0)
> >           {
> >           double tmpbounds[6];
> >     +      // points0->GetNumberOfPoints() is equal to the upper bound
> >     +      // on the points in the final merged grid.  We need to
> temporarily
> >     +      // set it to the number of points added to the merged grid so
> far.
> >     +      points0->GetData()->SetNumberOfTuples(npoints0);
> >           grid->GetBounds(tmpbounds);
> >     +
>  points0->GetData()->SetNumberOfTuples(this->TotalNumberOfPoints);
> >
> >           bounds[0] = ((tmpbounds[0] < bounds[0]) ? tmpbounds[0] :
> bounds[0]);
> >           bounds[2] = ((tmpbounds[2] < bounds[2]) ? tmpbounds[2] :
> bounds[2]);
> >
> >     Regards,
> >     Takuya
> >
> >     Takuya OSHIMA, Ph.D.
> >     Faculty of Engineering, Niigata University
> >     8050 Ikarashi-Ninocho, Nishi-ku, Niigata, 950-2181, JAPAN
> >
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-- 
Zhanping Liu, PhD
Kitware, Inc.
28 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-371-3971 x 138
http://www.zhanpingliu.org
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