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

[Zhanping Liu]

Hi Takuya:

  I have checked the code segment that you mentioned and I think your fix is
correct.

 Thanks.

 -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 8:15 AM, John Biddiscombe <biddisco at cscs.ch> wrote:

> Takuya
>
> Good work. If the kitware/Sandia guys don't respond, then I'll look at your
> patch in a week or two and get it in. (A lot of locator changes have been
> made recently, so do make sure you're using CVS pv)
>
> JB
>
>   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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> --
> John Biddiscombe,                            email:biddisco @ cscs.chhttp://www.cscs.ch/
> CSCS, Swiss National Supercomputing Centre  | Tel:  +41 (91) 610.82.07
> Via Cantonale, 6928 Manno, Switzerland      | Fax:  +41 (91) 610.82.82
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