[Paraview-developers] "Unable to build k-d tree structure" error with D3 filter and PV 4.4.0 on large datasets

[Cory Quammen]

Hi Michael,

Sorry to just getting around to responding to your question.

It looks like you are running out of memory on at least one compute node,
but I'm guessing you already figured that out. You'll either need to reduce
the data size somehow, increase the memory per core, or increase the number
of cores.

HTH,
Cory

On Tue, Mar 8, 2016 at 9:36 AM, Schlottke-Lakemper, Michael <
m.schlottke-lakemper at aia.rwth-aachen.de> wrote:

> Dear all,
>
> We have recently come across the following error when using the D3 filter
> on large and distributed vtkUnstructuredGrids. We have our own reader that
> locally creates a vtkUnstructuredGrid by reading the according subdomain
> from a file in netcdf format and I would like to use the D3 filter to have
> halo cells available on all domains (e.g. for gradient computations). For
> small scale meshes containing about 260 x 10^6 cells there is no problem.
> However, when I want to execute the filter on 1.8 x 10^9 cells I get the
> following error messages:
>
> Warning: In
> /dev/shm/domini/ParaView/4.4.0/intel-para-2015.07-mpi-devel/ParaView-v4.4.0-source/VTK/Filters/Parallel/vtkPKdTree.cxx,
> line 207
> vtkPKdTree (0x2943d0c0): (process 490) memory allocation on my node
> (BreadthFirstDivide)
>
> ERROR: In
> /dev/shm/domini/ParaView/4.4.0/intel-para-2015.07-mpi-devel/ParaView-v4.4.0-source/VTK/Filters/ParallelMPI/vtkDistributedDataFilter.cxx,
> line 796
> vtkDistributedDataFilter (0x29433cd0): Unable to build k-d tree structure
>
>
> the same is happening with other remote nodes, i.e.,
>
> Warning: In
> /dev/shm/domini/ParaView/4.4.0/intel-para-2015.07-mpi-devel/ParaView-v4.4.0-source/VTK/Filters/Parallel/vtkPKdTree.cxx,
> line 207
> vtkPKdTree (0x2a9fdf20): (process 137) memory allocation on a remote node
> (BreadthFirstDivide)
>
>
> I run a server on 576 cores using ParaView version 4.4.0. The program does
> not crash after this error, however, it is not creating any output. I have
> tracked down the error to the following (potential) location. I noticed
> that this error seems to be generated in the function BreadthFirstDivision,
> which somehow returns the error code 1, which is then in AllCheckForFailure
> summarized to a value > 0 on all MPI ranks leading to the error message. I
> also noticed that this cannot be a VTKERROR as it is not printed to the
> terminal. I believe that the error might reside in the check for midpt <
> -1, which would also return an error code of 1 in BreatdhFirstDivision.
>
> I hope you can help me with this problem. Thanks a lot in advance!
>
> Michael
>
>
> --
> Michael Schlottke-Lakemper
>
> Chair of Fluid Mechanics and Institute of Aerodynamics
> RWTH Aachen University
> Wüllnerstraße 5a
> 52062 Aachen
> Germany
>
> Phone: +49 (241) 80 95188
> Fax: +49 (241) 80 92257
> Mail: m.schlottke-lakemper at aia.rwth-aachen.de
> Web: http://www.aia.rwth-aachen.de
>
>
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-- 
Cory Quammen
R&D Engineer
Kitware, Inc.
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