[Paraview] [vtkusers] vtkDistributedDataFilter and ghost cells

[Andrew Parker]

Hi mate, how goes it?

How do you set the ghost level to be one rather than default zero then?
 Have you written your own "downstream" filter to update the number of
ghost levels?  If so any tips?

"If you know the name of a global node ID array in the input dataset, set
that name with this method"... Which method??  How do I set this?  I could
probably work out the global node and cell numbers and stick them into the
meshes that I pass to D3.  But how do I do that?  What method do I call to
set them, and what name do I give them.... "this method" ain't that helpful
in the docs ;-)

Cheers,
Andy

On 8 November 2012 01:18, Paul Edwards <paul.m.edwards at gmail.com> wrote:

> Hi Andy,
>
> I've had a few problems with D3.  The limitation I find is that global
> node ids are slow to generate and the point merging (I think) is only
> performed in single precision.  Also, remember that everything will be
> redone each time the number of ghost levels that are requested changes -
> this means the global ids are recalculated, it is repartitioned and then
> the number of ghost levels are added.  In some ways it might be better to
> have D3 split into 3 filters for the different steps although it would make
> a long pipeline.
>
> Btw looking at the docs it seems to suggest that it only creates temporary
> arrays for global ids within d3 (although I think in the past I have had
> access to the global ids it created):
>
> If you know the name of a global node ID array in the input dataset, set
> that name with this method. If you leave it unset, D3 will search the input
> data set for certain common names of global node ID arrays. If none is
> found, and ghost cells have been requested,* D3 will create a temporary
> global node ID array* before acquiring ghost cells. It is also desirable
> to have global element IDs. However, if they don't exist D3 can create them
> relatively quickly. Set the name of the global element ID array if you have
> it. If it is not set, D3 will search for it using common names. If still
> not found, D3 will create a temporary array of global element IDs.
>
>
> My filters now add their own global ids so I don't use d3 for that.
>
> Regards,
> Paul
>
>
> On 7 November 2012 14:50, George Zagaris <george.zagaris at kitware.com>wrote:
>
>> On Wed, Nov 7, 2012 at 9:34 AM, Andrew Parker
>> <andy.john.parker at googlemail.com> wrote:
>> > Many thanks for that.  I perform some threshold stuff early on, so
>> basically
>> >
>>
>> Perhaps an easy solution is to append a "GlobalCellID" and
>> "GlobalNodeID" before thresholding. To the best of my knowledge,
>> threshold will extract vtkUnstructuredGrid instance from whatever goes
>> in the input and not automatically retain this type of global
>> information.
>>
>> Hope this helps.
>>
>> Best,
>> George
>>
>> > On 7 November 2012 13:00, George Zagaris <george.zagaris at kitware.com>
>> wrote:
>> >>
>> >> Hello,
>> >>
>> >> Since the data is essentially structured (rectilinear grids), I think
>> >> the best way to get the global/local mapping is to use extent
>> >> information. Specifically, you need the whole extent of the grid and
>> >> the global extent of each partition. Then from the global IJK of a
>> >> point or cell, and the whole extent you can use methods from
>> >> vtkStructuredData to compute the corresponding global linear index for
>> >> a point or cell. Do you have extent information?
>> >>
>> >> Also, I have done some work on ghost generation in VTK for structured
>> >> (and AMR) data. Unfortunately, currently it doesn't work outside the
>> >> box with rectilinear grids. This functionality can still be used to
>> >> create ghost layers and exchange the fields (node and/or cell data) on
>> >> the grid but, it doesn't communicate the coordindates on the
>> >> rectilinear grid. Alternatively, you may be able to converge to a
>> >> solution faster if you convert the rectilinear grid to a
>> >> vtkStructuredGrid and use vtkPStructuredGridConnectivity or
>> >> vtkPStructuredGridGhostDataGenerator to generate ghost layers. There
>> >> are tests that illustrate how to use these classes and I can provide
>> >> more information if you are interested.
>> >>
>> >> Best,
>> >> George
>> >>
>> >> On Wed, Nov 7, 2012 at 7:22 AM, Moreland, Kenneth <kmorel at sandia.gov>
>> >> wrote:
>> >> > Hmmm. I thought global point IDs were always created. Maybe it only
>> >> > happens
>> >> > when ghost cells are created. Try getting that working first.
>> >> >
>> >> > As far as global cell IDs are concerned, you are out of luck.
>> >> > vtkDistributedDataFilter does not create them. But they are not all
>> that
>> >> > useful anyway since, unlike points, once you remove the out cells
>> there
>> >> > is
>> >> > no overlap. Usually you can get all the information you want from the
>> >> > ghost
>> >> > level.
>> >> >
>> >> > If you really need global cell IDs, I'm sure you would have no
>> trouble
>> >> > making them yourself. I would do it before running
>> >> > vtkDistributedDataFilter.
>> >> > Assuming when you first read in your data you have no duplicate
>> cells,
>> >> > just
>> >> > label those on process 0 as 0..N_0, those on process 1 as N_0+1..N_1,
>> >> > and so
>> >> > on.
>> >> >
>> >> > -Ken
>> >> >
>> >> > Sent from my iPad so blame autocorrect.
>> >> >
>> >> > On Nov 7, 2012, at 2:38 AM, "Andrew Parker"
>> >> > <andy.john.parker at googlemail.com> wrote:
>> >> >
>> >> > So that's working now in terms of the cast, forgot GetOutput() inside
>> >> > the
>> >> > cast operator!  The returned vtkUGrid is now fully populated and
>> >> > contains
>> >> > sensible information.
>> >> >
>> >> > However, both getPointData()->GetGlobalIds()  and
>> >> > getCellData()->GetGlobalIds() return null pointers.  Any thoughts?
>> >> >
>> >> > Also, should I be using CellData since I want the cell global to
>> local
>> >> > mapping for cells not the nodes, at the moment at least?
>> >> >
>> >> > On 6 November 2012 19:05, Moreland, Kenneth <kmorel at sandia.gov>
>> wrote:
>> >> >>
>> >> >> Perhaps it is outputting a composite data set of some type?  Try
>> >> >> running
>> >> >> GetClassName() to see what type of data object it really is.
>> >> >>
>> >> >> -Ken
>> >> >>
>> >> >> From: Andrew Parker <andy.john.parker at googlemail.com>
>> >> >> Date: Tuesday, November 6, 2012 9:50 AM
>> >> >>
>> >> >> To: Kenneth Moreland <kmorel at sandia.gov>
>> >> >> Cc: "vtkusers at vtk.org" <vtkusers at vtk.org>, "paraview at paraview.org"
>> >> >> <paraview at paraview.org>
>> >> >> Subject: [EXTERNAL] Re: [Paraview] vtkDistributedDataFilter and
>> ghost
>> >> >> cells
>> >> >>
>> >> >> Thanks on both accounts.  Any thoughts why the downcast called after
>> >> >> dd->Update() on distributedDataFilter is a null pointer?  As in, dd
>> is
>> >> >> working perfectly properly, but I don't seem to be able to extract a
>> >> >> valid
>> >> >> unstructuredgrid.  For a follow up question I assume
>> >> >> getPointData()->GetGlobalIds() gives the local to global for the
>> mesh
>> >> >> nodes,
>> >> >> and I should use getCellData()->GetGlobalIds() to get the local to
>> >> >> global
>> >> >> for the cells?  Once I get a valid pointer that is....
>> >> >>
>> >> >> Cheers again,
>> >> >> Andy
>> >> >>
>> >> >> On 6 November 2012 16:40, Moreland, Kenneth <kmorel at sandia.gov>
>> wrote:
>> >> >>>
>> >> >>> You should be able to do a vtkUnstructuredGrid::SafeDownCast() to
>> the
>> >> >>> data to get the unstructured mesh (and access to the point data).
>> >> >>>
>> >> >>> -Ken
>> >> >>>
>> >> >>> From: Andrew Parker <andy.john.parker at googlemail.com>
>> >> >>> Date: Tuesday, November 6, 2012 9:32 AM
>> >> >>> To: Kenneth Moreland <kmorel at sandia.gov>
>> >> >>> Cc: "vtkusers at vtk.org" <vtkusers at vtk.org>, "paraview at paraview.org"
>> >> >>> <paraview at paraview.org>
>> >> >>> Subject: [EXTERNAL] Re: [Paraview] vtkDistributedDataFilter and
>> ghost
>> >> >>> cells
>> >> >>>
>> >> >>> Another question which I'd forgotten, how do I get to a
>> >> >>> vtkUnstructuredGrid per processor from the
>> vtkDistributedDataFilter.
>> >> >>>
>> >> >>> For instance, dd->GetOutput()->GetPointData()->GetGlobalIds()
>> doesn't
>> >> >>> work as it's a vtkDataObject
>> >> >>>
>> >> >>> Stupid question I'm sure but the doxy notes say this type returns
>> an
>> >> >>> unstructured mesh, but I can't seem to get it out?
>> >> >>>
>> >> >>> Also, why exactly do I need the vtkPieceScalars and
>> >> >>> vtkDataSetSurfaceFilter again? If the above can be made to work and
>> >> >>> return
>> >> >>> the mapping, what are they adding in terms of information?
>> >> >>>
>> >> >>> Thanks again,
>> >> >>> Andy
>> >> >>>
>> >> >>> On 6 November 2012 16:00, Moreland, Kenneth <kmorel at sandia.gov>
>> wrote:
>> >> >>>>
>> >> >>>> I believe vtkDistributedDataFilter will always return with global
>> >> >>>> point
>> >> >>>> ids (a mapping from local point ids to global point ids),
>> although it
>> >> >>>> might
>> >> >>>> pass them if they already exist.  So
>> >> >>>> dd->GetOutput()->GetPointData()->GetGlobalIds() should return the
>> >> >>>> array that
>> >> >>>> gives this mapping.
>> >> >>>>
>> >> >>>> Ghost cells are only created on demand, and this is usually done
>> by
>> >> >>>> pipeline convention.  If you have a filter that needs a layer of
>> >> >>>> ghost
>> >> >>>> cells, it should override the RequestUpdateExtent method to
>> increment
>> >> >>>> the
>> >> >>>> value of UPDATE_NUMBER_OF_GHOST_LEVELS from the output
>> information to
>> >> >>>> the
>> >> >>>> input information.  This method would look something like this.
>> >> >>>>
>> >> >>>> int vtkDistributedDataFilter::RequestUpdateExtent(
>> >> >>>>   vtkInformation *vtkNotUsed(request),
>> >> >>>>   vtkInformationVector **inputVector,
>> >> >>>>   vtkInformationVector *outputVector)
>> >> >>>> {
>> >> >>>>   // get the info objects
>> >> >>>>   vtkInformation *inInfo =
>> inputVector[0]->GetInformationObject(0);
>> >> >>>>   vtkInformation *outInfo = outputVector->GetInformationObject(0);
>> >> >>>>
>> >> >>>>   int piece, numPieces, ghostLevels;
>> >> >>>>
>> >> >>>>   // We require an extra layer of ghost cells from upstream.
>> >> >>>>
>> >> >>>>   piece =
>> >> >>>>
>> >> >>>>
>> outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER());
>> >> >>>>   numPieces =
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_PIECES());
>> >> >>>>   ghostLevels =
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> outInfo->Get(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS());
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> inInfo->Set(vtkStreamingDemandDrivenPipeline::UPDATE_PIECE_NUMBER(),
>> >> >>>> piece);
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> inInfo->Set(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_PIECES(),
>> >> >>>>               numPieces);
>> >> >>>>
>> >> >>>>
>> >> >>>>
>> inInfo->Set(vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS(),
>> >> >>>>               ghostLevels);
>> >> >>>>
>> >> >>>>   return 1;
>> >> >>>> }
>> >> >>>>
>> >> >>>>
>> >> >>>> The operation of the RequestData method should also strip off this
>> >> >>>> layer
>> >> >>>> of ghost cells.  It might be possible to request a layer of ghost
>> >> >>>> cells by
>> >> >>>> setting UPDATE_NUMBER_OF_GHOST_LEVELS at the bottom of the
>> pipeline,
>> >> >>>> but I'm
>> >> >>>> not totally sure how to make that work.  It's probably easier (or
>> at
>> >> >>>> least
>> >> >>>> cleaner) to do it from within a filter.
>> >> >>>>
>> >> >>>> -Ken
>> >> >>>>
>> >> >>>> From: Andrew Parker <andy.john.parker at googlemail.com>
>> >> >>>> Date: Tuesday, November 6, 2012 8:25 AM
>> >> >>>> To: "vtkusers at vtk.org" <vtkusers at vtk.org>, "paraview at paraview.org
>> "
>> >> >>>> <paraview at paraview.org>
>> >> >>>> Subject: [EXTERNAL] [Paraview] vtkDistributedDataFilter and ghost
>> >> >>>> cells
>> >> >>>>
>> >> >>>> Hi,
>> >> >>>>
>> >> >>>> Hope you can help.  I have some code running in parallel, that by
>> >> >>>> other
>> >> >>>> means I have constructed nprocs worth of vtkRectilinearGrids, one
>> per
>> >> >>>> process.  Each of which is a valid nprocs-worth of the whole
>> serial
>> >> >>>> mesh,
>> >> >>>> I've check this and I am happy with that i.e. it's partitioned
>> >> >>>> properly and
>> >> >>>> nothing is missing.  I need the following information to process
>> my
>> >> >>>> data in
>> >> >>>> parallel:
>> >> >>>>
>> >> >>>> 1) I would like the local -> global cell mapping between the local
>> >> >>>> rgrid
>> >> >>>> and the corresponding global single mesh.
>> >> >>>> 2) I would like to know which cells are on processor boundaries
>> for
>> >> >>>> parallel exchange purposes.
>> >> >>>> 3) I would like all the double arrays per processor to be
>> "expanded"
>> >> >>>> by
>> >> >>>> the amount of (1 level of) ghost cells such that I can properly do
>> >> >>>> the
>> >> >>>> computations I want with the ability to exchange only those
>> >> >>>> additional cells
>> >> >>>> given the local to global mapping.
>> >> >>>>
>> >> >>>> I have tried from the examples to use the following code, which I
>> >> >>>> call
>> >> >>>> on every process, each of which has it's own local rgrid as I
>> said.
>> >> >>>> I do
>> >> >>>> the following:
>> >> >>>>
>> >> >>>>  vtkSmartPointer<vtkDistributedDataFilter> dd =
>> >> >>>> vtkSmartPointer<vtkDistributedDataFilter>::New();
>> >> >>>>  dd->SetInput(rgrid);
>> >> >>>>
>> >> >>>>  dd->SetController(getVtkController());
>> >> >>>>  dd->SetBoundaryModeToSplitBoundaryCells();
>> >> >>>>  //dd->SetBoundaryModeToAssignToOneRegion();
>> >> >>>>  //dd->SetBoundaryModeToAssignToAllIntersectingRegions();
>> >> >>>>  dd->UseMinimalMemoryOff();
>> >> >>>>  dd->Update();
>> >> >>>>  vtkPieceScalars *ps = vtkPieceScalars::New();
>> >> >>>>  ps->SetInputConnection(dd->GetOutputPort());
>> >> >>>>  ps->SetScalarModeToCellData();
>> >> >>>>  vtkDataSetSurfaceFilter *dss = vtkDataSetSurfaceFilter::New();
>> >> >>>>  dss->SetInputConnection(ps->GetOutputPort());
>> >> >>>>
>> >> >>>> The dd object works fine and writing its contents out on each
>> >> >>>> processor
>> >> >>>> gives nprocs worth of meshes, each of which look slightly
>> different
>> >> >>>> to the
>> >> >>>> way I've partitioned them up, but sum to the same serial mesh so
>> I am
>> >> >>>> happy
>> >> >>>> with that working correctly. But I can't for the life of me figure
>> >> >>>> out how
>> >> >>>> to obtain local to global cell mappings, allocate ghost cells, or
>> >> >>>> work out
>> >> >>>> how to exchange data given the above partition info and comms....
>> >> >>>>
>> >> >>>> Note I have not provided any additional information to "dd"
>> regarding
>> >> >>>> global cells as per the doxy notes so I assume it went away and
>> >> >>>> computed it.
>> >> >>>> I can't figure out how to extract it however.  I also have no idea
>> >> >>>> how to
>> >> >>>> modify each local processor rgrid to include the ghost cells for
>> that
>> >> >>>> processor.  Finally given that info, I could exchange between
>> >> >>>> processors to
>> >> >>>> write to each local processors ghost cells the corresponding
>> "real"
>> >> >>>> cell
>> >> >>>> data from the neighbouring meshes and continue the code.
>> >> >>>>
>> >> >>>> Any help really appreciated!
>> >> >>>>
>> >> >>>> Cheers,
>> >> >>>> Andy
>> >> >>>>
>> >> >>>
>> >> >>>
>> >> >>>
>> >> >>> --
>> >> >>>
>> >> >>> __________________________________
>> >> >>>
>> >> >>>    Dr Andrew Parker
>> >> >>>
>> >> >>>    Em at il:  andrew.parker at cantab.net
>> >> >>>
>> >> >>>
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >> __________________________________
>> >> >>
>> >> >>    Dr Andrew Parker
>> >> >>
>> >> >>    Em at il:  andrew.parker at cantab.net
>> >> >>
>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> >
>> >> > __________________________________
>> >> >
>> >> >    Dr Andrew Parker
>> >> >
>> >> >    Em at il:  andrew.parker at cantab.net
>> >> >
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > Powered by www.kitware.com
>> >> >
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>> >> > Please keep messages on-topic and check the VTK FAQ at:
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>> >> >
>> >
>> >
>> >
>> >
>> > --
>> >
>> > __________________________________
>> >
>> >    Dr Andrew Parker
>> >
>> >    Em at il:  andrew.parker at cantab.net
>> >
>> >
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
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>


-- 

__________________________________

   Dr Andrew Parker

   Em at il:  andrew.parker at cantab.net
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