[vtkusers] [Paraview] vtkDistributedDataFilter and ghost cells
Andrew Parker
andy.john.parker at googlemail.com
Wed Nov 7 09:34:35 EST 2012
Many thanks for that. I perform some threshold stuff early on, so
basically I'm working with unstructured grids pretty much from zero. I
think I need to try to populate the ghost cells using the approach Ken
suggested, but I'm not sure how to do that both from a conceptual point of
view - I'd just be copying Ken's code, but also from the perspective of
fitting into my code design.
There does seem to be some confusion surrounding ghost cells and local to
global cell mappings both in terms of which class computes/owns them and
when and how. Is that fair? I had assumed that given the massive amount of
work that D3 is doing, it would (must have) computed this info and have
been readily available via get methods, rather than going down the route of
extending the class just to define my own virtual methods....
These things are basic sets of info for parallel computing and I would have
assumed others would have wanted them but there is a lack of usage examples
and posts....not a complaint just surprised given that basically you can't
get going with vtk in parallel unless you use something like D3 for the
type of things I want to do. i.e. local processing and some exchange over
halos....
It is odd that I also can't get cell local to global out of the box as Ken
said...
Going to have a go with Ken's method and see where I get to. Are there any
good examples of creating and using ghost cells with unstructured meshes
that you could recommend??
Cheers again,
Andy
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
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
> > Please keep messages on-topic and check the VTK FAQ at:
> > http://www.vtk.org/Wiki/VTK_FAQ
> >
> > Follow this link to subscribe/unsubscribe:
> > http://www.vtk.org/mailman/listinfo/vtkusers
> >
>
--
__________________________________
Dr Andrew Parker
Em at il: andrew.parker at cantab.net
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.vtk.org/pipermail/vtkusers/attachments/20121107/5ebf0517/attachment.htm>
More information about the vtkusers
mailing list