Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Berk Geveci
self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
1)


in RequestUpdateExtent script. Of course, this requires that the reader or
a filter before the programmable filter is able to provide ghost levels.


-berk

On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Hello,

 I am trying to request ghost data in my python programmable filter but I
 am not sure how to go about and do so. I am assuming the call would go into
 the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to is
 something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() , and
 there are examples of that in the Paraview source but the way the objects
 are defined and called does not translate into Paraview VTK Python. What
 would be the appropriate call?

 Thank you,
 Jesus


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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Jesus Pulido
Thank you Berk.

I was under the impression that this command would trigger the reader to
automatically load in the additional # of requested ghost levels. I tested
the command and each data piece still has the same extents as before.

Is there any additional way to load in ghost level that's parallel
friendly? I am aware of the D3 filter but, from the memory usage, it seems
that it will load in the entire dataset into each processor and this is not
feasible for large datasets.

I am using binary, raw vti piece files each with their own extent of the
data and a header pvti file.
The data has no encoded ghost layers between pieces so I was hoping to have
paraview do that for me.

Jesus

On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci berk.gev...@kitware.comwrote:

 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the reader or
 a filter before the programmable filter is able to provide ghost levels.


 -berk

 On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Hello,

 I am trying to request ghost data in my python programmable filter but I
 am not sure how to go about and do so. I am assuming the call would go into
 the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to is
 something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() , and
 there are examples of that in the Paraview source but the way the objects
 are defined and called does not translate into Paraview VTK Python. What
 would be the appropriate call?

 Thank you,
 Jesus


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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Burlen Loring
There is also ghost cell generator for image data that does not convert 
to multi block. It's called SQImageGhosts and resides in the 
SciberQuestToolKit pluign.


You would need to ensure the plugin is loaded and insert this filter 
upstream of your python filter.


In your filter's RequestUpdateExtent you'll need to set both 
UPDATE_NUMBER_OF_GHOST_LEVELS() and UPDATE_EXTENT() to reflect the 
number of ghost cells that you need. When you set UPDATE_EXTENT() to 
include ghost cells you must ensure that it is contained by WHOLE_EXTENT().


In your filter's RequestData you'll need to give PV the extent he 
initially asked for and process the input and output arrays according to 
the modified input extents and requested output extents respectively. 
The following c++ code illustrates. You'll have to build PV from source 
and turn on the plugin during the build. I would recommend pulling the 
sources from PV git repo since a number of windows and mac build issues 
were recently fixed.


Burlen

this illustrates how ghost cells are requested in a filter:

//-
int vtkSQKernelConvolution::RequestUpdateExtent(
  vtkInformation *req,
  vtkInformationVector **inInfos,
  vtkInformationVector *outInfos)
{
  // ...

  // We will modify the extents we request from our input so
  // that we will have a layers of ghost cells. We also pass
  // the number of ghosts through the piece based key.
  int nGhosts = this-KernelWidth/2;

  inInfo-Set(
vtkSDDPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS(),
nGhosts);

  CartesianExtent outputExt;
  outInfo-Get(
vtkSDDPipeline::UPDATE_EXTENT(),
outputExt.GetData());

  CartesianExtent wholeExt;
  inInfo-Get(
vtkSDDPipeline::WHOLE_EXTENT(),
wholeExt.GetData());

  outputExt = CartesianExtent::Grow(
outputExt,
wholeExt,
nGhosts,
this-Mode);

  inInfo-Set(
vtkSDDPipeline::UPDATE_EXTENT(),
outputExt.GetData(),
6);

  int piece
= outInfo-Get(vtkSDDPipeline::UPDATE_PIECE_NUMBER());

  int numPieces
= outInfo-Get(vtkSDDPipeline::UPDATE_NUMBER_OF_PIECES());

  inInfo-Set(vtkSDDPipeline::UPDATE_PIECE_NUMBER(), piece);
  inInfo-Set(vtkSDDPipeline::UPDATE_NUMBER_OF_PIECES(), numPieces);
  inInfo-Set(vtkSDDPipeline::EXACT_EXTENT(), 1);

  return 1;
}

//-
int vtkSQKernelConvolution::RequestData(
vtkInformation * /*req*/,
vtkInformationVector **inInfoVec,
vtkInformationVector *outInfoVec)
{

  // ...

  // Get the input and output extents.
  CartesianExtent inputExt;
  inInfo-Get(
vtkStreamingDemandDrivenPipeline::UPDATE_EXTENT(),
inputExt.GetData());

  CartesianExtent inputDom;
  inInfo-Get(
vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(),
inputDom.GetData());

  CartesianExtent outputExt;
  outInfo-Get(
vtkStreamingDemandDrivenPipeline::UPDATE_EXTENT(),
outputExt.GetData());

  CartesianExtent domainExt;
  outInfo-Get(
vtkStreamingDemandDrivenPipeline::WHOLE_EXTENT(),
domainExt.GetData());

  // Check that we have the ghost cells that we need (more is OK).
  int nGhost = this-KernelWidth/2;

  CartesianExtent inputBox(inputExt);
  CartesianExtent outputBox
= CartesianExtent::Grow(outputExt, nGhost, this-Mode);

  if (!inputBox.Contains(outputBox))
{
vtkErrorMacro(
 This filter requires ghost cells to function correctly. 
 The input must contain the output plus   nGhost
  layers of ghosts. The input is   inputBox
 , but it must be at least 
 outputBox  .);
return 1;
}

  // NOTE You can't do a shallow copy because the array dimensions are
  // different on output and input because of the ghost layers.

  vtkImageData *inImData=dynamic_castvtkImageData *(inData);
  vtkImageData *outImData=dynamic_castvtkImageData *(outData);

  // set up the output.
  double X0[3];
  outInfo-Get(vtkDataObject::ORIGIN(),X0);
  outImData-SetOrigin(X0);

  double dX[3];
  outInfo-Get(vtkDataObject::SPACING(),dX);
  outImData-SetSpacing(dX);

  outImData-SetExtent(outputExt.GetData());

  // ...
}


On 07/17/2012 10:24 AM, George Zagaris wrote:

Since you have structured grids, one other possibility is using:
vtkPUniformGridGhostDataGenerator
(http://www.vtk.org/doc/nightly/html/classvtkPUniformGridGhostDataGenerator.html)

Each process constructs a vtkMultiBlockDataSet instance consisting of
the grids/blocks owned by the process with NULL entries for all remote
blocks.
The resulting output of the filter is a vtkMultiBlockDataSet
consisting of the ghosted grid/block instances. Make sure that you
specify the whole-extent for the entire dataset and that for each
block you attach PIECE_EXTENT() in the corresponding vtkInformation.

Let me know if you need more help on this.

Best,
George


On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulidojpul...@ucdavis.edu  

Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Berk Geveci
Actually, I think that I noticed this too. It may be a bug specific to the
programmable filter. I will check it out. By the way, what do you mean by
raw vti? Appended raw mode?

-berk

On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Thank you Berk.

 I was under the impression that this command would trigger the reader to
 automatically load in the additional # of requested ghost levels. I tested
 the command and each data piece still has the same extents as before.

 Is there any additional way to load in ghost level that's parallel
 friendly? I am aware of the D3 filter but, from the memory usage, it seems
 that it will load in the entire dataset into each processor and this is not
 feasible for large datasets.

 I am using binary, raw vti piece files each with their own extent of the
 data and a header pvti file.
 The data has no encoded ghost layers between pieces so I was hoping to
 have paraview do that for me.

 Jesus


 On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci berk.gev...@kitware.comwrote:

 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the reader
 or a filter before the programmable filter is able to provide ghost levels.


 -berk

  On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

  Hello,

 I am trying to request ghost data in my python programmable filter but I
 am not sure how to go about and do so. I am assuming the call would go into
 the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to is
 something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() , and
 there are examples of that in the Paraview source but the way the objects
 are defined and called does not translate into Paraview VTK Python. What
 would be the appropriate call?

 Thank you,
 Jesus


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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Jesus Pulido
Yes, appended raw mode. It has an ascii header then the data itself is
binary after a specified underscore delimiter.

Jesus

On Tue, Jul 17, 2012 at 1:17 PM, Berk Geveci berk.gev...@kitware.comwrote:

 Actually, I think that I noticed this too. It may be a bug specific to the
 programmable filter. I will check it out. By the way, what do you mean by
 raw vti? Appended raw mode?

 -berk


 On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

 Thank you Berk.

 I was under the impression that this command would trigger the reader to
 automatically load in the additional # of requested ghost levels. I tested
 the command and each data piece still has the same extents as before.

 Is there any additional way to load in ghost level that's parallel
 friendly? I am aware of the D3 filter but, from the memory usage, it seems
 that it will load in the entire dataset into each processor and this is not
 feasible for large datasets.

 I am using binary, raw vti piece files each with their own extent of
 the data and a header pvti file.
 The data has no encoded ghost layers between pieces so I was hoping to
 have paraview do that for me.

 Jesus


 On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci berk.gev...@kitware.comwrote:

 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the reader
 or a filter before the programmable filter is able to provide ghost levels.


 -berk

  On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

  Hello,

 I am trying to request ghost data in my python programmable filter but
 I am not sure how to go about and do so. I am assuming the call would go
 into the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to
 is something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() , and
 there are examples of that in the Paraview source but the way the objects
 are defined and called does not translate into Paraview VTK Python. What
 would be the appropriate call?

 Thank you,
 Jesus


 ___
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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Berk Geveci
One more question. What are you doing after reading the data? Depending on
what you are doing, I might be able to give you a piece of code that uses
George's filter to generate ghost levels using MPI. You will need to use
ParaView built from git.

Next week, George and I will start working on updating ParaView's
structured data readers to generate ghost levels using MPI under covers. We
waited way too long to do it...

-berk

On Tue, Jul 17, 2012 at 3:34 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Yes, appended raw mode. It has an ascii header then the data itself is
 binary after a specified underscore delimiter.

 Jesus


 On Tue, Jul 17, 2012 at 1:17 PM, Berk Geveci berk.gev...@kitware.comwrote:

 Actually, I think that I noticed this too. It may be a bug specific to
 the programmable filter. I will check it out. By the way, what do you mean
 by raw vti? Appended raw mode?

 -berk


 On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

 Thank you Berk.

 I was under the impression that this command would trigger the reader to
 automatically load in the additional # of requested ghost levels. I tested
 the command and each data piece still has the same extents as before.

 Is there any additional way to load in ghost level that's parallel
 friendly? I am aware of the D3 filter but, from the memory usage, it seems
 that it will load in the entire dataset into each processor and this is not
 feasible for large datasets.

 I am using binary, raw vti piece files each with their own extent of
 the data and a header pvti file.
 The data has no encoded ghost layers between pieces so I was hoping to
 have paraview do that for me.

 Jesus


 On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci berk.gev...@kitware.comwrote:

 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the reader
 or a filter before the programmable filter is able to provide ghost levels.


 -berk

  On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

  Hello,

 I am trying to request ghost data in my python programmable filter but
 I am not sure how to go about and do so. I am assuming the call would go
 into the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to
 is something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() ,
 and there are examples of that in the Paraview source but the way the
 objects are defined and called does not translate into Paraview VTK 
 Python.
 What would be the appropriate call?

 Thank you,
 Jesus


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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread David E DeMarle
Also remember this gem, which may help you.

Note also that there is a feature in the python programmable filter
that comes into play with structured data. That feature says that
structured data is not split at all by default. If you want structured
data to actually be parallel you need to put this code in your python
programmable filter.

from paraview import util
self.GetExecutive().SetExtentTranslator(self.GetExecutive().GetOutputInformation(0),
vtk.vtkExtentTranslator())

David E DeMarle
Kitware, Inc.
RD Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909


On Tue, Jul 17, 2012 at 4:02 PM, Berk Geveci berk.gev...@kitware.com wrote:
 One more question. What are you doing after reading the data? Depending on
 what you are doing, I might be able to give you a piece of code that uses
 George's filter to generate ghost levels using MPI. You will need to use
 ParaView built from git.

 Next week, George and I will start working on updating ParaView's structured
 data readers to generate ghost levels using MPI under covers. We waited way
 too long to do it...

 -berk


 On Tue, Jul 17, 2012 at 3:34 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Yes, appended raw mode. It has an ascii header then the data itself is
 binary after a specified underscore delimiter.

 Jesus


 On Tue, Jul 17, 2012 at 1:17 PM, Berk Geveci berk.gev...@kitware.com
 wrote:

 Actually, I think that I noticed this too. It may be a bug specific to
 the programmable filter. I will check it out. By the way, what do you mean
 by raw vti? Appended raw mode?

 -berk


 On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulido jpul...@ucdavis.edu
 wrote:

 Thank you Berk.

 I was under the impression that this command would trigger the reader to
 automatically load in the additional # of requested ghost levels. I tested
 the command and each data piece still has the same extents as before.

 Is there any additional way to load in ghost level that's parallel
 friendly? I am aware of the D3 filter but, from the memory usage, it seems
 that it will load in the entire dataset into each processor and this is not
 feasible for large datasets.

 I am using binary, raw vti piece files each with their own extent of
 the data and a header pvti file.
 The data has no encoded ghost layers between pieces so I was hoping to
 have paraview do that for me.

 Jesus


 On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci berk.gev...@kitware.com
 wrote:


 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the reader
 or a filter before the programmable filter is able to provide ghost 
 levels.


 -berk


 On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.edu
 wrote:

 Hello,

 I am trying to request ghost data in my python programmable filter but
 I am not sure how to go about and do so. I am assuming the call would go
 into the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to
 is something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() ,
 and there are examples of that in the Paraview source but the way the
 objects are defined and called does not translate into Paraview VTK 
 Python.
 What would be the appropriate call?

 Thank you,
 Jesus


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Re: [Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-17 Thread Jesus Pulido
I am simply applying a (Python) Programmable Filter after loading in the
data so the data itself does not get touched or modified before the
Programmable Filter is applied. Rebuilding paraview from git won't be a
problem since I've branched a few git versions in the past. If possible,
any workaround (including the previously suggested) would be great since
I'd rather not code my own MPI ghost cell trading logic inside of my
parallel programmable filter as I'm already performing computations every
single time I run the filter. I'd imagine it would be much slower than
having the ghost data already present or generating such ghost data
beforehand.

On Tue, Jul 17, 2012 at 2:05 PM, David E DeMarle
dave.dema...@kitware.comwrote:

 Also remember this gem, which may help you.

 Note also that there is a feature in the python programmable filter
 that comes into play with structured data. That feature says that
 structured data is not split at all by default. If you want structured
 data to actually be parallel you need to put this code in your python
 programmable filter.
 
 from paraview import util
 self.GetExecutive().

 SetExtentTranslator(self.GetExecutive().GetOutputInformation(0),
 vtk.vtkExtentTranslator())


Yes, I currently use that command to split my data for my Programmable
Filter. I ran into this feature last year.

Thank you,
Jesus

On Tue, Jul 17, 2012 at 2:02 PM, Berk Geveci berk.gev...@kitware.comwrote:

 One more question. What are you doing after reading the data? Depending on
 what you are doing, I might be able to give you a piece of code that uses
 George's filter to generate ghost levels using MPI. You will need to use
 ParaView built from git.

 Next week, George and I will start working on updating ParaView's
 structured data readers to generate ghost levels using MPI under covers. We
 waited way too long to do it...

 -berk


 On Tue, Jul 17, 2012 at 3:34 PM, Jesus Pulido jpul...@ucdavis.edu wrote:

 Yes, appended raw mode. It has an ascii header then the data itself is
 binary after a specified underscore delimiter.

 Jesus


 On Tue, Jul 17, 2012 at 1:17 PM, Berk Geveci berk.gev...@kitware.comwrote:

 Actually, I think that I noticed this too. It may be a bug specific to
 the programmable filter. I will check it out. By the way, what do you mean
 by raw vti? Appended raw mode?

 -berk


 On Tue, Jul 17, 2012 at 12:22 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

 Thank you Berk.

 I was under the impression that this command would trigger the reader
 to automatically load in the additional # of requested ghost levels. I
 tested the command and each data piece still has the same extents as 
 before.

 Is there any additional way to load in ghost level that's parallel
 friendly? I am aware of the D3 filter but, from the memory usage, it seems
 that it will load in the entire dataset into each processor and this is not
 feasible for large datasets.

 I am using binary, raw vti piece files each with their own extent of
 the data and a header pvti file.
 The data has no encoded ghost layers between pieces so I was hoping to
 have paraview do that for me.

 Jesus


 On Tue, Jul 17, 2012 at 7:29 AM, Berk Geveci 
 berk.gev...@kitware.comwrote:

 self.GetExecutive().GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_GHOST_LEVELS(),
 1)


 in RequestUpdateExtent script. Of course, this requires that the
 reader or a filter before the programmable filter is able to provide ghost
 levels.


 -berk

  On Wed, Jul 11, 2012 at 3:04 PM, Jesus Pulido jpul...@ucdavis.eduwrote:

  Hello,

 I am trying to request ghost data in my python programmable filter
 but I am not sure how to go about and do so. I am assuming the call would
 go into the RequestUpdateExtent Script.

 In the C++ equivalent filters that do request ghost data, the call to
 is something along the lines of
 vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() ,
 and there are examples of that in the Paraview source but the way the
 objects are defined and called does not translate into Paraview VTK 
 Python.
 What would be the appropriate call?

 Thank you,
 Jesus


 ___
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 http://paraview.org/Wiki/ParaView

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[Paraview] Parallel Python Programmable Filter Requesting Additional Ghost Data

2012-07-11 Thread Jesus Pulido
Hello,

I am trying to request ghost data in my python programmable filter but I am
not sure how to go about and do so. I am assuming the call would go into
the RequestUpdateExtent Script.

In the C++ equivalent filters that do request ghost data, the call to is
something along the lines of
vtkStreamingDemandDrivenPipeline::UPDATE_NUMBER_OF_GHOST_LEVELS() , and
there are examples of that in the Paraview source but the way the objects
are defined and called does not translate into Paraview VTK Python. What
would be the appropriate call?

Thank you,
Jesus
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