date:20161221

Re: [Paraview] [Non-DoD Source] color mapping of XDMF and HDF5 file is not shown

2016-12-21 Thread Seong Mo Yeon

I have tested color map problem a little.
Problem is due to the field value at initial time.
Initial value of field of the time series is zero.
I guess the behavior for the zero field is dependent on os. In MS windows, 
mapping data is visible in color map editor but in Linux mapping data for the 
initial time is gone until I remap the data after time marching

On 2016년 12월 22일 AM 4:37 +0900, Burns, Andrew J CTR USARMY RDECOM ARL (US) 
, wrote:
> Looked into this. There are two errors going on.
>
> 1: The type should be "Float" not "Double" Xdmf defines double as float with 
> precision 8.
>
> 2: There is an order of operations error in the handling of the X_Y_Z type. 
> We'll put a fix for it into the next Xdmf3 reader.
>
> -Andrew Burns
>
> -Original Message-
> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of SeongMo 
> Yeon
> Sent: Wednesday, December 21, 2016 11:20 AM
> To: paraview@paraview.org
> Subject: [Non-DoD Source] [Paraview] color mapping of XDMF and HDF5 file is 
> not shown
>
> Hi,
>
>
> I am woking with HDF5 and XDMF file to visualize in ParaView.
>
> three problems are found in reading xdmf reader.
>
> 1) in MS Windows, color map is shown correctly but in Linux, color map is 
> gone and nothing is shown but grid surface.
>
> 2) in Linux (not sure in Windows), Paraview 5.1.2 has problem in reading 
> attribute data
>
> 3) xdmf3 reader cannot read my xdmf file. which part should I correct in 
> order for xdmf3 reader working
>
>
> Thanks in advance.
>
>
> --
> Seong Mo Yeon
> E-mail : seongmo.y...@gmail.com
> Tel :
> 
> Fluctuat nec mergitur
>
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[Paraview] moving streamlines with flow

2016-12-21 Thread Jan Deca


Hello,

I am running simulations of magnetized plasma flow through a 
computational domain. In the simulation the magnetic field lines are 
moving with the flow. When generating an animation over different time 
steps (frames), however, the streamtracer uses the same seeds for each 
frame, and hence the resulting impression is that the field lines do not 
move in time.


Would anybody have an idea on how to accomplish moving field lines?

Thank you!

Jan
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Re: [Paraview] [vtkusers] vtk.vtkDistributedDataFilter() not works

2016-12-21 Thread Cory Quammen

Magician,

I am transitioning this thread over to the ParaView users mailing list
as you are using pvpython, and this is actually simpler to do using
the paraview.simple module rather than with VTK directly.

What you are trying to do is not going to work with pvpython. pvpython
is a client that you can use with either the built-in server or by
connecting to a remote server, much like the ParaView application. You
won't be able to run it in parallel and run parallel VTK code with it.

Instead, you will need to invoke pvpython with a script that connects
to a running pvserver with 2 processors.

Here's something that worked for me for partitioning a point source:

* Launch pvserver with two processes (mpirun -np 2 pvserver)
* Launch pvpython script.py
* The contents of script.py should be:

from paraview.simple import *

Connect("localhost")

pointSource = PointSource()
pointSource.NumberOfPoints = 1
pointSource.Radius = 1.0

glyph = Glyph(Input=pointSource, GlyphType='Arrow')
glyph.GlyphType = '2D Glyph'
glyph.GlyphType.GlyphType = 'Vertex'
glyph.GlyphMode = 'All Points'

d3 = D3(Input=glyph)

SaveData('tmp.pvtu', proxy=d3)

The Glyph filter is needed to add vertex cells at each point. D3 needs
these cells to do the partitioning properly.

Can you get this script to work?

Thanks,
Cory

On Mon, Dec 19, 2016 at 4:54 PM, Magician  wrote:
> Hi Cory,
>
>
> Sorry again. (My mailer has some trouble...)
>
> I tried Sphere Source too, but the results are same.
>
>> src = vtk.vtkSphereSource()
>> src.SetCenter(0.0, 0.0, 0.0)
>> src.SetRadius(1.0)
>> src.SetThetaResolution(8)
>> src.SetPhiResolution(5)
>> src.Update()
>
> If the code runs on native VTK environments, maybe my ParaView’s VTK has some 
> trouble.
>
>
> Magician
>
>
>> On Dec 13, 2016, at 12:03, Cory Quammen  wrote:
>>
>> Hmm, I'm not sure. Could you try setting the input to d3 to the output
>> of a vtkSphereSource and see if you get the expected results there?
>> You should get half the sphere in one piece and the other half sphere
>> in the other piece.
>>
>> Thanks,
>> Cory
>>
>> On Sat, Dec 10, 2016 at 10:35 AM, Magician  wrote:
>>> Hi Cory,
>>>
>>>
>>> Sorry for my late reply.
>>> I modified my code for splitting the points, but the filter doesn’t work.
>>>
>>>
>>>import vtk
>>>
>>>src = vtk.vtkPointSource()
>>>src.SetCenter((0.0, 0.0, 0.0))
>>>src.SetNumberOfPoints(1000)
>>>src.SetRadius(1.0)
>>>src.Update()
>>>
>>>dst = vtk.vtkPolyData()
>>>pts = vtk.vtkPoints()
>>>pts.SetData(src.GetOutput().GetPoints().GetData())
>>>dst.SetPoints(pts)
>>>cells = vtk.vtkCellArray()
>>>for i in range(src.GetOutput().GetNumberOfPoints()):
>>>ptIds = vtk.vtkIdList()
>>>ptIds.InsertNextId(i)
>>>cells.InsertNextCell(ptIds)
>>>dst.SetVerts(cells)
>>>
>>>d3 = vtk.vtkDistributedDataFilter()
>>>d3.UseMinimalMemoryOff()
>>>d3.SetInputData(dst)
>>>d3.SetBoundaryMode(0)
>>>d3.SetBoundaryModeToSplitBoundaryCells()
>>>d3.Update()
>>>
>>>writer = vtk.vtkXMLPUnstructuredGridWriter()
>>>writer.SetInputData(d3.GetOutput())
>>>writer.SetFileName(’test.pvtu’)
>>>writer.SetNumberOfPieces(2)
>>>writer.WriteSummaryFileOn()
>>>writer.SetStartPiece(0)
>>>writer.SetEndPiece(1)
>>>writer.Write()
>>>
>>>
>>> Magician
>>>
>>>
 On Dec 6, 2016, at 01:33, Cory Quammen  wrote:

 I'm not 100% sure of this, but the vtkPointSource produces an output
 with only 1 cell. That may not be partitionable by the
 vtkDistributeDataFilter. You shouldn't get duplicate output in each
 piece, but let's not worry about that for now.

 Try swapping out the vtkPointSource with a vtkSphereSource and see if
 the data is partitioned.

 HTH,
 Cory

 On Sat, Dec 3, 2016 at 8:57 PM, Magician  wrote:
> Hi Cory,
>
>
> Thanks for your advice.
>
> Hmmm...I already run the script with MPI.
> The attached script is a minimal sample.
>
>
> If I execute it, pvtu file is exported.
> But the all piece sources are exactly same, and not partitioned.
>
>
>
> Magician
>
>
>> On Nov 28, 2016, at 06:19, Cory Quammen  wrote:
>>
>> I think you need to run your script in parallel with MPI for the
>> partitioning to work. See [1] for an example of how to use this
>> filter.
>>
>> Hope that helps,
>> Cory
>>
>> [1] 
>> http://www.vtk.org/gitweb?p=VTK.git;a=blob;f=Filters/Parallel/Testing/Cxx/DistributedData.cxx
>>
>> On Sun, Nov 27, 2016 at 10:39 AM, Magician  wrote:
>>> Does anyone use the vtkDistributedDataFilter?
>>>
>>>
>>> On Nov 19, 2016, at 18:16, Magician  wrote:
>>>
>>> Hi all,
>>>
>>>
>>> I posted the message

Re: [Paraview] [Non-DoD Source] color mapping of XDMF and HDF5 file is not shown

2016-12-21 Thread Burns, Andrew J CTR USARMY RDECOM ARL (US)

Looked into this. There are two errors going on.

1: The type should be "Float" not "Double" Xdmf defines double as float with 
precision 8.

2: There is an order of operations error in the handling of the X_Y_Z type. 
We'll put a fix for it into the next Xdmf3 reader.

-Andrew Burns

-Original Message-
From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of SeongMo Yeon
Sent: Wednesday, December 21, 2016 11:20 AM
To: paraview@paraview.org
Subject: [Non-DoD Source] [Paraview] color mapping of XDMF and HDF5 file is not 
shown

Hi,


I am woking with HDF5 and XDMF file to visualize in ParaView.

three problems are found in reading xdmf reader.

1) in MS Windows, color map is shown correctly but in Linux, color map is gone 
and nothing is shown but grid surface.

2) in Linux (not sure in Windows), Paraview 5.1.2 has problem in reading 
attribute data

3) xdmf3 reader cannot read my xdmf file. which part should I correct in order 
for xdmf3 reader working


Thanks in advance.


-- 
Seong Mo Yeon
E-mail : seongmo.y...@gmail.com
Tel :

Fluctuat nec mergitur

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[Paraview] plugins with 5.2

2016-12-21 Thread Burlen Loring

After upgrading to 5.2 my plugin is not compiling. When I configure the 
plugin I see a few pages of the following:


   CMake Warning (dev) at io/CMakeLists.txt:54 (add_library):
  Policy CMP0028 is not set: Double colon in target name means ALIAS or
  IMPORTED target.  Run "cmake --help-policy CMP0028" for policy
   details.
  Use the cmake_policy command to set the policy and suppress this
   warning.

  Target "teca_io" links to target "Qt4::QtCore" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED
   target, or
  an ALIAS target is missing?
   This warning is for project developers.  Use -Wno-dev to suppress it.

then linker errors

   [ 32%] Linking CXX shared library ../lib/libteca_io.so
   /bin/ld: cannot find -lQt4::QtCore
   /bin/ld: cannot find -lQt4::QtGui
   collect2: error: ld returned 1 exit status
   io/CMakeFiles/teca_io.dir/build.make:402: recipe for target
   'lib/libteca_io.so' failed
   make[2]: *** [lib/libteca_io.so] Error 1
   CMakeFiles/Makefile2:196: recipe for target
   'io/CMakeFiles/teca_io.dir/all' failed
   make[1]: *** [io/CMakeFiles/teca_io.dir/all] Error 2
   Makefile:127: recipe for target 'all' failed
   make: *** [all] Error 2

It's not a library so I set  the policy to new,  and the cmake configure 
errors out. Any idea what's missing?


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Re: [Paraview] ... not yet supported for more than 2147483647 bytes.

2016-12-21 Thread Berk Geveci

Besides what others said here, I am curious why ParaView is trying to move
> 2 GB over MPI. This wouldn't normally happen unless it was trying to
gather and deliver the entire dataset to the client. Which in itself would
be a problem with data this size. What operation leads to this error?

On Mon, Dec 19, 2016 at 5:25 PM, Kashiwa, Bucky  wrote:

> Andy, Ashton:  I will bring up v5.2 to see if it works for me.  Thanks, b.
>
> ===73
> <>Bucky Kashiwa PhD, PE  <> Post: MS B216, Los Alamos, NM  87545   <>
> <>  Ofc: TA3-SM123-RM276 <>Email: b...@lanl.gov, kash...@qwest.net  <>
> <>Voice: 505-667-8812 <(505)%20667-8812><>  Fax: 505-665-5926
> <(505)%20665-5926>  <>
>  <> Home: 505-988-7332 <(505)%20988-7332>  <>
> Cell: 505-795-5581 <(505)%20795-5581>  <>
> ===73
>
> From: Andy Bauer 
> Date: Monday, December 19, 2016 at 3:17 PM
> To: andrealphus 
> Cc: Bucky Kashiwa , "ParaView@ParaView.org" <
> ParaView@paraview.org>
> Subject: Re: [Paraview] ... not yet supported for more than 2147483647
> <(214)%20748-3647> bytes.
>
> There are two parts to this issue. The first is that that
> vtkMPICommunicator for PV 4.3.1 won't communicate data that is over 2^31
> bytes of data. This is fixed in PV 5.2. The other issue is due to MPI
> having a limit of 2^31 objects to be communicated in a single shot. This is
> MPI's API in that the count for objects that are typically sent/received is
> an int. See  http://www.mpich.org/static/docs/v3.1/www3/MPI_Send.html for
> example.
>
> On Mon, Dec 19, 2016 at 4:59 PM, andrealphus 
> wrote:
>
>> That is a 32 bit error, from trying to index something with more than
>> (2^32)/2 elements or indices. Are you using any custom
>> libraries/packages/modules which might not be 64 bit compliant? Are
>> you sure you built a 64 bit version (check your gcc -v).
>>
>> -ashton
>>
>> On Mon, Dec 19, 2016 at 1:32 PM, Kashiwa, Bucky  wrote:
>> > On Linux using ParaView version 4.3.1 built with OSMesa-9.0.1, OpenMPI,
>> > etc.  Running pvserver with 12 PEs, client-server mode, Standard Release
>> > ParaView-4.3.1-Linux-64bit client.  With large point data (>2Gb) we get
>> > this error, upon trying to display a large number of points:
>> >
>> > Generic Warning: In
>> > ../ParaView-v4.3.1-source/VTK/Parallel/MPI/vtkMPICommunicator.cxx,
>> > line 194
>> >
>> > This operation not yet supported for more than 2147483647
>> <(214)%20748-3647> bytes.
>> >
>> > Our CMakeCache.txt is attached, in case it may provide helpful clues.
>> >
>> > Thanks much.  B. Kashiwa
>> >
>> >
>> >
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>
>
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Re: [Paraview] [Non-DoD Source] color mapping of XDMF and HDF5 file is not shown

[Paraview] moving streamlines with flow

Re: [Paraview] [vtkusers] vtk.vtkDistributedDataFilter() not works

Re: [Paraview] [Non-DoD Source] color mapping of XDMF and HDF5 file is not shown

[Paraview] plugins with 5.2

Re: [Paraview] ... not yet supported for more than 2147483647 bytes.

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