Re: [Paraview] Question about Paraview and parallel processing
Hi Adam, The legacy VTK format was never upgraded to support domain decomposition. The VisIt folks added an extra layer to do that. In ParaView, you need to use another format. I would recommend the new VTK format (in your case pvts). See http://www.vtk.org/VTK/img/file-formats.pdf for more information. I don't know what your workflow is. If you want to convert existing VTK files, it is very easy to do that with some Python scripting. Let us know if you need help. If you absolutely must stick to the legacy format, I actually lied. There are ways of reading partitioned VTK files into ParaView but it is not as trivial as the solution above. Best, -berk On Wed, Jan 2, 2013 at 3:45 PM, Adam Larios alar...@math.tamu.edu wrote: To whom it may concern, I have some data which takes on different values in space, which normally would be easy to view in Paraview. The problem is that the space (which is a big cube) is decomposed into different subdomains since the data was processed in parallel, and each subdomain is saved in a different file. Currently, paraview interprets each subdomain as a different time-step. Is it possible to get paraview to load all of the parallelized data and view it as a single time step? Of course, I could parse all of these files into one big file, but I would like to avoid this extra step if necessary, since the files are updated regularly, and an extra post-processing step would slow things down significantly. My files are in legacy VTK format. They look like this, for example (the real runs are much larger than this): # myData_00.vtk # vtk myData ASCII DATASET STRUCTURED_GRID DIMENSIONS 12 12 12 POINTS1728 float 0.9519978E-01 0.9519978E-01 0.9519978E-01 0.2855993E+00 0.9519978E-01 0.9519978E-01 0.4759989E+00 0.9519978E-01 0.9519978E-01 .. # myData_01.vtk # vtk myData ASCII DATASET STRUCTURED_GRID DIMENSIONS 12 12 12 POINTS1728 float 0.9519978E-01 0.9519978E-01 0.2189595E+01 0.2855993E+00 0.9519978E-01 0.2189595E+01 0.4759989E+00 0.9519978E-01 0.2189595E+01 .. and so on up to myData_07.vtk. Visit can stitch all of these domains together with a simple file that tells what all the other files are: # myData.visit # !NBLOCKS 8 myData_00.vtk myData_01.vtk myData_02.vtk myData_03.vtk myData_04.vtk myData_05.vtk myData_06.vtk myData_07.vtk Is there anything I can do to get Paraview to interpret these as a single data set? Any help would be much appreciated! (Also, my apologies in advance if this is not the right place to post this kind of thing.) Best regards, Adam ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] Linker error with OpenMPI 1.6.2
Happy new year, I've tried to use a newer version of OpenMPI (1.4.4 = 1.6.2) with PV from git master. Unfortunately, I was not able to build ParaView successfully. A linker error comes from the vtkParallelMPI project. When I look into the project file I can see that libmpi.lib and libmpi_cxx.lib are set correctly. vtkMPICommunicator.cxx.obj : error LNK2001: Unknown external Symbol ompi_mpi_file_null. vtkMPIController.cxx.obj : error LNK2001: Unknown external Symbol ompi_mpi_file_null. . I have no idea, why this failure occurs. Compiling the same PV from git master with OpenMPI 1.4.4 still works. Thanks, Stephan ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] Linker error with OpenMPI 1.6.2
What version of ParaView is this? Can you attach your CmakeCache.txt file? Utkarsh On Thu, Jan 3, 2013 at 9:46 AM, Stephan Rogge stephan.ro...@tu-cottbus.de wrote: Happy new year, I’ve tried to use a newer version of OpenMPI (1.4.4 = 1.6.2) with PV from git master. Unfortunately, I was not able to build ParaView successfully. A linker error comes from the vtkParallelMPI project. When I look into the project file I can see that libmpi.lib and libmpi_cxx.lib are set correctly. vtkMPICommunicator.cxx.obj : error LNK2001: Unknown external Symbol ompi_mpi_file_null. vtkMPIController.cxx.obj : error LNK2001: Unknown external Symbol ompi_mpi_file_null. … I have no idea, why this failure occurs. Compiling the same PV from git master with OpenMPI 1.4.4 still works. Thanks, Stephan ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] How to change the Representation within a Plugin ?
Try: vtkSMPropertyHelper(repr-getProxy(), RadiusArray).Set(4, radius); ... repr-getProxy()-UpdateVTKObjects(); Utkarsh On Wed, Jan 2, 2013 at 2:57 PM, Christian Richter christian.rich...@ovgu.de wrote: Thank you Utkarsh, thas does the trick. Can you give me a hint how I can do DataRepresentation1.RadiusArray = [None, 'radius'] //python trace in C++ ? Thanks, Christian Zitat von Utkarsh Ayachit utkarsh.ayac...@kitware.com: Try calling the following before src-updatePipeline() before attempting to create the representation. The reader hasn't been executed yet and hence it doesn't provide any information about what type of data it will produce and hence createDataRepresentation() cannot create any data-representation for it. updatePipeline() forces the reader to execute i.e. it's RequestData() will get called and then the rest should work as expected. Utkarsh On Tue, Jan 1, 2013 at 5:50 AM, Christian Richter christian.rich...@ovgu.de wrote: Hi, I've written a Plugin to use Paraview as LiveView for our simulation Data. With a QFileSystemWatcher the Plugin updates the filenames of the fileseries-reader everytime a new result-file was written to disk. Now I want to change the Representation from Point to Point Sprite automaticly after the source is created and set some standard properties. In Pythion I used: xreader=liggghts_Reader(guiName=liggghts_dump) xreader.FileNames=files SetDisplayProperties(xreader, Representation=Point Sprite) DataRepresentation1 = Show() DataRepresentation1.PointSpriteDefaultsInitialized = 1 DataRepresentation1.Texture = [] DataRepresentation1.RadiusTransferFunctionEnabled = 1 DataRepresentation1.RadiusMode = 'Scalar' DataRepresentation1.Representation = 'Point Sprite' DataRepresentation1.RadiusArray = [None, 'radius'] DataRepresentation1.RadiusIsProportional = 1 And I tried this in my C++Plugin: src = builder-createReader(QString(sources),type, files, s); //works src-rename(type); pqActiveView myActiveView=pqActiveView::instance(); this-RenderView=myActiveView.current(); pqDataRepresentation *repr = builder-createDataRepresentation(src-getOutputPort(0), this-RenderView); vtkSMPropertyHelper(repr-getProxy(),Representation).Set(Point Sprite); //segfault but get segfault at last line because repr is still NULL. I attached the code and here is a video where you can see the Plugin working. http://youtu.be/5CGGf-kPcEQ best, Christian ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
[Paraview] External plugin menu behavior
Hi, I have a set of external plugins that we have made a menu entry that is visible in the ParaView GUI Filters menu. I'm seeing a strange problem in ParaView 3.98. When I use a plugin for the first time, all is fine. However, when I exit PV, restart and go to use the same plugin, the entry is missing from our menu. It is in the Filters/Recent menu entry and is still searchable. Does anyone know why the original menu entry would be deleted? I blew away my config file and tried again, but I see the same behavior. Thanks, M -- Dr. Michael Reuter Data Analaysis and Visualization Group Neutron Data Analysis and Visualization Division Oak Ridge National Laboratory Office: 1-865-241-7216 Fax: 1-865-574-6080 Email: reute...@ornl.gov ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] External plugin menu behavior
Sounds like a bug to me. Any details on how I could try to reproduce this? If you could reproduce with one of the packaged plugins or examples, that'd be even better. Utkarsh On Thu, Jan 3, 2013 at 3:04 PM, Michael Reuter reute...@ornl.gov wrote: Hi, I have a set of external plugins that we have made a menu entry that is visible in the ParaView GUI Filters menu. I'm seeing a strange problem in ParaView 3.98. When I use a plugin for the first time, all is fine. However, when I exit PV, restart and go to use the same plugin, the entry is missing from our menu. It is in the Filters/Recent menu entry and is still searchable. Does anyone know why the original menu entry would be deleted? I blew away my config file and tried again, but I see the same behavior. Thanks, M -- Dr. Michael Reuter Data Analaysis and Visualization Group Neutron Data Analysis and Visualization Division Oak Ridge National Laboratory Office: 1-865-241-7216 Fax: 1-865-574-6080 Email: reute...@ornl.gov ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] External plugin menu behavior
I tried Plot Over Line, Clip and Histogram. Now those are gone from their original menus. M On 1/3/13 3:20 PM, Utkarsh Ayachit utkarsh.ayac...@kitware.com wrote: Sounds like a bug to me. Any details on how I could try to reproduce this? If you could reproduce with one of the packaged plugins or examples, that'd be even better. Utkarsh On Thu, Jan 3, 2013 at 3:04 PM, Michael Reuter reute...@ornl.gov wrote: Hi, I have a set of external plugins that we have made a menu entry that is visible in the ParaView GUI Filters menu. I'm seeing a strange problem in ParaView 3.98. When I use a plugin for the first time, all is fine. However, when I exit PV, restart and go to use the same plugin, the entry is missing from our menu. It is in the Filters/Recent menu entry and is still searchable. Does anyone know why the original menu entry would be deleted? I blew away my config file and tried again, but I see the same behavior. Thanks, M -- Dr. Michael Reuter Data Analaysis and Visualization Group Neutron Data Analysis and Visualization Division Oak Ridge National Laboratory Office: 1-865-241-7216 Fax: 1-865-574-6080 Email: reute...@ornl.gov ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] HDF5 and Paraview
Hello Jens, thanks for the response. It explained a lot. I have been reading up about XDMF and am trying to implement it. My filename.h5 file just contains a scalar value for 512*512*512 grid points in a structured uniform cube. I don't store any grid coordinates information in any files. But all the material I have been reading for XDMF mention that I have to give grid information. Is there a simple way of conveying my uniform grid structure to XDMF or should I create a file with grid coordinates and make XDMF read it? Thank you, Pradeep On 2 janv. 2013, at 05:50, Jens Kleimann j...@tp4.rub.de wrote: Am 21.12.2012 03:28, schrieb Pradeep Jha: Thanks for the response everyone and thanks for the detailed response Ken. It made things a bit more clearer. But still I dont understand that once I create a Hdf5 data, and even I create a XDMF file, how can I be sure which reader to use for the data? So every time I switch to a new data, chances are I might have to try out all the readers one by one, till one of them plots it fine? Is there something I am missing? Once you have created the corresponding filename.xmf that belongs to your filename.h5, you just open filename.xmf in PV. It contains the location and structural info on the HDF5 and thus knows how to open and interpret it. You will no longer be prompted to pick a reader. Cheers, Jens. ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview ___ 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 ParaView Wiki at: http://paraview.org/Wiki/ParaView Follow this link to subscribe/unsubscribe: http://www.paraview.org/mailman/listinfo/paraview
Re: [Paraview] HDF5 and Paraview
If you look on the Xdmf Model and Format website
(http://www.xdmf.org/index.php/XDMF_Model_and_Format) you can see that there is
a 2DCoRectMesh and 3DCoRectMesh topology which can be used to make 2/3D
constant spacing meshes with axis aligned to X,Y,Z.
And example of how to write this is on the API portion
(http://www.xdmf.org/index.php/XDMF_API). The relevant section is:
# Domain
dm = XdmfDomain()
root.Insert(dm)
# Grid
g = XdmfGrid()
g.SetName(Structured Grid)
# Topology
t = g.GetTopology()
t.SetTopologyType(XDMF_3DCORECTMESH)
t.GetShapeDesc().SetShapeFromString('10 20 30')
# Geometry
geo = g.GetGeometry()
geo.SetGeometryType(XDMF_GEOMETRY_ORIGIN_DXDYDZ)
geo.SetOrigin(1, 2, 3)
geo.SetDxDyDz(0.1, 0.2, 0.3)
Which is using the python bindings, but you can easily determine what the
resulting xml file looks at by looking at the Model and Format page to see what
the resulting tags would be. Or you can use the Python or C++ bindings to write
your file. Basically you tell it that your grid is constant and rectilinear,
and then you give it the origin and the spacing.
Tim
- Original Message -
From: Pradeep Jha pradeep.kumar@gmail.com
To: Jens Kleimann j...@tp4.rub.de
Cc: paraview@paraview.org
Sent: Thursday, January 3, 2013 10:19:42 PM
Subject: Re: [Paraview] HDF5 and Paraview
Hello Jens,
thanks for the response. It explained a lot.
I have been reading up about XDMF and am trying to implement it. My filename.h5
file just contains a scalar value for 512*512*512 grid points in a structured
uniform cube. I don't store any grid coordinates information in any files. But
all the material I have been reading for XDMF mention that I have to give grid
information. Is there a simple way of conveying my uniform grid structure to
XDMF or should I create a file with grid coordinates and make XDMF read it?
Thank you,
Pradeep
On 2 janv. 2013, at 05:50, Jens Kleimann j...@tp4.rub.de wrote:
Am 21.12.2012 03:28, schrieb Pradeep Jha:
Thanks for the response everyone and thanks for the detailed response
Ken. It made things a bit more clearer.
But still I dont understand that once I create a Hdf5 data, and even I
create a XDMF file, how can I be sure which reader to use for the data?
So every time I switch to a new data, chances are I might have to try
out all the readers one by one, till one of them plots it fine?
Is there something I am missing?
Once you have created the corresponding filename.xmf that belongs to your
filename.h5, you just open filename.xmf in PV. It contains the location and
structural info on the HDF5 and thus knows how to open and interpret it. You
will no longer be prompted to pick a reader.
Cheers, Jens.
___
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