Re: [Paraview] Broken Streamlines

[Andy Bauer]

Additionally, you can view the ReasonForTermination cell data output to see
why the streamlines terminated. Click on the ? button to see what the
values correspond to.


On Wed, Feb 7, 2018 at 12:23 PM, Andy Bauer <andy.ba...@kitware.com> wrote:

> Hi,
>
> You may want to try playing with some of the advanced options for
> computing streamlines (click on the gear button in the upper right corner
> of the parameters for the filter).
>
> If that doesn't help, you may want to share your dataset so that we can
> investigate. Also, is this a 2D simulation? It may be that the streamline
> is going out of the plane of your grid and therefore terminating.
>
> --Andy
>
> On Wed, Feb 7, 2018 at 12:06 PM, Steytler, Louis Louw <
> steyt...@illinois.edu> wrote:
>
>> Hi Everyone,
>>
>> When generating streamlines from a 3D computation, in some parts, the
>> streamlines appear broken. This is shown in the attached image (the arrows
>> point to the broken parts).
>>
>> Increasing the "Maximum Streamline Length" parameter did not help.
>>
>> Using the "Point to Cell Data" filter, and then generating streamlines on
>> the cell data did not help.
>>
>> Although in the image shown the broken parts are in an area of low
>> velocity, this happens in regions of high velocity as well. It also does
>> not seem to depend on grid resolution, as the broken parts show up all over.
>>
>> Has anyone experienced anything like this? Any ideas how to work around
>> this?
>>
>> Thanks very much,
>>
>> Louis Steytler
>> Department of Mechanical Science and Engineering
>> University of Illinois at Urbana-Champaign
>> 1206 West Green Street
>> Urbana, Il 61801
>> steyt...@illinois.edu
>>
>> ___
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>>
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>>
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>>
>>
>
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Re: [Paraview] Broken Streamlines

[Andy Bauer]

Hi,

You may want to try playing with some of the advanced options for computing
streamlines (click on the gear button in the upper right corner of the
parameters for the filter).

If that doesn't help, you may want to share your dataset so that we can
investigate. Also, is this a 2D simulation? It may be that the streamline
is going out of the plane of your grid and therefore terminating.

--Andy

On Wed, Feb 7, 2018 at 12:06 PM, Steytler, Louis Louw  wrote:

> Hi Everyone,
>
> When generating streamlines from a 3D computation, in some parts, the
> streamlines appear broken. This is shown in the attached image (the arrows
> point to the broken parts).
>
> Increasing the "Maximum Streamline Length" parameter did not help.
>
> Using the "Point to Cell Data" filter, and then generating streamlines on
> the cell data did not help.
>
> Although in the image shown the broken parts are in an area of low
> velocity, this happens in regions of high velocity as well. It also does
> not seem to depend on grid resolution, as the broken parts show up all over.
>
> Has anyone experienced anything like this? Any ideas how to work around
> this?
>
> Thanks very much,
>
> Louis Steytler
> Department of Mechanical Science and Engineering
> University of Illinois at Urbana-Champaign
> 1206 West Green Street
> Urbana, Il 61801
> steyt...@illinois.edu
>
> ___
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> opensource/opensource.html
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> Please keep messages on-topic and check the ParaView Wiki at:
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>
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Re: [Paraview] PythonFullExample does not send any data

[Andy Bauer]

Hi Simon,

I'm confused a to where the data is being sent from and to. If it's from
the simulation and to the adaptor then all of that would get done before
Catalyst would ever see it. If it's from the adaptor to Catalyst or to the
PV GUI through the Live connection you'll probably want to look at
coprocessing.py and grep through it for "live". I don't look too often at
the Live sections of the code so it would take a bit of time to go through
all of the details on it properly.

Best,
Andy

On Tue, Feb 6, 2018 at 10:44 AM, Michalke, Simon <simon.micha...@fau.de>
wrote:

> Thank you very much, it works now.
>
> Since I am getting the initial data via http and process it manually, is
> there a way to "directly" open a connection and send data? I think the
> coprocessor structure is not suitable for my case. Something like:
>
> con = openConnection()
>
> con.sendData(data)
> con.sendData(data)
> con.sendData(data)
>
> con.close()
>
> where data is something like vtkPolyData. Or, alternatively transfer the
> grid at the beginning and only send the data as vtk*Array itself after
> first initialization.
>
> Cheers,
> Simon
>
>
> Am 2018-02-06 14:18, schrieb Andy Bauer:
>
>> In  cpscript.py you will need to change the following line:
>> coprocessor.EnableLiveVisualization(False, 1)
>>
>> to:
>> coprocessor.EnableLiveVisualization(True, 1)
>>
>> As for building VTK objects through the Python API, the VTK Examples at
>> https://lorensen.github.io/VTKExamples/site/Python/ should have several
>> will help you out.
>>
>> Cheers,
>> Andy
>>
>> On Tue, Feb 6, 2018 at 4:37 AM, Michalke, Simon <simon.micha...@fau.de>
>> wrote:
>>
>> Hello,
>>>
>>> I am trying to code a tool to send live data from a simulation to
>>> paraview. I build my paraview with the latest superbuild and with system
>>> python (3.4m). Then I tried to run the "PythonFullExample". After
>>> un-commenting line 25 in fedriver.py:
>>> coprocessor.addscript("cpscript.py")
>>> the script still does not send any data. There are no error messages as
>>> well. I made sure that paraview is listening to the correct port.
>>>
>>> In general, I cannot find any python example on how to attach values to a
>>> poly element or a point.
>>>
>>> Regards,
>>> Simon Michalke
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>>>
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Re: [Paraview] PythonFullExample does not send any data

[Andy Bauer]

In  cpscript.py you will need to change the following line:
coprocessor.EnableLiveVisualization(False, 1)

to:
coprocessor.EnableLiveVisualization(True, 1)

As for building VTK objects through the Python API, the VTK Examples at
https://lorensen.github.io/VTKExamples/site/Python/ should have several
will help you out.

Cheers,
Andy

On Tue, Feb 6, 2018 at 4:37 AM, Michalke, Simon 
wrote:

> Hello,
>
> I am trying to code a tool to send live data from a simulation to
> paraview. I build my paraview with the latest superbuild and with system
> python (3.4m). Then I tried to run the "PythonFullExample". After
> un-commenting line 25 in fedriver.py:
> coprocessor.addscript("cpscript.py")
> the script still does not send any data. There are no error messages as
> well. I made sure that paraview is listening to the correct port.
>
> In general, I cannot find any python example on how to attach values to a
> poly element or a point.
>
> Regards,
> Simon Michalke
> ___
> Powered by www.kitware.com
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> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
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Re: [Paraview] How to insert annotate time info into catalyst?

[Andy Bauer]

For Catalyst Live you can use the Python Annotation filter to show the time
after you've extracted the Annotate Time Filter from the Calalyst
simulation run. You'll need to change the Array Association to Row Data and
put in "Text.GetValue(0)" in the Expression.

On Mon, Jan 29, 2018 at 8:59 PM, Seong Mo Yeon <seongmo.y...@gmail.com>
wrote:

> Hi, Andi Bauer,
>
> I found that annotate time filter works in live visualization and the
> error occurs when output rendering components is activated.
> gdb says the error occurs at vtkSMBoundsDomain.cxx: 60
>   vtkPVDataInformation* info = this->GetInputInformation();
>   if (info)
>   {
> double bounds[6];
> info->GetBounds(bounds);
> this->SetDomainValues(bounds);
>   }
>
> and the vtkPVDataInformation has the following information:
>
> members of vtkPVDataInformation:
>   DataSetType = 19,
>   CompositeDataSetType = -1,
>   NumberOfDataSets = 1,
>   NumberOfPoints = 0,
>   NumberOfCells = 1,
>   NumberOfRows = 1,
>   MemorySize = 1,
>   PolygonCount = 0,
>   Bounds = {1.0001e+299, -1.0001e+299,
> 1.0001e+299, -1.0001e+299, 1.0001e+299,
> -1.0001e+299},
>   Extent = {2147483647 <(214)%20748-3647>, -2147483647 <(214)%20748-3647>,
> 2147483647 <(214)%20748-3647>, -2147483647 <(214)%20748-3647>, 2147483647
> <(214)%20748-3647>, -2147483647 <(214)%20748-3647>},
>   TimeSpan = {-1.0001e+299, 1.0001e+299},
>   Time = 0.0050001,
>   HasTime = 1,
>   NumberOfTimeSteps = 0,
>   DataClassName = 0x5996b050 "vtkTable",
>   TimeLabel = 0x0,
>   CompositeDataClassName = 0x0,
>   CompositeDataSetName = 0x0,
>   PointDataInformation = 0x58ec6430,
>   CellDataInformation = 0x58ec66d0,
>   FieldDataInformation = 0x58ec6770,
>   VertexDataInformation = 0x58ec6890,
>   EdgeDataInformation = 0x58ec67f0,
>   RowDataInformation = 0x58ec6370,
>   CompositeDataInformation = 0x58eb5430,
>   PointArrayInformation = 0x58ec6c50,
>   PortNumber = 0
>
> my guess is that annotate time filter is a type of vtkTable and Bounds
> member variable has too large values. Any idea?
>
> Regards
>
> SeongMo
>
> On 2018년 1월 27일 AM 2:06 +0900, Andy Bauer <andy.ba...@kitware.com>, wrote:
>
> Hi SeongMo,
>
> The AnnotateTime source should work with Catalyst. See the attached images
> and the annotatetime.py script which I used to create it.
>
> With your script, what do your images look like?
>
> You could also try what Ufuk mentioned. I think his work is based on
> weather/climate time scales so he has to handle months, leap years, etc.
> which ParaView itself doesn't handle naturally. You can see some of the
> things he's done with Catalyst at https://blog.kitware.com/
> integration-of-paraview-catalyst-with-regional-earth-system-model/.
>
> Best,
> Andy
>
> On Thu, Jan 25, 2018 at 10:47 AM, SeongMo <seongmo.y...@gmail.com> wrote:
>
>> Dear Andy Bauer,
>>
>> For the color map issue, I think ParaView 5.4.1 resolved it. But, I could
>> not figure out annotate time filter issue. may be it is just simple problem
>> but I am not sure. Coprocess routine is as follows and python script is
>> attached.
>>
>> It would be appreciated if you make some advice.
>>
>>
>> void CoProcess(Foam::fvMesh& mesh, Foam::Time& runTime)
>> {
>>vtkNew dataDescription;
>>dataDescription->AddInput("input");
>>const double time = runTime.value();
>>const unsigned int timeStep = runTime.timeIndex();
>>dataDescription->SetTimeData(time, timeStep);
>>
>>if (runTime.end())
>>{
>>// assume that we want to all the pipelines to execute
>>// if it is the last time step
>>dataDescription->ForceOutputOn();
>>}
>>if (Processor->RequestDataDescription(dataDescription.GetPointer())
>> != 0)
>>{
>>Foam::polyMesh::readUpdateState meshState = mesh.readUpdate();
>>
>>if(meshState != Foam::polyMesh::UNCHANGED)
>>{
>>// mesh moved? or mesh topology changed?
>>BuildVTKGrid(mesh, true);
>>}
>>UpdateVTKAttributes(mesh);
>>dataDescription->GetInputDescriptionByName("input")->
>>SetGrid(multiBlockDataSet);
>>Processor->CoProcess(dataDescription.GetPointer());
>>}
>&

Re: [Paraview] Paraview Not Reading Some Fields in Dataset

[Andy Bauer]

Glad to hear that you're able to read the file correctly now -- thanks for
reporting back to everyone!

On Wed, Jan 31, 2018 at 11:07 AM, Tate Fanning <t8fann...@gmail.com> wrote:

> I found a solution to the problem. The CFD code was writing the offsets
> incorrectly. When I adjust them manually, Paraview can read the file just
> fine.
>
> This thread goes into a little more detail: https://www.cfd-
> online.com/Forums/paraview/198220-paraview-not-reading-
> some-fields-dataset.html
>
> On Tue, Jan 30, 2018 at 1:24 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> It looks like you have integer overflow (https://en.wikipedia.org/wiki
>> /Integer_overflow). I'd suggest using a datatype with more precision and
>> see if that fixes the issue.
>>
>> On Tue, Jan 30, 2018 at 3:15 PM, Tate Fanning <t8fann...@gmail.com>
>> wrote:
>>
>>> I've output a vtu file from a CFD code. When trying to load the dataset
>>> into Paraview I get the following errors:
>>>
>>> [CODE]Error reading uncompressed binary data header. Read 0 of 4 bytes.
>>> ERROR: In 
>>> C:\bbd\7cc78367\source-paraview\VTK\IO\XMLParser\vtkXMLDataParser.cxx,
>>> line 609 vtkXMLDataParser (009CC7674520): Error reading uncompressed
>>> binary data header. Read 0 of 4 bytes.
>>>
>>> Cannot read point data array "Cyl_Velocity" from PointData in piece 0.
>>> The data array in the element may be too short. ERROR: In
>>> C:\bbd\7cc78367\source-paraview\VTK\IO\XML\vtkXMLDataReader.cxx, line
>>> 443 vtkXMLUnstructuredGridReader (009C837CFCE0): Cannot read point data
>>> array "Cyl_Velocity" from PointData in piece 0. The data array in the
>>> element may be too short.[/CODE]
>>>
>>> If I ask Paraview to not read the offending arrays, it reads the other
>>> arrays in fine. From these errors, it seems the data file has some issues
>>> with a few specific arrays.
>>>
>>> Upon inspection of the first part of the vtu file, the offending arrays
>>> (Cyl_Velocity and Rel_Velocity) have negative offsets.
>>>
>>> [CODE]>> byte_order="BigEndian">
>>> 
>>> 
>>>   
>>> >> NumberOfComponents="3" format="appended" offset="   0" />
>>>   
>>>   
>>> >> offset="   236520940" />
>>> >> offset="   541266416" />
>>> 
>>>   
>>>   
>>>  >> offset="   617452792" />
>>>  
>>>  >> offset="   775133424" />
>>>  >> offset="   853973740" />
>>>  >> offset="   932814056" />
>>>  >> offset="  1011654372" />
>>>  >> offset="  1090494688" />
>>>  >> offset="  1169335004" />
>>>  
>>>  >> offset="  1327015636" />
>>>  >> offset="  1405855952" />
>>>  >> offset="  1484696268" />
>>>  >> offset="  1563536584" />
>>>  >> offset="  1642376900" />
>>>  >> offset="  1721217216" />
>>>  >> offset="  1800057532" />
>>>  >> offset="  1878897848" />
>>>  >> offset="  1957738164" />
>>>  >> NumberOfComponents="3" format="appended" offset="  2036578480
>>> <(203)%20657-8480>" />
>>>  >> NumberOfComponents="3" format="appended" offset=" -2021867876" />
>>>  >> NumberOfComponents="3" format="appended" offset=" -1785346936" />
>>>   
>>> [/CODE]
>>>
>>> The CFD code also can output data files for a specific surface. When I
>>> load one of those into Paraview, it has no issues with any data array in
>>> that file, and everything works fine.
>>>
>>> Upon inspection of the first part of a single surface vtu file with no
>>> issues, no array has a negative offset.
>>>
>>> [CODE] >> byte_order="BigEndian">
>>> 
>>> 
>>>   
>>> >> NumberOfComponents="3&quo

Re: [Paraview] Paraview Not Reading Some Fields in Dataset

[Andy Bauer]

It looks like you have integer overflow (
https://en.wikipedia.org/wiki/Integer_overflow). I'd suggest using a
datatype with more precision and see if that fixes the issue.

On Tue, Jan 30, 2018 at 3:15 PM, Tate Fanning  wrote:

> I've output a vtu file from a CFD code. When trying to load the dataset
> into Paraview I get the following errors:
>
> [CODE]Error reading uncompressed binary data header. Read 0 of 4 bytes.
> ERROR: In 
> C:\bbd\7cc78367\source-paraview\VTK\IO\XMLParser\vtkXMLDataParser.cxx,
> line 609 vtkXMLDataParser (009CC7674520): Error reading uncompressed
> binary data header. Read 0 of 4 bytes.
>
> Cannot read point data array "Cyl_Velocity" from PointData in piece 0. The
> data array in the element may be too short. ERROR: In
> C:\bbd\7cc78367\source-paraview\VTK\IO\XML\vtkXMLDataReader.cxx, line 443
> vtkXMLUnstructuredGridReader (009C837CFCE0): Cannot read point data
> array "Cyl_Velocity" from PointData in piece 0. The data array in the
> element may be too short.[/CODE]
>
> If I ask Paraview to not read the offending arrays, it reads the other
> arrays in fine. From these errors, it seems the data file has some issues
> with a few specific arrays.
>
> Upon inspection of the first part of the vtu file, the offending arrays
> (Cyl_Velocity and Rel_Velocity) have negative offsets.
>
> [CODE] byte_order="BigEndian">
> 
> 
>   
>  NumberOfComponents="3" format="appended" offset="   0" />
>   
>   
>  offset="   236520940" />
> 
> 
>   
>   
>  
>  
>  
>  
>  
>   offset="  1011654372" />
>   offset="  1090494688" />
>   offset="  1169335004" />
>  
>   offset="  1327015636" />
>   offset="  1405855952" />
>   offset="  1484696268" />
>   offset="  1563536584" />
>   offset="  1642376900" />
>   offset="  1721217216" />
>   offset="  1800057532" />
>   offset="  1878897848" />
>   offset="  1957738164" />
>   format="appended" offset="  2036578480 <(203)%20657-8480>" />
>   NumberOfComponents="3" format="appended" offset=" -2021867876" />
>   NumberOfComponents="3" format="appended" offset=" -1785346936" />
>   
> [/CODE]
>
> The CFD code also can output data files for a specific surface. When I
> load one of those into Paraview, it has no issues with any data array in
> that file, and everything works fine.
>
> Upon inspection of the first part of a single surface vtu file with no
> issues, no array has a negative offset.
>
> [CODE]  byte_order="BigEndian">
> 
> 
>   
>  NumberOfComponents="3" format="appended" offset="   0" />
>   
>   
>  offset=" 4224604" />
> 
> 
>   
>   
>  
>  
>  
>  
>  
>   offset="15454308" />
>   offset="16862512" />
>   offset="18270716" />
>  
>   offset="21087124" />
>   offset="22495328" />
>   offset="23903532" />
>   offset="25311736" />
>   offset="26719940" />
>   offset="28128144" />
>   offset="29536348" />
>   offset="30944552" />
>   offset="32352756" />
>   format="appended" offset="33760960" />
>   NumberOfComponents="3" format="appended" offset="37985564" />
>   NumberOfComponents="3" format="appended" offset="42210168" />
>   
> [/CODE]
>
> So I think the offset sign is relevant to my problem, but I don't really
> know what it means or how to fix it. Does anyone know what I can do to fix
> my data set, or at least know what the underlying problem is?
>
> Thank you.
>
> --
> *Tate Fanning*
> Ph.D. Candidate
> Turbomachinery Research Lab
> BYU Mechanical Engineering
> 360-953-7457 <(360)%20953-7457>
> t8fann...@gmail.com
>
>
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Re: [Paraview] Plain text data with white space delimiters; Use raw array as axis/variables

[Andy Bauer]

Hi,

ParaView should be able to handle this. Try giving the filename a .csv
extension and then add a space for the Field Delimiter Characters options.
Optionally, you may also want to enable the Merge Consecutive Delimiters
option.

On Fri, Jan 26, 2018 at 8:33 AM, Liang Wang  wrote:

> Hi All,
>
> 1) Does the ParaView GUI read a plain text file with white space as
> delimiters?
> 2) Can ParaView use a giving 1d array as an axis?
>
> My problem:
>
> I have a plain text data file, each column is a different variable, and
> delimiters are white space, e.g.,
>
> x y z variable1 variable 2
>
> Is there a way to read such a file and use x, y, z as coordinates of the
> resulting variables?
>
> For example, in TecPlot you can read in such a file and set axises to use
> the x, y, z (or any other named variables).
>
> For 1), does ParaView have an extra setting to set common options for
> plain text data like delimiter, header, skiprow, etc.?
>
> For 2), it appears to me that in ParaView all field/cell data is
> associated with a predefined axis, so it is not that straightforward to use
> a raw array as axis or as variable, though this is possible in the Python
> interface. Is this correct.
>
> Best,
>
> Liang
>
>
>
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Re: [Paraview] How to insert annotate time info into catalyst?

[Andy Bauer]

Hi Seongmo,

Please keep the conversations on the mailing list so that anyone can follow
along or participate. Also, these types of things often get lost in my
inbox when they don't make it back to the ParaView mailing list.

What version of ParaView Catalyst are you using? I think the annotate time
filter should work with Catalyst but I haven't verified that. I vaguely
remember others using that filter with Catalyst though. Also, I think the
colormap bug was fixed. If you have a way of sharing a sample that
demonstrates either of those bugs I can try taking a look at the issue.

Best,
Andy

On Thu, Jan 18, 2018 at 6:40 PM, Seong Mo Yeon <seongmo.y...@gmail.com>
wrote:

> Dear Andy Bauer
>
> I have a quick question.
> Is it possible to have annotate time filter processed in catalyst adaptor?
> Current my code cannot that filter.
>
> BTW, image extracted from catalyst looks different from render view of
> paraview at the time of writing a script. e.g., pressure colormap legend is
> missing.
>
> Regards
> Seongmo
>
> On 2018년 1월 18일 AM 1:17 +0900, Andy Bauer <andy.ba...@kitware.com>, wrote:
>
> Hi,
>
> My guess is that the TimeStep isn't getting set properly in the adaptor
> (though it looks like it should be in 
> "dataDescription->SetTimeData(runTime.value(),
> runTime.deltaTValue());"). My suggestion would be to add in the following
> to either the RequestDataDescription() or DoCoProcessing() methods in the
> python script to see what Catalyst thinks the time step is:
> print("In script2.py, the data time step is ",
> datadescription.GetTimeStep())
>
>
> On Wed, Jan 17, 2018 at 9:57 AM, SeongMo <seongmo.y...@gmail.com> wrote:
>
>> Hi,
>>
>> I wrote a OpenFOAM adaptor for Catalyst.
>>
>> In the ParaView, the connection is made good and shows filtered flow
>> field as written in the python script.
>>
>> However, filename_%t and image_%t is not expanded as time marching but
>> just write filename_0 and image_0.png.
>>
>> As far as I know, %t should be replaced with current time as given in
>> dataDescription->SetTimeData.
>>
>> Any help would be appreciated.
>>
>>
>> FYI, python script is attached and snippet of my OpenFOAM Adaptor code
>> for Catalyst is as follows:
>>
>> // icoFoam.C
>>
>> #ifdef USE_CATALYST
>> Foam::HashTable options = args.options();
>> IStringStream is(options["scriptList"]);
>> wordList scriptList = readList(is);
>> OFAdaptor::Initialize(scriptList, mesh);
>> #endif
>> while (runTime.loop())
>> {
>> runTime.write();
>> #ifdef USE_CATALYST
>> OFAdaptor::CoProcess(mesh, runTime);
>> #endif
>> }
>> #ifdef USE_CATALYST
>> OFAdaptor::Finalize();
>> #endif
>>
>>
>> // OFAdaptor.C
>>
>> void CoProcess(Foam::fvMesh& mesh, Foam::Time& runTime)
>> {
>>vtkNew dataDescription;
>>dataDescription->AddInput("input");
>>dataDescription->SetTimeData(runTime.value(),
>> runTime.deltaTValue());
>>if (runTime.end())
>>{
>>// assume that we want to all the pipelines to execute
>>// if it is the last time step
>>dataDescription->ForceOutputOn();
>>}
>>if (Processor->RequestDataDescription(dataDescription.GetPointer())
>> != 0)
>>{
>>Foam::polyMesh::readUpdateState meshState = mesh.readUpdate();
>>
>>if(meshState != Foam::polyMesh::UNCHANGED)
>>{
>>BuildVTKGrid(mesh);
>>}
>>UpdateVTKAttributes(mesh);
>> dataDescription->GetInputDescriptionByName("input")->SetGrid
>> (multiBlockDataSet);
>>Processor->CoProcess(dataDescription.GetPointer());
>>}
>> }
>>
>>
>> --
>> SeongMo Yeon, Ph.D, Senior Engineer
>> Offshore Hydrodynamics Research
>> SAMSUNG HEAVY INDUSTRIES CO., LTD.
>> Central Research Institute
>> E-mail : seongmo.y...@gmail.com
>> Tel :
>> 
>> Fluctuat nec mergitur
>>
>>
>> ___
>> 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
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> https://paraview.org/mailman/listinfo/paraview
>>
>>
>
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Re: [Paraview] [EXTERNAL] Re: Material Interface Filter

[Andy Bauer]

It sounds like it. I believe that the user would have to use the extract
surface filter first though.

On Tue, Jan 23, 2018 at 2:00 PM, Scott, W Alan <wasc...@sandia.gov> wrote:

> Andy,
> Wouldn't the upcoming volume filter calculate the volume of fragments
> coming from the Connectivity filter?
>
> Alan
>
> > -Original Message-
> > From: Cory Quammen [mailto:cory.quam...@kitware.com]
> > Sent: Monday, January 22, 2018 9:29 PM
> > To: Scott, W Alan <wasc...@sandia.gov>
> > Cc: Bauer, Andy (External Contacts) <andy.ba...@kitware.com>;
> > paraview@paraview.org
> > Subject: Re: [EXTERNAL] Re: [Paraview] Material Interface Filter
> >
> > On Wed, Jan 17, 2018 at 9:42 PM, Scott, W Alan <wasc...@sandia.gov>
> > wrote:
> > > Thanks Andy!  Although I will take a round about method, I would love
> > > a real solution.
> > >
> > >
> > >
> > > Cory?  Thoughts?
> > >
> > >
> > >
> > > Alan
> > >
> > >
> > >
> > > From: Andy Bauer [mailto:andy.ba...@kitware.com]
> > > Sent: Wednesday, January 17, 2018 9:24 AM
> > > To: Scott, W Alan <wasc...@sandia.gov>; Quammen, Cory (External
> > > Contacts) <cory.quam...@kitware.com>
> > > Cc: paraview@paraview.org
> > > Subject: [EXTERNAL] Re: [Paraview] Material Interface Filter
> > >
> > >
> > >
> > > The best way I can think of is to then use the threshold filter to
> > > isolate each of the pieces and then use the cell size filter on each
> > > piece. This would be fairly easy to automate in a Python script to
> > > just print out the values.
> > >
> > > Alternatively, I don't see a reason why the Connectivity filter
> > > couldn't have an option added to output a field data array with the
> > > summed sizes of each piece. Since Cory just made the connectivity
> > > filter work correctly in parallel it would surprise me that he may be
> > > familiar enough with the code to do the change in a couple of hours.
> >
> > I'm hesitant to add an option in the Connectivity filter to do this.
> > Instead, I can imagine uses for a volume computation for surfaces/volumes
> > labeled by a RegionId that isn't necessarily assigned as a function of
> > connectivity. Instead, I would prefer to create a separate filter that
> computes
> > volumes for each RegionId in the input dataset. You would feed the output
> > of the Connectivity filter to this new filter and get the
> volume-per-region
> > information you want.
> >
> > Cory
> >
> > >
> > >
> > > On Tue, Jan 16, 2018 at 1:32 PM, Scott, W Alan <wasc...@sandia.gov>
> > wrote:
> > >
> > > I have a user that wants to use the equivalent of the Material
> > > Interface Filter on VTK files.  Is there a way to do this?  I did find
> > > the Connectivity filter, that gets me half way.  I then want to find
> > > the mass of these individual fragments.
> > >
> > >
> > >
> > > To test, I used Wavelet, the Clip by Sphere, then made the Radius 15,
> > > then ran the connectivity filter.
> > >
> > >
> > >
> > > Thanks,
> > >
> > >
> > >
> > > Alan
> > >
> > >
> > >
> > >
> > >
> > >
> > > ___
> > > 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
> > >
> > > Search the list archives at: http://markmail.org/search/?q=ParaView
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > https://paraview.org/mailman/listinfo/paraview
> > >
> > >
> >
> >
> >
> > --
> > Cory Quammen
> > Staff R Engineer
> > Kitware, Inc.
>
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Re: [Paraview] Catalyst dlopen issues with OpenGL2 support for off-screen Mesa

[Andy Bauer]

Hi Yvan,

Thanks for the update.

I haven't seen anything like this yet but if I'm able to reproduce it I'll
see if I can track down the issue.

Best,
Andy

On Mon, Jan 22, 2018 at 9:16 PM,  wrote:

> Hello,
>
> I made further progress on this old thread, so am answering myself to
> close this issue...
>
> With recent versions of OSMesa (17.2 or 17.8), I observed that using
> LD_PRELOAD with OSMesa.so.8 also avoided the incorrect initialization issue
> of OSMesa leading to Catalyst complaining aboit OpenGL2 features not being
> available.
>
> On an Arch Linux system, I had also reproduced the reported issue at one
> time, but do not reproduce it anymore with Mesa 17.3.
> On a Debian 8 based system, I still reproduce it, but running new tests,
> instead of LD_PRELOAD, using RTLD_LAZY | RTLD_GLOBAL as dlopen flags solves
> the issue (either RTLD_LAZY or RTLD_NOW work with RTLD_GLOBAL, none work
> wth RTLD_LOCAL). I am pretty sure I had run similar tests a few month ago
> with older versions, with less success.
>
> I assume the improvements come from Mesa updates, though as the behavior
> of dlopen is concerned, it might also be due to lower level patches.
>
> In any case, I started building a small test case to reproduce this, but
> it was not working yet (trying to get the
> correct libraries to link in a minimal setting, or other options correct
> while not being familiar with CMake), so as I have a good work, I guess
> I'll leave it there and hope the issue does not resurfaces.
>
> Best regards,
>
>   Yvan
>
> - Mail original -
> De: "Yvan Fournier" 
> À: paraview@paraview.org
> Envoyé: Jeudi 25 Mai 2017 02:18:04
> Objet: Re: [Paraview] Catalyst dlopen issues with OpenGL2 support for
> off-screen Mesa
>
> Hello,
>
> I reproduced the issue described 2 months ago relative to detection of
> OSMesa
> OpenGL2 support using dynamically loaded shared libraries on another
> machine.
>
> I had reproduced this issue on Debian-9 based systems, but not with the
> preconfigured Mesa/OSMesa from Arch Linux. Recently, I had other issues
> with the
>  packaged library on Arch (Mesa 17.1.0, including both off-screen and
> on-screen
> drivers), as glGetString and a few other symbols were not found.
>
> So I recompiled Mesa for off-screen mode, using the recommendations from
> the
> ParaView Wiki (with the packaged LLVM 4.0), and encounter the following
> error
> again when starting Catalyst:
>
> 
> ERROR: In
> /home/yvan/src/ParaView/VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx,
> line
> 831
>
> vtkOSOpenGLRenderWindow (0x72e3c00): GL version 2.1 with the gpu_shader4
> extension is not supported by your graphics driver but is required fo
> r the new OpenGL rendering backend. Please update your OpenGL driver. If
> you are
> using Mesa please make sure you have version 10.6.5 or later
> and make sure your driver in Mesa supports OpenGL 3.2.
> 
>
> Trying to force usage of OpenSWR (using "export GALLIUM_DRIVER=swr") I have
> another error:
>
> 
> SWR detected AVX2
>
> SWR library load failure: /home/yvan/opt/osmesa/lib/libswrAVX2.so:
> undefined
> symbol: _glapi_tls_Dispatch
> 
>
> So this seems quite reproducible on various systems, and both with LLVM
> 3.9 or
> LLVM 4, Mesa 13 or 17.
>
> When linking ParaView (Catalyst) normally (rather than linking them with a
> smaller module loaded as a plugin with dlopen), both the default LLVMpipe
> and
> OpenSwr errors dissapear, and things work fine
>
> Does anybody have an idea what I may be missing when loading with dlopen ?
>
> Best regards,
>
>   Yvan
>
>
> From: Yvan Fournier 
> To: paraview@paraview.org
> Objet: Re: [Paraview] Issues with OpenGL2 support for off-screen Mesa
> Date: Sat, 11 Mar 2017 00:36:00 +0100
>
> > Hello,
> >
> > I made some progress using OpenGL2 for offs-screen Mesa on a Debian
> 8-based
> > system:
> >
> > I don't need to compile my code or ParaView in static: compiling
> everything
> > with
> > dyanmic libraries works, as long as I link everything together instead of
> > loading a plugin (consisting of some Code_Saturne libraries, ParaView
> > Libraries,
> > and OSMesa/Gallium).
> >
> > So it seems some things re not initialized correctly when I load
> ParaView and
> > OSMesa as a plugin, so I'm not took sure the problem comes from ParaView,
> > OSMesa, or LLVM. I tried OSMesa 13.0.3 and 17.0.1, and LLVM 3.5
> (packaged with
> > Debian 8) and 3.9 (local build), with identical results.
> >
> > I also tried using RTLD_NOW and even RTLD_NOW | RTLD_GLOBAL instead of
> the
> > usual
> >  RTLD_LAZY when using dlopen, with no difference in behavior (I have not
> tried
> > RTLD_DEEPBIND).
> >
> > Has anyone encountered similar issues or does anyone have an idea what
> could
> > be
> > missing in the initialization stage using dlopen for a plugin linked 

Re: [Paraview] Material Interface Filter

[Andy Bauer]

The best way I can think of is to then use the threshold filter to isolate
each of the pieces and then use the cell size filter on each piece. This
would be fairly easy to automate in a Python script to just print out the
values.

Alternatively, I don't see a reason why the Connectivity filter couldn't
have an option added to output a field data array with the summed sizes of
each piece. Since Cory just made the connectivity filter work correctly in
parallel it would surprise me that he may be familiar enough with the code
to do the change in a couple of hours.

On Tue, Jan 16, 2018 at 1:32 PM, Scott, W Alan  wrote:

> I have a user that wants to use the equivalent of the Material Interface
> Filter on VTK files.  Is there a way to do this?  I did find the
> Connectivity filter, that gets me half way.  I then want to find the mass
> of these individual fragments.
>
>
>
> To test, I used Wavelet, the Clip by Sphere, then made the Radius 15, then
> ran the connectivity filter.
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
>
>
> ___
> 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
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> https://paraview.org/mailman/listinfo/paraview
>
>
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Re: [Paraview] filename_%t is not expanded to current time in Catalyst

[Andy Bauer]

Hi,

My guess is that the TimeStep isn't getting set properly in the adaptor
(though it looks like it should be in
"dataDescription->SetTimeData(runTime.value(),
runTime.deltaTValue());"). My suggestion would be to add in the following
to either the RequestDataDescription() or DoCoProcessing() methods in the
python script to see what Catalyst thinks the time step is:
print("In script2.py, the data time step is ",
datadescription.GetTimeStep())


On Wed, Jan 17, 2018 at 9:57 AM, SeongMo  wrote:

> Hi,
>
> I wrote a OpenFOAM adaptor for Catalyst.
>
> In the ParaView, the connection is made good and shows filtered flow field
> as written in the python script.
>
> However, filename_%t and image_%t is not expanded as time marching but
> just write filename_0 and image_0.png.
>
> As far as I know, %t should be replaced with current time as given in
> dataDescription->SetTimeData.
>
> Any help would be appreciated.
>
>
> FYI, python script is attached and snippet of my OpenFOAM Adaptor code for
> Catalyst is as follows:
>
> // icoFoam.C
>
> #ifdef USE_CATALYST
> Foam::HashTable options = args.options();
> IStringStream is(options["scriptList"]);
> wordList scriptList = readList(is);
> OFAdaptor::Initialize(scriptList, mesh);
> #endif
> while (runTime.loop())
> {
> runTime.write();
> #ifdef USE_CATALYST
> OFAdaptor::CoProcess(mesh, runTime);
> #endif
> }
> #ifdef USE_CATALYST
> OFAdaptor::Finalize();
> #endif
>
>
> // OFAdaptor.C
>
> void CoProcess(Foam::fvMesh& mesh, Foam::Time& runTime)
> {
>vtkNew dataDescription;
>dataDescription->AddInput("input");
>dataDescription->SetTimeData(runTime.value(),
> runTime.deltaTValue());
>if (runTime.end())
>{
>// assume that we want to all the pipelines to execute
>// if it is the last time step
>dataDescription->ForceOutputOn();
>}
>if (Processor->RequestDataDescription(dataDescription.GetPointer())
> != 0)
>{
>Foam::polyMesh::readUpdateState meshState = mesh.readUpdate();
>
>if(meshState != Foam::polyMesh::UNCHANGED)
>{
>BuildVTKGrid(mesh);
>}
>UpdateVTKAttributes(mesh);
> dataDescription->GetInputDescriptionByName("input")->
> SetGrid(multiBlockDataSet);
>Processor->CoProcess(dataDescription.GetPointer());
>}
> }
>
>
> --
> SeongMo Yeon, Ph.D, Senior Engineer
> Offshore Hydrodynamics Research
> SAMSUNG HEAVY INDUSTRIES CO., LTD.
> Central Research Institute
> E-mail : seongmo.y...@gmail.com
> Tel :
> 
> Fluctuat nec mergitur
>
>
> ___
> 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
>
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>
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>
>
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Re: [Paraview] PV4.10 extracting a surface

[Andy Bauer]

The Threshold filter works by selecting cells that have cell data in the
selected range. If you're requesting to do thresholding on a point data
array then it will use the point data to cell data filter to create a cell
data array and threshold on that. With this, it's very unlikely that any
cell data ends up with exactly a value of .1. It sounds like what you want
is to use the Contour filter on your rad array.

On Wed, Dec 20, 2017 at 10:32 AM, Utkarsh Ayachit <
utkarsh.ayac...@kitware.com> wrote:

> I believe you're getting  the warning because the threshold ended up
> not producing any output. If you can attach the state/data file, I may
> be able to can give more info.
>
> Utkarsh
>
> On Wed, Dec 20, 2017 at 10:15 AM, Stephen Wornom
>  wrote:
> > The geometry is a cylinder.
> > Using the calculator I do
> > rad =sqrt( x**2+y**2)
> > I would like to extract the cylinder surface which is rad = 0.1
> > I click on threshold then information to see rad 0.1 > I click on extract and enter the values min = 0.1 and max 0.1 for rad
> > I get this message
> > warning: In
> > /home/utkarsh/Dashboards/MyTests/NightlyMaster/
> ParaViewSuperbuild-Release/paraview/src/paraview/
> ParaViewCore/ServerManager/Rendering/vtkSMPVRepresentationProxy.cxx,
> > line 279
> >
> > vtkSMPVRepresentationProxy (0x359fd080): Could not determine array range.
> >
> >
> > Any ideas to the solution of my problem?
> > Thanks in advance,
> > Stephen
> >
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Re: [Paraview] wallShearStress Calculation in Paraview

[Andy Bauer]

There's no general way to compute gradients normal to the surface so you
need to compute the gradient on the simulation's cells (e.g. volumetric
cells for 3D). You can use the Gradient Of Unstructured Data set to do
that. Then extract the surface as Mathi said, use the Normals filter to
compute the normals, use the Calculator filter to multiply the normals by
the gradient and the viscosity and you'll have the wall shear stress over
the entire boundary surface. You can then select the cells you want to show
the WSS over the exact portion of the desired boundary.

On Wed, Dec 6, 2017 at 9:05 AM, Ezhilmathi Krishnasamy <
ezhkr...@student.liu.se> wrote:

> Hi Ahmet,
>
> What you can do that is, use the filter name called extract surface.
> once you get that surface either you can export those values in form of
> from elements or from the points.
>
> It might work, or you may get more clear explanation from this forum.
>
> Cheers,
> Mathi
>
>
>
> On 6 December 2017 at 15:00, Ahmet Ahmet  wrote:
>
>> Hello everyone,
>>
>> I have results with OpenFOAM including p,T,U outputs. Due to some
>> reasons, I can't use wallShearStress or wallgradU utility in OF. So, I have
>> to calculate it on Paraview. I saw many topics related to that on google,
>> but I could not find a satisfactory answer. My case is 3-D, compressible
>> and laminar but we can think about incompressible and may be 2-D.
>>
>> I think the most important part for WSS is to calculate velocity
>> gradient. My unsolved problem is to calculate that. How can I calculate
>> gradients on the wall? I have no-slip wall, that is u=0 and with *Gradient
>> of Unstructured DataSet/Compute Derivatives *filters, I obtained 0 on
>> the wall. I think the values in the nearest mesh to the wall should be
>> accounted for. To do that, what should I do?
>>
>> *Note:*
>>
>>1. The walls are not aligned with a coordinate axis. For this part, I
>>tried to extract the wall surface and generate normal vectors.
>>2. As an alternative to get directly on wall, I tried to get slice a
>>little bit over the wall surface and then take surface vector on slice 
>> then
>>gradient of unstructured dataset on surface vector. That gives me a result
>>but I am not sure it's true.
>>
>>
>> This may be simple for you, sorry for that.
>> Thank you in advance,
>> Ahmet
>>
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Re: [Paraview] Integrate variable filter

[Andy Bauer]

You may also want to look at the Cell Size filter which has the advanced
option to globally sum the values.

The Integrate Variable filter can give unexpected results with mixed
dimension elements since it will integrate all 0D, 1D, 2D and 3D cells.

On Fri, Dec 1, 2017 at 5:02 AM, Andrew  wrote:

> Hello.
> For calculationg volumes and areas, the "Cell Data" attribute type of
> Integrate variables filter is usable. You don't need to define additional
> constant field for this. I checked it now and it seems to give the correct
> domain volume (554 m3 in SolidWorks, 557 m3 in ParaView). The error may be
> due to unequality of mesh and "ideal" geometry. You can also use the
> Threshold filter before the Intergate variables to define the custom volume
> (with particular scalar values).
>
> 2017-12-01 12:08 GMT+03:00 Lionel Wilhelm :
>
>> Dear Paraviewers,
>>
>> I'm trying to compute a closed volume in paraview. For that purpose, I
>> define a constant field with value 1 on the domain and use the integrate
>> filter. Unfortunately the result does not seem to be correct.
>>
>> Attached a screenshot of the GUI where I try to compute the volume of a
>> cube which volume is  0.075^3.
>>
>> I guess that floating point operations error might result in this error
>> but I'm unsure. Furthermore could you tell me if there is a mean for
>> computing such small volumes enclosed in complex surfaces?
>>
>> Kindly,
>>
>> Lionel Wilhelm
>>
>>
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Re: [Paraview] rendering window problem

[Andy Bauer]

I'm guessing your view size is locked in your settings. If that's the case
you can change that by going to Tools and uncheck either "Lock View Size"
or "Lock View Size Custom..."

On Wed, Nov 8, 2017 at 3:36 PM,  wrote:

> Hello all
>
>
>
> I recently switch to Paraview 5.4.1. It used to work well for a week.
> Then, every time I start Paraview, it only shows a part of the rendering
> window (as shown in the attached figure). I already un-install and
> re-install Paraview. But the problem persists. So how can I do to fix this?
>
>
>
> Thank you very much
>
>
>
> Chih-Hao
>
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Re: [Paraview] PythonFullExample Error: Must use ParaView v4.2 or greater

[Andy Bauer]

Hi,

I'm not able to reproduce this issue on my Linux machine. Can you verify
that the GUI version of ParaView that you're running is also v5.4? That's
the only thing I can think of right now that could be causing the issue.

Best,
Andy

On Fri, Nov 3, 2017 at 7:06 PM, the lily  wrote:

> Hello,
>
>
> I built paraview 5.4 from the repo https://gitlab.kitware.
> com/paraview/paraview/blob/master/Documentation/dev/git/download.md on
> MacOS Sierra
>
> I'm trying to run the PythonFullExample downloaded from here
> https://gitlab.kitware.com/paraview/paraview/tree/master/
> Examples/Catalyst/PythonFullExample
>
>
> I run it as the following:
>
>
> export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/Users/a/ParaView/
> paraview_build/lib
>
> export PYTHONPATH=/Users/a/ParaView/paraview_build/lib/site-packages
>
> /Users/a/ParaView/paraview_build/bin/pvpython fedriver.py cpscript.py
>
> I connect to Catalyst, then I get an error '*Must use ParaView v4.2 or
> greater*'
>
> Any guide on how to solve this?
>
>
>
>
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Re: [Paraview] Does Catalyst add MPI processes or use TCP communication?

[Andy Bauer]

Currently Catalyst sends its data to pvserver through sockets which will
not likely not utilize an HPC's fast interconnect. We hope to address this
in the future using ADIOS but I don't have a timetable on when that will be
done.

On Sat, Oct 28, 2017 at 12:57 PM, Kolja Petersen <petersenko...@gmail.com>
wrote:

>
>
> On Sat, Oct 28, 2017 at 5:07 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> FYI: pvserver will likely be run in a separate MPI job if you're doing a
>> Live connection.
>>
>
> Yes, so the pvserver MPI job will have one MPI_COMM_WORLD, and the
> Catalyst enabled simulation will have a different MPI_COMM_WORLD.
>
> The question is how does Catalyst send its data to the other communicator?
> Afaik, their is no connection between the two unless the second
> communicator is spawned from the first by MPI_Comm_spawn().
> Kolja
>
>
>> On Sat, Oct 28, 2017 at 11:05 AM, Andy Bauer <andy.ba...@kitware.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Catalyst by default uses MPI_COMM_WORLD of the existing MPI library that
>>> the simulation code is linked with. You can use another MPI communicator as
>>> well. An example of that is in the 
>>> Examples/Catalyst/MPISubCommunicatorExample
>>> source directory.
>>>
>>> Best,
>>> Andy
>>>
>>> On Sat, Oct 28, 2017 at 7:50 AM, Kolja Petersen <petersenko...@gmail.com
>>> > wrote:
>>>
>>>> Hello,
>>>> I am trying to understand a Catalyst implementation detail.
>>>>
>>>> Because parallel Catalyst may transfer huge data to a parallel
>>>> pvserver, I thought the Catalyst processes would have themselves added to
>>>> the pvserver's MPI communicator. However, MPI_Comm_spawn() is the only
>>>> function that I know of for this task, and I find "MPI_Comm_spawn" nowhere
>>>> in the code (searched case insensitive).
>>>>
>>>> I thought that the standard Catalyst TCP port 2 was only used for
>>>> control messages between Catalyst and pvserver, and data exchange would go
>>>> via MPI. But apparently there is no MPI connection between Catalyst and
>>>> pvserver, and all data are sent via TCP:2, which could explain observed
>>>> network bottlenecks.
>>>>
>>>> Can somebody clarify this implementation detail?
>>>> Thanks
>>>> Kolja
>>>>
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>>>>
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>>>>
>>>
>>
>
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Re: [Paraview] Does Catalyst add MPI processes or use TCP communication?

[Andy Bauer]

FYI: pvserver will likely be run in a separate MPI job if you're doing a
Live connection.

On Sat, Oct 28, 2017 at 11:05 AM, Andy Bauer <andy.ba...@kitware.com> wrote:

> Hi,
>
> Catalyst by default uses MPI_COMM_WORLD of the existing MPI library that
> the simulation code is linked with. You can use another MPI communicator as
> well. An example of that is in the Examples/Catalyst/MPISubCommunicatorExample
> source directory.
>
> Best,
> Andy
>
> On Sat, Oct 28, 2017 at 7:50 AM, Kolja Petersen <petersenko...@gmail.com>
> wrote:
>
>> Hello,
>> I am trying to understand a Catalyst implementation detail.
>>
>> Because parallel Catalyst may transfer huge data to a parallel pvserver,
>> I thought the Catalyst processes would have themselves added to the
>> pvserver's MPI communicator. However, MPI_Comm_spawn() is the only function
>> that I know of for this task, and I find "MPI_Comm_spawn" nowhere in the
>> code (searched case insensitive).
>>
>> I thought that the standard Catalyst TCP port 2 was only used for
>> control messages between Catalyst and pvserver, and data exchange would go
>> via MPI. But apparently there is no MPI connection between Catalyst and
>> pvserver, and all data are sent via TCP:2, which could explain observed
>> network bottlenecks.
>>
>> Can somebody clarify this implementation detail?
>> Thanks
>> Kolja
>>
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>>
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Re: [Paraview] Does Catalyst add MPI processes or use TCP communication?

[Andy Bauer]

Hi,

Catalyst by default uses MPI_COMM_WORLD of the existing MPI library that
the simulation code is linked with. You can use another MPI communicator as
well. An example of that is in the
Examples/Catalyst/MPISubCommunicatorExample source directory.

Best,
Andy

On Sat, Oct 28, 2017 at 7:50 AM, Kolja Petersen 
wrote:

> Hello,
> I am trying to understand a Catalyst implementation detail.
>
> Because parallel Catalyst may transfer huge data to a parallel pvserver, I
> thought the Catalyst processes would have themselves added to the
> pvserver's MPI communicator. However, MPI_Comm_spawn() is the only function
> that I know of for this task, and I find "MPI_Comm_spawn" nowhere in the
> code (searched case insensitive).
>
> I thought that the standard Catalyst TCP port 2 was only used for
> control messages between Catalyst and pvserver, and data exchange would go
> via MPI. But apparently there is no MPI connection between Catalyst and
> pvserver, and all data are sent via TCP:2, which could explain observed
> network bottlenecks.
>
> Can somebody clarify this implementation detail?
> Thanks
> Kolja
>
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Re: [Paraview] LiveInsituLink proxy in pvpython client

[Andy Bauer]

Unfortunately there's no comprehensive "developing paraview" guide. It can
be used as a framework for other applications and has been designed to do
that but we haven't had any funding to work on a comprehensive guide for
that.

I haven't looked at the Live parts in depth in a while so my memory is
probably fuzzy on that and it would take a good bit of time for me to
familiarize myself with that part of the code. By murky I mean that things
get a bit confusing when you're looking at the classes for both the client,
server and in situ side. Kitware does offer support services if this is
important to get working for you.

Best,
Andy

On Fri, Oct 27, 2017 at 12:51 PM, Kolja Petersen <petersenko...@gmail.com>
wrote:

> More questions below...
>
> On Thu, Oct 26, 2017 at 5:54 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> I inlined some answers below...
>>
>> On Wed, Oct 25, 2017 at 1:42 PM, Kolja Petersen <petersenko...@gmail.com>
>> wrote:
>>
>>> Thank you, Andy,
>>> unfortunately your answer has shown me how little I understand about
>>> Catalyst. But maybe it leads in the right direction after some work from my
>>> side.
>>>
>>> Just to make sure that we are talking about the same thing: My pvpython
>>> client is supposed to automate some of the visualization functionality of
>>> the paraview GUI. The coprocessing.py is in charge of the other side of the
>>> link, namely to provide data to the visualization side, if I understand
>>> correctly? I rather followed what happens in the constructor
>>> pqLiveInsituVisualizationManager::pqLiveInsituVisualizationManager(int
>>> connection_port, pqServer* server), which creates a
>>> vtkSMLiveInsituLinkProxy, not a vtkLiveInsituLink as coprocessing.py.
>>>
>>
>> Yes, coprocessing.py should only be used on the simulation side.
>>
>
> So, did you suggest, coprocessing.py could also help to develop the
> visualization side? If yes, how? Or was my first email too unclear, so that
> my intention was not obvious?
>
>
>>
>>>
>>> Now I saw that the vtkLiveInsituLink class can have ProcessType LIVE
>>> (for the visualization side? as server side object of the proxy created by
>>> paraview?) or INSITU (for the simulation side?). So apparently the same
>>> class can take both roles? If yes, that'd clarify some of my confusion. But
>>> still I don't see how coprocessing.py helps me to implement a python
>>> visualization client?
>>>
>>>
>> Yes, the same class does work in both roles with the LIVE ProcessType
>> being the visualization side and the INSITU being the simulation side.
>> Things get a little murkier when there is a separate pvserver from the
>> client that connects to the simulation.
>>
>
> What do you mean by "murkier"? Paraview also uses a proxy (to a
> vtkLiveInsituLink instance either on a pvserver or on the builtin server),
> not  the class itself. Do you have an easier solution (C++ or python) by
> using vtkInsituLink directly?
>
> Are there any design documents from Kitware that show the timings and
> message exchange between Catalyst, pvserver and Paraview (or other
> clients)? I don't know Kitware's publishing policies. My impression was
> always that you are not just developing the Paraview application but also
> an open source visualization programming framework. Maybe I'm wrong, but I
> am missing some kind of "Paraview Programming Guide" that goes beyond a
> User's Guide, to enable others understand the concepts behind Paraview and
> contribute at a deeper level than just adding filters and data processing
> algorithms.
> Anyway, thanks for your explanations, although I couldn't make much
> progress.
> Kolja
>
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Re: [Paraview] LiveInsituLink proxy in pvpython client

[Andy Bauer]

I inlined some answers below...

On Wed, Oct 25, 2017 at 1:42 PM, Kolja Petersen <petersenko...@gmail.com>
wrote:

> Thank you, Andy,
> unfortunately your answer has shown me how little I understand about
> Catalyst. But maybe it leads in the right direction after some work from my
> side.
>
> Just to make sure that we are talking about the same thing: My pvpython
> client is supposed to automate some of the visualization functionality of
> the paraview GUI. The coprocessing.py is in charge of the other side of the
> link, namely to provide data to the visualization side, if I understand
> correctly? I rather followed what happens in the constructor
> pqLiveInsituVisualizationManager::pqLiveInsituVisualizationManager(int
> connection_port, pqServer* server), which creates a
> vtkSMLiveInsituLinkProxy, not a vtkLiveInsituLink as coprocessing.py.
>

Yes, coprocessing.py should only be used on the simulation side.


>
> Now I saw that the vtkLiveInsituLink class can have ProcessType LIVE (for
> the visualization side? as server side object of the proxy created by
> paraview?) or INSITU (for the simulation side?). So apparently the same
> class can take both roles? If yes, that'd clarify some of my confusion. But
> still I don't see how coprocessing.py helps me to implement a python
> visualization client?
>
>
Yes, the same class does work in both roles with the LIVE ProcessType being
the visualization side and the INSITU being the simulation side. Things get
a little murkier when there is a separate pvserver from the client that
connects to the simulation.


> Then, following the creation of a vtkSMLiveInsituLinkProxy in the
> pqLiveInsituVisualizationManager constructor, this proxy's server side
> vtkLiveInsituLink calls 
> "parallelController->TriggerRMIOnAllChildren(INITIALIZE_CONNECTION);"
> inside vtkLiveInsituLink::InsituConnect(vtkMultiProcessController*
> proc0NodesController). This seems to be the first RMI sent over the link.
> Is there any possibility to log the transmission or reception of this RMI?
> I don't find it in the cslogs.
> I think I could make some progress if I am able to debug where those
> messages are sent to, and why the python client doesn't react to them.
>

I believe the cslogs are only between the client and server. You may be
able to print the cslogs on the simulation side as well but I haven't tried
that to verify that it works.


> Thank you
> Kolja
>
> On Wed, Oct 25, 2017 at 4:05 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> Hi Kolja,
>>
>> I can't recall if anyone tried the Catalyst Live connection through
>> pvpython but I don't think anyone has done that yet. The design was meant
>> to go through the GUI. My suggestion would be to start looking at the
>> DoLiveVisualization() method in coprocessing.py.
>>
>> Cheers,
>> Andy
>>
>> On Tue, Oct 24, 2017 at 12:49 PM, Kolja Petersen <petersenko...@gmail.com
>> > wrote:
>>
>>> Hello,
>>> Are there any examples how to receive extracts from Catalyst simulations
>>> in a batch pvpython script?
>>>
>>> My first attempt looks as attached. I connect to a pvserver running on
>>> localhost. Then I create a LiveInsituLink proxy, set the insitu port to
>>> 2 and initialize the proxy. Finally, I repeat ProcessEvents(), which I
>>> hoped would allow me to interact with the Catalyst simulation.
>>>
>>> However, when I first start pvserver, then the "coproc.py" script
>>> (attached), and finally a Catalyst example (e.g.
>>> Examples/Catalyst/CFullExample/FEDriver.c), nothing useful happens. The
>>> callback, which should react to any LiveInsituLink events, is only called
>>> during initialization (UpdatePropertyEvent and ModifiedEvent), then never
>>> again. lil.GetTimeStep() in the endless loop shows always the same
>>> (uninitialized?) value, there are no Debug messages from the LiveInsituLink
>>> proxy.
>>>
>>> How can I receive a notification, when a Catalyst simulation connects?
>>> How can I get a list of available extracts?
>>> Thank you
>>> Kolja
>>>
>>> ___
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>>>
>>
>
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Re: [Paraview] LiveInsituLink proxy in pvpython client

[Andy Bauer]

Hi Kolja,

I can't recall if anyone tried the Catalyst Live connection through
pvpython but I don't think anyone has done that yet. The design was meant
to go through the GUI. My suggestion would be to start looking at the
DoLiveVisualization() method in coprocessing.py.

Cheers,
Andy

On Tue, Oct 24, 2017 at 12:49 PM, Kolja Petersen 
wrote:

> Hello,
> Are there any examples how to receive extracts from Catalyst simulations
> in a batch pvpython script?
>
> My first attempt looks as attached. I connect to a pvserver running on
> localhost. Then I create a LiveInsituLink proxy, set the insitu port to
> 2 and initialize the proxy. Finally, I repeat ProcessEvents(), which I
> hoped would allow me to interact with the Catalyst simulation.
>
> However, when I first start pvserver, then the "coproc.py" script
> (attached), and finally a Catalyst example (e.g.
> Examples/Catalyst/CFullExample/FEDriver.c), nothing useful happens. The
> callback, which should react to any LiveInsituLink events, is only called
> during initialization (UpdatePropertyEvent and ModifiedEvent), then never
> again. lil.GetTimeStep() in the endless loop shows always the same
> (uninitialized?) value, there are no Debug messages from the LiveInsituLink
> proxy.
>
> How can I receive a notification, when a Catalyst simulation connects?
> How can I get a list of available extracts?
> Thank you
> Kolja
>
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Re: [Paraview] Paraview v5.4.1 using EGL on ppc64le RHEL7.2

[Andy Bauer]

Hi,

It should do hardware rendering in all cases. If you're connecting the GUI
to the EGL pvserver though the rendering can switch from being done on the
client vs. being done on the server. You can control where the rendering is
being done in your settings under the Render View by setting the Remote
Render Threshold.

Also, what kind of dataset do you have? It's possible that the dataset type
can only be rendered with a single process.

Best,
Andy

On Tue, Oct 24, 2017 at 7:11 AM, Bruce D'Amora <dam...@us.ibm.com> wrote:

> using 384.61 driver. Does pvserver use software rendering for surface,
> wireframe, outline, points? Rendering in those modes works, but when I
> switch to volume rendering it crashes. I wonder if I'm just switching to
> H/W rendering when I switch to volume mode and it is crashing.
>
> ___
> Bruce D'Amora
> Senior Technical Staff Member
> Manager, Cognitive and Cloud Solutions
> Data Centric Solutions
> IBM T. J. Watson Research Center
> 914-945-4514 <(914)%20945-4514> (T/L 862-4514)
>
>
>
> From:Andy Bauer <andy.ba...@kitware.com>
> To:"Bruce D'Amora" <dam...@us.ibm.com>
> Cc:"paraview@paraview.org" <paraview@paraview.org>
> Date:10/23/2017 08:44 PM
> Subject:Re: [Paraview] Paraview v5.4.1 using EGL on ppc64le
> RHEL7.2
> --
>
>
>
> Hi,
>
> It may be a driver issue. Which NVIDIA driver version are you using?
> According to
> *https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/*
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__blog.kitware.com_off-2Dscreen-2Drendering-2Dthrough-2Dthe-2Dnative-2Dplatform-2Dinterface-2Degl_=DwMFaQ=jf_iaSHvJObTbx-siA1ZOg=nFZHTDwwrtvRFMAKk-cL1lSblvQ2XZraApJR7VBntn4=R-cqnFfkFSXbKukKqz4rPqKveoxdFitLcz6RTmgXyZo=vg5d5KFutIWZlFK5GgmZDA-Rs68eKk8NTDa02LahtmA=>you'll
> need at lest 355.11.
>
> Cheers,
> Andy
>
> On Mon, Oct 23, 2017 at 5:25 PM, Bruce D'Amora <*dam...@us.ibm.com*
> <dam...@us.ibm.com>> wrote:
> I think there is an issue with volume rendering on Paraview v5.4.1 using
> EGL on ppc64le RHEL 7.2 and client-server rendering. Any model that I try
> to volume render results in a segfault.
> Always seem to get these errors, but only when I try volume rendering.
>
> Warning: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkEGLRenderWindow.cxx, line 272
> vtkEGLRenderWindow (0x1003dad7340): Setting an EGL display to device
> index: 0 require EGL_EXT_device_base EGL_EXT_platform_device
> EGL_EXT_platform_base extensions
>
> ERROR: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkEGLRenderWindow.cxx, line 341
> vtkEGLRenderWindow (0x1003dad7340): Only EGL 1.4 and greater allows OpenGL
> as client API. See eglBindAPI for more information.
>
> ERROR: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
> vtkEGLRenderWindow (0x1003dad7340): GLEW could not be initialized.
> ___
> Bruce D'Amora
>
>
>
> ___
> Powered by *www.kitware.com*
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.kitware.com=DwMFaQ=jf_iaSHvJObTbx-siA1ZOg=nFZHTDwwrtvRFMAKk-cL1lSblvQ2XZraApJR7VBntn4=R-cqnFfkFSXbKukKqz4rPqKveoxdFitLcz6RTmgXyZo=MuqBW1BSoPm8NvK6FrW4hMVojop5uAg24zsjVLFeob8=>
>
>
> Visit other Kitware open-source projects at
> *http://www.kitware.com/opensource/opensource.html*
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.kitware.com_opensource_opensource.html=DwMFaQ=jf_iaSHvJObTbx-siA1ZOg=nFZHTDwwrtvRFMAKk-cL1lSblvQ2XZraApJR7VBntn4=R-cqnFfkFSXbKukKqz4rPqKveoxdFitLcz6RTmgXyZo=ZIXVgkrSBK1EIf5L2CxMS3qFlWBQS_06Mo1wE4YteKw=>
>
> Please keep messages on-topic and check the ParaView Wiki at:
> *http://paraview.org/Wiki/ParaView*
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__paraview.org_Wiki_ParaView=DwMFaQ=jf_iaSHvJObTbx-siA1ZOg=nFZHTDwwrtvRFMAKk-cL1lSblvQ2XZraApJR7VBntn4=R-cqnFfkFSXbKukKqz4rPqKveoxdFitLcz6RTmgXyZo=K_X55oWmgRkJFPXYnmQ7T0LI_yMxiOkWwAlCFYgP56A=>
>
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>
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Re: [Paraview] Paraview v5.4.1 using EGL on ppc64le RHEL7.2

[Andy Bauer]

Hi,

It may be a driver issue. Which NVIDIA driver version are you using?
According to
https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/
you'll need at lest 355.11.

Cheers,
Andy

On Mon, Oct 23, 2017 at 5:25 PM, Bruce D'Amora  wrote:

> I think there is an issue with volume rendering on Paraview v5.4.1 using
> EGL on ppc64le RHEL 7.2 and client-server rendering. Any model that I try
> to volume render results in a segfault.
> Always seem to get these errors, but only when I try volume rendering.
>
> Warning: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkEGLRenderWindow.cxx, line 272
> vtkEGLRenderWindow (0x1003dad7340): Setting an EGL display to device
> index: 0 require EGL_EXT_device_base EGL_EXT_platform_device
> EGL_EXT_platform_base extensions
>
> ERROR: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkEGLRenderWindow.cxx, line 341
> vtkEGLRenderWindow (0x1003dad7340): Only EGL 1.4 and greater allows OpenGL
> as client API. See eglBindAPI for more information.
>
> ERROR: In /gsa/yktgsa/home/s/a/sawkor/ess/ParaView-v5.4.1/VTK/
> Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
> vtkEGLRenderWindow (0x1003dad7340): GLEW could not be initialized.
> ___
> Bruce D'Amora
>
>
> ___
> 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
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
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>
>
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Re: [Paraview] [EXT] Re: How to test for empty block in multi-block dataset

[Andy Bauer]

Glad to hear it works! A disclaimer -- I don't profess to write good Python
code, just mildly functional Python code :)

On Wed, Oct 18, 2017 at 2:11 PM, Dennis Conklin <dennis_conk...@goodyear.com
> wrote:

> Andy,
>
>
>
> That works!   Thanks much!
>
>
>
> Now I just have to add it to every filter I’ve ever written to protect
> them all against empty blocks!  I’m amazed it took this long for this to
> come up!
>
>
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 1:47 PM
>
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* Re: [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
> Maybe try the following:
>
>if hasattr(block, "GetNumberOfCells") and block.GetNumberOfCells()
> > 0 and block.GetCellType(0)==12:
>
>   process_block(block)
>
>
>
> On Wed, Oct 18, 2017 at 1:05 PM, Dennis Conklin <
> dennis_conk...@goodyear.com> wrote:
>
> Andy,
>
>
>
> GetCellType works fine when I have cells in the block, but in this recent
> case I had zero cells in the block after a Threshold filter,   my code is
> of the form:
>
>
>
> Def process_block(block):
>
> Print block.GetNumberOfCells()
>
>
>
>
>
>
>
>
>
> ###
>
>
> # main routine starts here
>
> output.CopyStructure(inputs[0].VTKObject)
>
> # if you ShallowCopy, then new variables created in input to filter
>
> output.DeepCopy(inputs[0].VTKObject)
>
>
>
> #
>
> # Loop over blocks in composite (Exodus) data set
>
> for block in output:
>
>
>
># VTK element types:
>
># 12 = VTK_HEXAHEDRON (Gdyr Hex)
>
>#  9 = VTK_QUAD  (Gdyr Membrane)
>
>#  3 = VTK_LINE  (Gdyr 3D Truss)
>
># since EXODUS requires single element type per block, test 1st
> element only
>
>if block.GetCellType(0)==12:
>
>   process_block(block)
>
>
>
> I think GetCellType is dying as there is no element(0)
>
> I need a way to test the block before calling anything to see if it is
> empty
>
>
>
> Thanks!
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 11:39 AM
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* Re: [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
> Hi Dennis,
>
> Maybe the block isn't a vtkDataSet and thus wouldn't have the
> GetCellType() method. You could try a print statement after the for loop to
> see what each block is by doing something like:
>
> print block
>
>
>
> Could you share your full python code for the programmable filter? That
> may make it easier to track down.
>
>
>
> Best,
>
> Andy
>
>
>
> On Wed, Oct 18, 2017 at 11:01 AM, Dennis Conklin <
> dennis_conk...@goodyear.com> wrote:
>
> Andy,
>
>
>
> I’m not sure about the multiblock, my routines generally look like:
>
>
>
> For block in output:
>
>  If block.GetCellType(0)=12;
>
>process_block(block)
>
>
>
> would this be
>
>
>
> If input.GetBlock(i)
>
> And I might not have loaded all the blocks in the set, then I might have
> eliminated some loaded blocks with earlier operations – what is the i in
> GetBlock?  Is it block_number as displayed in Spreadsheet or block index as
> in:
>
>
>
> block_index = block.FieldData.GetArray(‘ElementBlockIds’) - 1
>
>
>
> Sorry for such a basic question, but I only know the stuff I have used
> previously.
>
>
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 10:44 AM
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
>  *WARNING - External email; exercise caution.*
>
>
>
> Hi Dennis,
>
> I think something like:
>
> if multiblock.GetBlock(i) != None:
>   ...
>
> should work. You probably don't even need the "!=None" part.
>
> Cheers,
>
> Andy
>
>
>
> On Wed, Oct 18, 2017 at 10:41 AM, Dennis Conklin <
> dennis_conk...@

Re: [Paraview] [EXT] Re: How to test for empty block in multi-block dataset

[Andy Bauer]

Maybe try the following:

   if hasattr(block, "GetNumberOfCells") and block.GetNumberOfCells() >
0 and block.GetCellType(0)==12:

  process_block(block)

On Wed, Oct 18, 2017 at 1:05 PM, Dennis Conklin <dennis_conk...@goodyear.com
> wrote:

> Andy,
>
>
>
> GetCellType works fine when I have cells in the block, but in this recent
> case I had zero cells in the block after a Threshold filter,   my code is
> of the form:
>
>
>
> Def process_block(block):
>
> Print block.GetNumberOfCells()
>
>
>
>
>
>
>
>
>
> ###
>
>
> # main routine starts here
>
> output.CopyStructure(inputs[0].VTKObject)
>
> # if you ShallowCopy, then new variables created in input to filter
>
> output.DeepCopy(inputs[0].VTKObject)
>
>
>
> #
>
> # Loop over blocks in composite (Exodus) data set
>
> for block in output:
>
>
>
># VTK element types:
>
># 12 = VTK_HEXAHEDRON (Gdyr Hex)
>
>#  9 = VTK_QUAD  (Gdyr Membrane)
>
>#  3 = VTK_LINE  (Gdyr 3D Truss)
>
># since EXODUS requires single element type per block, test 1st
> element only
>
>if block.GetCellType(0)==12:
>
>   process_block(block)
>
>
>
> I think GetCellType is dying as there is no element(0)
>
> I need a way to test the block before calling anything to see if it is
> empty
>
>
>
> Thanks!
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 11:39 AM
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* Re: [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
> Hi Dennis,
>
> Maybe the block isn't a vtkDataSet and thus wouldn't have the
> GetCellType() method. You could try a print statement after the for loop to
> see what each block is by doing something like:
>
> print block
>
>
>
> Could you share your full python code for the programmable filter? That
> may make it easier to track down.
>
>
>
> Best,
>
> Andy
>
>
>
> On Wed, Oct 18, 2017 at 11:01 AM, Dennis Conklin <
> dennis_conk...@goodyear.com> wrote:
>
> Andy,
>
>
>
> I’m not sure about the multiblock, my routines generally look like:
>
>
>
> For block in output:
>
>  If block.GetCellType(0)=12;
>
>process_block(block)
>
>
>
> would this be
>
>
>
> If input.GetBlock(i)
>
> And I might not have loaded all the blocks in the set, then I might have
> eliminated some loaded blocks with earlier operations – what is the i in
> GetBlock?  Is it block_number as displayed in Spreadsheet or block index as
> in:
>
>
>
> block_index = block.FieldData.GetArray(‘ElementBlockIds’) - 1
>
>
>
> Sorry for such a basic question, but I only know the stuff I have used
> previously.
>
>
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 10:44 AM
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
>  *WARNING - External email; exercise caution.*
>
>
>
> Hi Dennis,
>
> I think something like:
>
> if multiblock.GetBlock(i) != None:
>   ...
>
> should work. You probably don't even need the "!=None" part.
>
> Cheers,
>
> Andy
>
>
>
> On Wed, Oct 18, 2017 at 10:41 AM, Dennis Conklin <
> dennis_conk...@goodyear.com> wrote:
>
> P.S.  I’m writing python inside a Programmable Filter
>
>
>
> Thanks again
>
> Dennis
>
>
> ___
> Powered by www.kitware.com
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com=01%7C01%7Cdennis_conklin%40goodyear.com%7C9dc270fb009a4b0639b908d51636b731%7C939e896692854a9a9f040887efe8aae0%7C0=99HLWFzFakz2A2flWuPb%2BjcOwf%2FEEemG9UURNHalZKc%3D=0>
>
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> opensource/opensource.html
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Re: [Paraview] [EXT] Re: How to test for empty block in multi-block dataset

[Andy Bauer]

Hi Dennis,

Maybe the block isn't a vtkDataSet and thus wouldn't have the GetCellType()
method. You could try a print statement after the for loop to see what each
block is by doing something like:
print block

Could you share your full python code for the programmable filter? That may
make it easier to track down.

Best,
Andy

On Wed, Oct 18, 2017 at 11:01 AM, Dennis Conklin <
dennis_conk...@goodyear.com> wrote:

> Andy,
>
>
>
> I’m not sure about the multiblock, my routines generally look like:
>
>
>
> For block in output:
>
>  If block.GetCellType(0)=12;
>
>process_block(block)
>
>
>
> would this be
>
>
>
> If input.GetBlock(i)
>
> And I might not have loaded all the blocks in the set, then I might have
> eliminated some loaded blocks with earlier operations – what is the i in
> GetBlock?  Is it block_number as displayed in Spreadsheet or block index as
> in:
>
>
>
> block_index = block.FieldData.GetArray(‘ElementBlockIds’) - 1
>
>
>
> Sorry for such a basic question, but I only know the stuff I have used
> previously.
>
>
>
> Dennis
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, October 18, 2017 10:44 AM
> *To:* Dennis Conklin <dennis_conk...@goodyear.com>
> *Cc:* Paraview (paraview@paraview.org) <paraview@paraview.org>
> *Subject:* [EXT] Re: [Paraview] How to test for empty block in
> multi-block dataset
>
>
>
>  *WARNING - External email; exercise caution.*
>
>
>
> Hi Dennis,
>
> I think something like:
>
> if multiblock.GetBlock(i) != None:
>   ...
>
> should work. You probably don't even need the "!=None" part.
>
> Cheers,
>
> Andy
>
>
>
> On Wed, Oct 18, 2017 at 10:41 AM, Dennis Conklin <
> dennis_conk...@goodyear.com> wrote:
>
> P.S.  I’m writing python inside a Programmable Filter
>
>
>
> Thanks again
>
> Dennis
>
>
> ___
> Powered by www.kitware.com
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com=01%7C01%7Cdennis_conklin%40goodyear.com%7C9dc270fb009a4b0639b908d51636b731%7C939e896692854a9a9f040887efe8aae0%7C0=99HLWFzFakz2A2flWuPb%2BjcOwf%2FEEemG9UURNHalZKc%3D=0>
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.kitware.com%2Fopensource%2Fopensource.html=01%7C01%7Cdennis_conklin%40goodyear.com%7C9dc270fb009a4b0639b908d51636b731%7C939e896692854a9a9f040887efe8aae0%7C0=3id87QE9dLu8DdNl%2BE7KX3z8TUWFHqotqxtAdGnj8uE%3D=0>
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fparaview.org%2FWiki%2FParaView=01%7C01%7Cdennis_conklin%40goodyear.com%7C9dc270fb009a4b0639b908d51636b731%7C939e896692854a9a9f040887efe8aae0%7C0=EMSmEDwRt9GGxILGWdVsG7NuX%2FNZN4a5aPJvzF8X2Rk%3D=0>
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Re: [Paraview] How to test for empty block in multi-block dataset

[Andy Bauer]

Hi Dennis,

I think something like:
if multiblock.GetBlock(i) != None:
  ...

should work. You probably don't even need the "!=None" part.

Cheers,
Andy

On Wed, Oct 18, 2017 at 10:41 AM, Dennis Conklin <
dennis_conk...@goodyear.com> wrote:

> P.S.  I’m writing python inside a Programmable Filter
>
>
>
> Thanks again
>
> Dennis
>
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Re: [Paraview] [paraview] visualize higher order element.

[Andy Bauer]

Hi Mathi,

When I looked at the file in ParaView it seems like the connectivity is
wrong with your cells. If you try the Clean to Grid filter that should fix
your problem. I would suggest fixing the connectivity though as the best
way to manage the data since the Clean to Grid filter will merge coincident
points and may inadvertently mess up your point data fields for the
coincident points. Note that the Clean to Grid filter reduced the number of
points in your grid from 2,006,480 to 451,792.

Cheers,
Andy

On Wed, Oct 11, 2017 at 10:17 AM, Ezhilmathi Krishnasamy <
ezhkr...@student.liu.se> wrote:

> Hi Andy,
>
> Any idea or info about this extracting the surface of the geometry
> in higher order element mesh (or solution).
>
> Kind regards,
> Mathi
>
> On 20 September 2017 at 21:32, Ezhilmathi Krishnasamy <
> ezhkr...@student.liu.se> wrote:
>
>> Hi Andy,
>>
>> Thanks!
>>
>> I am attaching you the image here, I would like to see the sphere surface
>> inside the
>> cube. Instead I am still seeing the elements.
>>
>> Kind regards,
>> Mathi​
>>  sol.vtu
>> <https://drive.google.com/a/student.liu.se/file/d/0B2nFsji7UDKueGZmU0g0dHZSb2s/view?usp=drive_web>
>> ​
>>
>> On 20 September 2017 at 21:15, Andy Bauer <andy.ba...@kitware.com> wrote:
>>
>>> Hi,
>>>
>>> What do you mean by the extract operator? ParaView has a variety of
>>> filters (similar to VisIt's operators) for performing extracts of different
>>> types. Could you also share your dataset? That may make it easier to
>>> diagnose the issue.
>>>
>>> Best,
>>> Andy
>>>
>>> On Wed, Sep 20, 2017 at 2:33 PM, Ezhilmathi Krishnasamy <
>>> ezhkr...@student.liu.se> wrote:
>>>
>>>> Hi,
>>>>
>>>> I have fluid domain as a cube and inside this cube I have sphere. In
>>>> the linear element mesh if I use extract operator and apply the clip as
>>>> well I can see the sphere surface.
>>>>
>>>> But where as in higher order element mesh.
>>>> If i follow the same procedure, I don't see the sphere surface instead
>>>> I see only the elements in the cube.
>>>>
>>>> Could anyone please tell me how to solve this problem.
>>>>
>>>> Kind regards,
>>>> Mathi
>>>>
>>>>
>>>> Sent from my iPhone
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>>>
>>>
>>
>
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Re: [Paraview] Lambda-2 vortices computation

[Andy Bauer]

Hi,

I think the best way is to use the Gradient of Unstructured DataSet filter
to compute the velocity gradient and then use the Calculator or Python
Calculator filter to compute lambda-2.

Cheers,
Andy

On Fri, Oct 6, 2017 at 4:40 PM, Ezhilmathi Krishnasamy <
ezhkr...@student.liu.se> wrote:

> Hi,
>
> Could anyone tell me how to calculate the lambda-2 vorticity computation
> in
> Paraview.
>
> Kind regards,
> Mathi
>
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Re: [Paraview] Coprocessing with many time steps

[Andy Bauer]

Hi,

The XML readers and writers don't properly support time so currently the
best way would be to create a pvd file which would contain the time and
time step information. I don't know of anything in VTK or ParaView that
writes out pvd files (I only see a vtkPVDReader in ParaView) but the format
is meant to be simple. I would suggest doing it directly in the Catalyst
Python script through some Python library as the best workaround for now.



On Thu, Sep 28, 2017 at 3:08 PM, Hermano Lustosa <hllust...@gmail.com>
wrote:

> Ohh I see...
>
> Just another quick question. Currently, I am creating a series of VTU and
> VTI files whose names follow the pattern mysimulation-t%d. With %d being
> replaced by an integer index identifying the time step. I am about to code
> a simple PVD writer to consolidate the output and also to assign the real
> time step value in seconds instead of maintaining this integer index.
>
> It doesn't seem to be very hard to create this PVD file by hand, but I was
> just wondering if there is something in the VTK library that could
> automatically create these files for me. I still could not understand how I
> can assign the real time step in seconds to a file, don't know if its even
> possible with VT? files. If this is possible, some directions that could
> help me implement that would be very nice!
>
> Thanks once again!
>
>
>
>
>
> On Thu, Sep 28, 2017 at 3:50 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> Hi,
>>
>> The TemporalStatistics filter (or any other filter that iterates through
>> time steps) doesn't currently work with Catalyst. We hope to change this in
>> the future but because of the way that the ParaView pipeline works it makes
>> it a non-trivial change.
>>
>> Andy
>>
>> On Thu, Sep 28, 2017 at 2:40 PM, Hermano Lustosa <hllust...@gmail.com>
>> wrote:
>>
>>> I have doubt about using paraview catalyst from my simulation code.
>>> Suppose I created a simple Paraview pipeline containing the
>>> TemporalStatistics filter only.
>>>
>>> Initially, it is not clear for which "dummy" source is adequate for the
>>> script. I used a simple programmable source or even a unstructured cell
>>> types source to create the python script. Then, I call the script from
>>> catalyst in my code like this:
>>>
>>> for each time step
>>> update grid;
>>> create data description;
>>> call coprocessing method;
>>>
>>> The problem is that I expect the TemporalStatistics filter to create a
>>> single file containing the statistics for all the time steps. However, this
>>> approach creates a file for every time step. What I should do in the
>>> catalyst (or during the script creation) to have a single output for this
>>> filter.
>>>
>>> Thanks in advance.
>>>
>>>
>>>
>>>
>>>
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>>>
>>
>
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Re: [Paraview] Coprocessing with many time steps

[Andy Bauer]

Hi,

The TemporalStatistics filter (or any other filter that iterates through
time steps) doesn't currently work with Catalyst. We hope to change this in
the future but because of the way that the ParaView pipeline works it makes
it a non-trivial change.

Andy

On Thu, Sep 28, 2017 at 2:40 PM, Hermano Lustosa 
wrote:

> I have doubt about using paraview catalyst from my simulation code.
> Suppose I created a simple Paraview pipeline containing the
> TemporalStatistics filter only.
>
> Initially, it is not clear for which "dummy" source is adequate for the
> script. I used a simple programmable source or even a unstructured cell
> types source to create the python script. Then, I call the script from
> catalyst in my code like this:
>
> for each time step
> update grid;
> create data description;
> call coprocessing method;
>
> The problem is that I expect the TemporalStatistics filter to create a
> single file containing the statistics for all the time steps. However, this
> approach creates a file for every time step. What I should do in the
> catalyst (or during the script creation) to have a single output for this
> filter.
>
> Thanks in advance.
>
>
>
>
>
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Re: [Paraview] parallel processing in volume rendering and Merge Blocks filter ...

[Andy Bauer]

Hi Ufuk,

The Merge Blocks filter will work locally on each process and shouldn't
move any of the data between MPI processes since it's a trivially parallel
operation. When doing volume rendering of unstructured grids (the output
dataset type of the merge blocks filter) with Ice-T in parallel, there will
be data moved around in order to simplify and reduce the parallel
communication by constructing convex partitions.

I don't know how NVIDIA's Index plugin works in parallel but my guess would
be that it also wants convex partitions.

Cheers,
Andy


On Thu, Sep 21, 2017 at 3:14 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi Andy,
>
> Thanks for the clarification. One minor question, after applying Merge
> Blocks is it still processing in serial mode or can i use MPI to improve
> the performance? By the way, i am also using NVIDIA Index plugin. I think
> that it supports parallel rendering but again not for multi block dataset.
> Right?
>
> Regards,
>
> --ufuk
>
>
> On 20/09/2017 22:12, Andy Bauer wrote:
>
> Hi Ufuk,
>
> ParaView doesn't currently support volume rendering of multiblock
> datasets, even in serial, so using the Merge Blocks filter is probably the
> best way to do any volume rendering of your dataset.
>
> Cheers,
> Andy
>
> On Wed, Sep 20, 2017 at 2:45 PM, Ufuk Turuncoglu <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Hi,
>>
>> I am trying to perform volume rendering (VR) using multi-block +
>> multi-piece dataset. In this case, the data file has single block that
>> contains multiple piece (created by MPI parallel simulation code) and it is
>> in structured grid. When I try to use volume rendering with raw data, it
>> creates empty output but if I use Merge Block filter before using volume
>> rendering, it works without any problem. So, I have to use Merge Blocks
>> to perform VR. At this point, I just wonder that is it typical behaviour
>> of ParaView for multi-block + multi-piece datasets? Is it still possible
>> to perform VR in parallel if I had a multiple core (such as enabling Auto
>> MPI from the settings)? If not is there any way to re-structure the data to
>> perform more efficient rendering?
>>
>> Best Regards,
>>
>> --ufuk
>>
>>
>>
>>
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>>
>
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Re: [Paraview] [paraview] visualize higher order element.

[Andy Bauer]

Hi,

What do you mean by the extract operator? ParaView has a variety of filters
(similar to VisIt's operators) for performing extracts of different types.
Could you also share your dataset? That may make it easier to diagnose the
issue.

Best,
Andy

On Wed, Sep 20, 2017 at 2:33 PM, Ezhilmathi Krishnasamy <
ezhkr...@student.liu.se> wrote:

> Hi,
>
> I have fluid domain as a cube and inside this cube I have sphere. In the
> linear element mesh if I use extract operator and apply the clip as well I
> can see the sphere surface.
>
> But where as in higher order element mesh.
> If i follow the same procedure, I don't see the sphere surface instead I
> see only the elements in the cube.
>
> Could anyone please tell me how to solve this problem.
>
> Kind regards,
> Mathi
>
>
> Sent from my iPhone
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Re: [Paraview] parallel processing in volume rendering and Merge Blocks filter ...

[Andy Bauer]

Hi Ufuk,

ParaView doesn't currently support volume rendering of multiblock datasets,
even in serial, so using the Merge Blocks filter is probably the best way
to do any volume rendering of your dataset.

Cheers,
Andy

On Wed, Sep 20, 2017 at 2:45 PM, Ufuk Turuncoglu <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi,
>
> I am trying to perform volume rendering (VR) using multi-block +
> multi-piece dataset. In this case, the data file has single block that
> contains multiple piece (created by MPI parallel simulation code) and it is
> in structured grid. When I try to use volume rendering with raw data, it
> creates empty output but if I use Merge Block filter before using volume
> rendering, it works without any problem. So, I have to use Merge Blocks
> to perform VR. At this point, I just wonder that is it typical behaviour
> of ParaView for multi-block + multi-piece datasets? Is it still possible
> to perform VR in parallel if I had a multiple core (such as enabling Auto
> MPI from the settings)? If not is there any way to re-structure the data to
> perform more efficient rendering?
>
> Best Regards,
>
> --ufuk
>
>
>
>
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Re: [Paraview] Connecting points

[Andy Bauer]

Hi,

Please keep the discussions on the mailing list so that everyone that wants
to see what was discussed can.

https://www.paraview.org/Wiki/ParaView/Data_formats#CSV_.28Comma_Separated_Variable.29_files
has information on reading in a csv file into ParaView. From this though
you will still need to convert this information into points and then add
cells as needed. The ParaView User's Guide is available at
https://www.paraview.org/paraview-guide/ and should be able to give you
more guidance on what you want to do.

Cheers,
Andy

On Mon, Sep 18, 2017 at 6:53 AM, Doina Gumeniuc (224252 MAHS) <224...@via.dk
> wrote:

> Hi Andy,
>
> I am very new with paraview and it is confusing. I have a csv file where I
> show x,y and z of the points. Now, between those points, in real life, I
> have timoshenko beams. How can I arrange this info (length, siftness, cross
> sectional area, etc) in csv so paraview can read it? I would really
> appreciate some directions. Thank you!
> ------
> *From:* Andy Bauer <andy.ba...@kitware.com>
> *Sent:* September 14, 2017 4:13:02 PM
> *To:* Doina Gumeniuc (224252 MAHS)
> *Cc:* paraview@paraview.org
> *Subject:* Re: [Paraview] Connecting points
>
> Hi,
>
> ParaView has line cells which is what you probably want to use. The line
> cells themselves have no concept of cross section but you can add that as
> field data.
>
> Beyond this, how are you getting your points into ParaView? Wherever that
> is being done you'll probably want to add in the line cells at that point
> in your workflow. Another option is using the Python Programmable Filter to
> make those cells -- see https://www.paraview.org/Wiki/Python_Programmable_
> Filter.
>
> Cheers,
> Andy
>
> On Thu, Sep 14, 2017 at 6:02 AM, Doina Gumeniuc (224252 MAHS) <
> 224...@via.dk> wrote:
>
>> Hi dear users,
>>
>> I would really appreciate if you could guide me on how to connect points
>> with beam elements, FEM style.
>>
>> Thank you!
>>
>> ___
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>>
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>>
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>>
>>
>
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Re: [Paraview] Connecting points

[Andy Bauer]

Hi,

ParaView has line cells which is what you probably want to use. The line
cells themselves have no concept of cross section but you can add that as
field data.

Beyond this, how are you getting your points into ParaView? Wherever that
is being done you'll probably want to add in the line cells at that point
in your workflow. Another option is using the Python Programmable Filter to
make those cells -- see
https://www.paraview.org/Wiki/Python_Programmable_Filter.

Cheers,
Andy

On Thu, Sep 14, 2017 at 6:02 AM, Doina Gumeniuc (224252 MAHS) <224...@via.dk
> wrote:

> Hi dear users,
>
> I would really appreciate if you could guide me on how to connect points
> with beam elements, FEM style.
>
> Thank you!
>
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Re: [Paraview] Using 64 or more cores on a single node when running client/server

[Andy Bauer]

If you're running on the DSRCs I'm guessing that the limit is coming from
the node selection option (i.e. "#PBS -l select=8:ncpus=36:mpiprocs=8").
mpiprocs here is the number of MPI processes per node while ncpus is the
number of cores per node (in this case only nodes that have 36 cores per
node will be used. I've never tried having mpiprocs higher than ncpus. I
would guess that a simple MPI helloworld would really show whether or not
this is where the limit is coming from.

Best,
Andy

On Wed, Sep 13, 2017 at 12:12 PM, Utkarsh Ayachit <
utkarsh.ayac...@kitware.com> wrote:

> > It should be related to your mpi environment: may be oversubscribing
> (more
> > than one mpi process by core) is not the default behavior.
>
> I am tempted to second that. There's nothing in ParaView that checks
> how many cores your node has, as a result if there's a cap, it's
> coming from the MPI implementation itself.
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Re: [Paraview] Catalyst distributed graph example

[Andy Bauer]

Hi Matthieu,

There isn't a Catalyst example for graphs but it shouldn't be too hard to
make. I'm not very familiar with the vtkGraph and derived classes but if I
were to to try doing that I'd just see how the graph object is generated in
some filter that generates one (look in the RequestData() method).

As for visualizing graphs in ParaView, hopefully someone else on the list
can provide insight on doing that.

Best,
Andy

On Wed, Sep 13, 2017 at 11:38 AM, Dorier, Matthieu  wrote:

> Hi,
>
>
> I would like to use Catalyst to visualize a distributed directed graph.
> Each node of the graph is characterized by an id (not necessarily
> contiguous, as some nodes are added and removed during the execution) and a
> list of connections (ids of "friends").
>
>
> The nodes can be assigned coordinates in a 2D or a 3D space.
>
>
> Do you have an example of adaptor for that?
>
>
> Also if I want to use coordinates in higher dimensions, would I need to
> project to a 3D subspace or is there a way for ParaView to figure out a
> layout to display the graph?
>
>
> Thanks,
>
>
> Matthieu
>
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Re: [Paraview] paraview display issue on parallel files

[Andy Bauer]

Hi,

You can remap the point variables back onto the points using the Resample
with Dataset filter but that won't work for cell data.

I believe that the D3 filter is only available if you have ParaView
built/installed with MPI. Even then it will only work if you're running
with more than a single MPI process.

I still suggest writing out the data with either marking the repeated cells
as ghost cells or not including them in the file as any other thing you do
to get around that can become fairly expensive and manually intensive as
you go to bigger datasets.

Andy

On Wed, Sep 6, 2017 at 3:28 PM, Rilin Shen <shenri...@gmail.com> wrote:

> Dear all,
>
> Thanks for your suggestions. It is exactly what you said.
>
> Marking ghost cell would be non-trival work and I tried the second idea.
> But only cell and points information is left, other field information
> associated with points seem to be lost. Is that the case? If that is the
> case, is there an easy way to attach point data to points again?
>
> BTW, I searched the internet and found that the D3 filter could be a good
> option for my unstructured grid information. But I cannot find the D3
> filter as Filters>Alphabetical>D3. So my second question is how to add D3
> filter to my paraview?
>
> Best regards,
>
>
> Rilin Shen
> Division of Solid Mechanics, School of Astronautics
> *Harbin Institute of Technology*, Harbin 150001, China
> Civil Engineering & Engineering Mechanics
> *Columbia University*, New York 10027, U.S.
> Tel: (+1) 646-200-2122 <(646)%20200-2122>
> Email: shenri...@gmail.com  /  rs3...@columbia.edu <shenri...@126.com>
>
> 2017-09-06 14:50 GMT-04:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> Please respond to the entire mailing list so that anyone that wants to
>> participate or follow along can.
>>
>> I think the issue here is that you have the same cell specified in
>> multiple vtu files and ParaView is getting confused when trying to render
>> them. These are the overlapping cells at the subdomain boundary. My
>> recommendation would be to either mark these repeated cells as ghost cells
>> (see https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for
>> information on that). Other than that, you could use the Clean to Grid
>> filter to get rid of coincident points and then use the Clean Cells to Grid
>> filter to get rid of extra copies of the cell.
>>
>> Cheers,
>> Andy
>>
>>
>> On Tue, Sep 5, 2017 at 6:24 PM, Rilin Shen <shenri...@gmail.com> wrote:
>>
>>> ​
>>>  Bone.7z
>>> <https://drive.google.com/file/d/0B1JLvkeOK5PQVXR3cTBHa2lfQjQ/view?usp=drive_web>
>>> ​​​Dear Andy,
>>>
>>> Thanks a lot for your help.
>>>
>>> As you said, It looks like a ghost cell issue. I attached my dataset.
>>> Please check it.
>>>
>>> If you need any additional information, please let me know.
>>>
>>> Best regards,
>>>
>>> Rilin Shen
>>> Division of Solid Mechanics, School of Astronautics
>>> *Harbin Institute of Technology*, Harbin 150001, China
>>> Civil Engineering & Engineering Mechanics
>>> *Columbia University*, New York 10027, U.S.
>>> Tel: (+1) 646-200-2122 <(646)%20200-2122>
>>> Email: shenri...@gmail.com  /  rs3...@columbia.edu <shenri...@126.com>
>>>
>>> 2017-09-05 16:54 GMT-04:00 Andy Bauer <andy.ba...@kitware.com>:
>>>
>>>> Hi,
>>>>
>>>> This typically happens when ghost cells are marked improperly or the
>>>> data set has a node/point partitioning and no cells to bridge between the
>>>> subdomains (though the point partitioning issue usually happens with finite
>>>> difference simulations instead of FEM simulations). If you could share your
>>>> dataset it would be easier to diagnose.
>>>>
>>>> Best,
>>>> Andy
>>>>
>>>> On Tue, Sep 5, 2017 at 4:23 PM, Rilin Shen <shenri...@gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I'm very happy to meet all of you in this society.
>>>>>
>>>>> I use a finite element software with multiprocessors(40) to solve
>>>>> problems.
>>>>>
>>>>> All the .vtu files. associated with each processor are output and then
>>>>> a file .pvtu is generated.
>>>>>
>>>>> The original file is displayed perfectly as shown in bone.png.
>>>>> However, when I try to cut it with a plane, it

Re: [Paraview] paraview display issue on parallel files

[Andy Bauer]

Hi,

Please respond to the entire mailing list so that anyone that wants to
participate or follow along can.

I think the issue here is that you have the same cell specified in multiple
vtu files and ParaView is getting confused when trying to render them.
These are the overlapping cells at the subdomain boundary. My
recommendation would be to either mark these repeated cells as ghost cells
(see https://blog.kitware.com/ghost-and-blanking-visibility-changes/ for
information on that). Other than that, you could use the Clean to Grid
filter to get rid of coincident points and then use the Clean Cells to Grid
filter to get rid of extra copies of the cell.

Cheers,
Andy


On Tue, Sep 5, 2017 at 6:24 PM, Rilin Shen <shenri...@gmail.com> wrote:

> ​
>  Bone.7z
> <https://drive.google.com/file/d/0B1JLvkeOK5PQVXR3cTBHa2lfQjQ/view?usp=drive_web>
> ​​​Dear Andy,
>
> Thanks a lot for your help.
>
> As you said, It looks like a ghost cell issue. I attached my dataset.
> Please check it.
>
> If you need any additional information, please let me know.
>
> Best regards,
>
> Rilin Shen
> Division of Solid Mechanics, School of Astronautics
> *Harbin Institute of Technology*, Harbin 150001, China
> Civil Engineering & Engineering Mechanics
> *Columbia University*, New York 10027, U.S.
> Tel: (+1) 646-200-2122 <(646)%20200-2122>
> Email: shenri...@gmail.com  /  rs3...@columbia.edu <shenri...@126.com>
>
> 2017-09-05 16:54 GMT-04:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> This typically happens when ghost cells are marked improperly or the data
>> set has a node/point partitioning and no cells to bridge between the
>> subdomains (though the point partitioning issue usually happens with finite
>> difference simulations instead of FEM simulations). If you could share your
>> dataset it would be easier to diagnose.
>>
>> Best,
>> Andy
>>
>> On Tue, Sep 5, 2017 at 4:23 PM, Rilin Shen <shenri...@gmail.com> wrote:
>>
>>> Dear all,
>>>
>>> I'm very happy to meet all of you in this society.
>>>
>>> I use a finite element software with multiprocessors(40) to solve
>>> problems.
>>>
>>> All the .vtu files. associated with each processor are output and then a
>>> file .pvtu is generated.
>>>
>>> The original file is displayed perfectly as shown in bone.png.  However,
>>> when I try to cut it with a plane, it occurs the following issue as
>>> clip.png, It seems not be displayed correctly.
>>>
>>> Would you please tell me what happened to my data?
>>>
>>> Best regards,
>>>
>>> Rilin Shen
>>> Division of Solid Mechanics, School of Astronautics
>>> *Harbin Institute of Technology*, Harbin 150001, China
>>> Civil Engineering & Engineering Mechanics
>>> *Columbia University*, New York 10027, U.S.
>>> Tel: (+1) 646-200-2122 <(646)%20200-2122>
>>> Email: shenri...@gmail.com  /  rs3...@columbia.edu <shenri...@126.com>
>>>
>>> ___
>>> 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
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/paraview
>>>
>>>
>>
>
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Re: [Paraview] Catalyst visualization not rendering without me clicking on the screen

[Andy Bauer]

Hi Jimmy,

I haven't heard of this issue before. Could you report an issue for this at
https://gitlab.kitware.com/paraview/paraview/issues ?

Thanks,
Andy

On Wed, Aug 30, 2017 at 11:37 AM, A .  wrote:

> Dear community,
>
>
> Whenever I am trying to visualize something live (i.e. with Catalyst), the
> rendering view is not being updated unless I pan over the view with my
> mouse.
>
>
> I noticed that automatic rendering happens when I am dealing with a larger
> dataset. There seems to be some kind of a threshold for when to update the
> rendering view, based on the data size (or based on the amount of change in
> data).
>
>
> I tried increasing the CoProcessor frequency 
> (coprocessor.SetUpdateFrequencies(freqs)),
> and also the EnableLiveVisualization(True, freq), but it didn't help.
>
>
> Anyone has a solution for this?
>
>
> Best,
>
> Jimmy
>
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Re: [Paraview] Shortcut for Catalyst server connection

[Andy Bauer]

Hi,

You may be able to save a Python trace of those actions as a macro. This
may require editing the Python trace output though as I'm not if all of
those actions would be tracked in a trace.

Best,
Andy

On Mon, Aug 28, 2017 at 5:41 PM, A .  wrote:

> Hi all,
>
>
> I was wondering if there is a faster way to open a Catalyst connection
> with ParaView. Currently I see myself doing the following routine
> "Catalyst" --> "Connect" --> "OK" --> "OK" --> "Pause Simulation" quite a
> lot.
>
>
> Is there a way to compress this into a single step?
>
>
> Best,
>
> Jimmy
>
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Re: [Paraview] Segmentation fault in protobuf

[Andy Bauer]

Hi Ufuk,

Glad to hear that things are working for you and thanks for reporting back.

Cheers,
Andy

On Wed, Aug 16, 2017 at 11:09 AM,  wrote:

> Hi,
>
> I add print statement to python script and it shows that three input port
> is ok but one of them is empty. The new allinputsgridwriter.py that has
> automatic detection of input port fail in this case but if I use old one
> with manual configuration of the ports (there is no definition of empty
> port in this case) work fine. Anyway, the issue seems solved with external
> installation of protobuf library and I tested both gcc and intel
> compilers. It could be the version issue of the internal protobuf library
> in PV. So, you may consider to update it. Thanks to both of you for your
> help.
>
> Regards,
>
> --ufuk
>
> > Hmm, can you check that you've set the vtkCPInputDataDescription grid
> > through the SetGrid() method? You can add in something like "print("input
> > is ", datadescription.GetInputDescriptionByName().GetGrid())" a
> > couple of places in your Python script to see if there is actually a grid
> > added there for that input.
> >
> > Best,
> > Andy
> >
> > On Tue, Aug 15, 2017 at 3:30 PM, 
> wrote:
> >
> >> Without support of you and also Ben, i could not even reach to this
> >> point.
> >> Thanks again. At least, code runs now. I think that this is big
> >> improvement.
> >>
> >> Anyway, both command is working as expected,
> >>
> >> > mpirun -np 4 pvbatch 
> >> > mpirun -np 4 pvbatch -sym 
> >>
> >> I also tested allinputsgridwriter_new.py with CFullExample (and also
> >> Fortran90FullExample) and it works without any problem. As I mentioned
> >> before, CFullExample was also working before upgrading protobuf (still,
> >> i
> >> don't know why). So, it is not a good way to find the source of the
> >> problem.
> >>
> >> --ufuk
> >>
> >>
> >> > Hmm, how about making that Python code into a file and running it with
> >> > both:
> >> > mpirun -np 4 pvbatch 
> >> > mpirun -np 4 pvbatch -sym 
> >> >
> >> > Just to verify, the allinputsgridwriter.py didn't work with any of the
> >> > Catalyst examples (e.g. CFullExample), correct?
> >> >
> >> > I think this is going to be some issue where we continually bisect the
> >> > problem space so I appreciate your patience on this.
> >> >
> >> > Best,
> >> > Andy
> >> >
> >> > On Tue, Aug 15, 2017 at 2:49 PM, 
> >> wrote:
> >> >
> >> >> Hi,
> >> >>
> >> >> Yes. It works and produces same output.
> >> >>
> >> >> --ufuk
> >> >>
> >> >> > Hi Ufuk,
> >> >> >
> >> >> > It looks like the script line that is not working properly is:
> >> >> > grid =
> >> >> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >> >> >
> >> >> > grid is set to None here for your build. Trying something simpler,
> >> in
> >> >> > pvpython can you try the following and let us know if it works:
> >> >> > =
> >> >> > from paraview.simple import *
> >> >> > a = Wavelet()
> >> >> > a.UpdatePipeline()
> >> >> > b = a.GetClientSideObject()
> >> >> > c = b.GetOutputDataObject(0)
> >> >> > print c
> >> >> > =
> >> >> >
> >> >> >
> >> >> >
> >> >> > It should give output like the following if it works:
> >> >> > vtkImageData (0x4586a00)
> >> >> >   Debug: Off
> >> >> >   Modified Time: 204809
> >> >> >   Reference Count: 2
> >> >> >   Registered Events: (none)
> >> >> >   Information: 0x4586450
> >> >> >   Data Released: False
> >> >> >   Global Release Data: Off
> >> >> >   UpdateTime: 204810
> >> >> >   Field Data:
> >> >> > Debug: Off
> >> >> > Modified Time: 204775
> >> >> > Reference Count: 1
> >> >> > Registered Events: (none)
> >> >> > Number Of Arrays: 0
> >> >> > Number Of Components: 0
> >> >> > Number Of Tuples: 0
> >> >> >   Number Of Points: 9261
> >> >> >   Number Of Cells: 8000
> >> >> >   Cell Data:
> >> >> > Debug: Off
> >> >> > Modified Time: 204783
> >> >> > Reference Count: 1
> >> >> > Registered Events:
> >> >> >   Registered Observers:
> >> >> > vtkObserver (0x4586550)
> >> >> >   Event: 33
> >> >> >   EventName: ModifiedEvent
> >> >> >   Command: 0x45864a0
> >> >> >   Priority: 0
> >> >> >   Tag: 1
> >> >> > Number Of Arrays: 0
> >> >> > Number Of Components: 0
> >> >> > Number Of Tuples: 0
> >> >> > Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
> >> >> > Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
> >> >> > Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
> >> >> > Scalars: (none)
> >> >> > Vectors: (none)
> >> >> > Normals: (none)
> >> >> > TCoords: (none)
> >> >> > Tensors: (none)
> >> >> > GlobalIds: (none)
> >> >> > PedigreeIds: (none)
> >> >> > EdgeFlag: (none)
> >> >> >   Point Data:
> >> >> > Debug: Off
> >> >> > Modified Time: 204809
> >> >> > Reference Count: 1
> >> >> > Registered Events:
> >> >> >   Registered Observers:

Re: [Paraview] Segmentation fault in protobuf

[Andy Bauer]

Hmm, can you check that you've set the vtkCPInputDataDescription grid
through the SetGrid() method? You can add in something like "print("input
is ", datadescription.GetInputDescriptionByName().GetGrid())" a
couple of places in your Python script to see if there is actually a grid
added there for that input.

Best,
Andy

On Tue, Aug 15, 2017 at 3:30 PM,  wrote:

> Without support of you and also Ben, i could not even reach to this point.
> Thanks again. At least, code runs now. I think that this is big
> improvement.
>
> Anyway, both command is working as expected,
>
> > mpirun -np 4 pvbatch 
> > mpirun -np 4 pvbatch -sym 
>
> I also tested allinputsgridwriter_new.py with CFullExample (and also
> Fortran90FullExample) and it works without any problem. As I mentioned
> before, CFullExample was also working before upgrading protobuf (still, i
> don't know why). So, it is not a good way to find the source of the
> problem.
>
> --ufuk
>
>
> > Hmm, how about making that Python code into a file and running it with
> > both:
> > mpirun -np 4 pvbatch 
> > mpirun -np 4 pvbatch -sym 
> >
> > Just to verify, the allinputsgridwriter.py didn't work with any of the
> > Catalyst examples (e.g. CFullExample), correct?
> >
> > I think this is going to be some issue where we continually bisect the
> > problem space so I appreciate your patience on this.
> >
> > Best,
> > Andy
> >
> > On Tue, Aug 15, 2017 at 2:49 PM, 
> wrote:
> >
> >> Hi,
> >>
> >> Yes. It works and produces same output.
> >>
> >> --ufuk
> >>
> >> > Hi Ufuk,
> >> >
> >> > It looks like the script line that is not working properly is:
> >> > grid =
> >> adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >> >
> >> > grid is set to None here for your build. Trying something simpler, in
> >> > pvpython can you try the following and let us know if it works:
> >> > =
> >> > from paraview.simple import *
> >> > a = Wavelet()
> >> > a.UpdatePipeline()
> >> > b = a.GetClientSideObject()
> >> > c = b.GetOutputDataObject(0)
> >> > print c
> >> > =
> >> >
> >> >
> >> >
> >> > It should give output like the following if it works:
> >> > vtkImageData (0x4586a00)
> >> >   Debug: Off
> >> >   Modified Time: 204809
> >> >   Reference Count: 2
> >> >   Registered Events: (none)
> >> >   Information: 0x4586450
> >> >   Data Released: False
> >> >   Global Release Data: Off
> >> >   UpdateTime: 204810
> >> >   Field Data:
> >> > Debug: Off
> >> > Modified Time: 204775
> >> > Reference Count: 1
> >> > Registered Events: (none)
> >> > Number Of Arrays: 0
> >> > Number Of Components: 0
> >> > Number Of Tuples: 0
> >> >   Number Of Points: 9261
> >> >   Number Of Cells: 8000
> >> >   Cell Data:
> >> > Debug: Off
> >> > Modified Time: 204783
> >> > Reference Count: 1
> >> > Registered Events:
> >> >   Registered Observers:
> >> > vtkObserver (0x4586550)
> >> >   Event: 33
> >> >   EventName: ModifiedEvent
> >> >   Command: 0x45864a0
> >> >   Priority: 0
> >> >   Tag: 1
> >> > Number Of Arrays: 0
> >> > Number Of Components: 0
> >> > Number Of Tuples: 0
> >> > Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
> >> > Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
> >> > Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
> >> > Scalars: (none)
> >> > Vectors: (none)
> >> > Normals: (none)
> >> > TCoords: (none)
> >> > Tensors: (none)
> >> > GlobalIds: (none)
> >> > PedigreeIds: (none)
> >> > EdgeFlag: (none)
> >> >   Point Data:
> >> > Debug: Off
> >> > Modified Time: 204809
> >> > Reference Count: 1
> >> > Registered Events:
> >> >   Registered Observers:
> >> > vtkObserver (0x45864f0)
> >> >   Event: 33
> >> >   EventName: ModifiedEvent
> >> >   Command: 0x45864a0
> >> >   Priority: 0
> >> >   Tag: 1
> >> > Number Of Arrays: 1
> >> > Array 0 name = RTData
> >> > Number Of Components: 1
> >> > Number Of Tuples: 9261
> >> > Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
> >> > Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
> >> > Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
> >> > Scalars:
> >> >   Debug: Off
> >> >   Modified Time: 204809
> >> >   Reference Count: 2
> >> >   Registered Events: (none)
> >> >   Name: RTData
> >> >   Data type: float
> >> >   Size: 9261
> >> >   MaxId: 9260
> >> >   NumberOfComponents: 1
> >> >   Information: 0
> >> >   Name: RTData
> >> >   Number Of Components: 1
> >> >   Number Of Tuples: 9261
> >> >   Size: 9261
> >> >   MaxId: 9260
> >> >   LookupTable: (none)
> >> > Vectors: (none)
> >> > Normals: (none)
> >> > TCoords: (none)
> >> > Tensors: (none)
> >> > GlobalIds: (none)
> >> > PedigreeIds: (none)
> >> > EdgeFlag: (none)
> >> >   Bounds:
> >> > 

Re: [Paraview] Segmentation fault in protobuf

[Andy Bauer]

Hmm, how about making that Python code into a file and running it with both:
mpirun -np 4 pvbatch 
mpirun -np 4 pvbatch -sym 

Just to verify, the allinputsgridwriter.py didn't work with any of the
Catalyst examples (e.g. CFullExample), correct?

I think this is going to be some issue where we continually bisect the
problem space so I appreciate your patience on this.

Best,
Andy

On Tue, Aug 15, 2017 at 2:49 PM,  wrote:

> Hi,
>
> Yes. It works and produces same output.
>
> --ufuk
>
> > Hi Ufuk,
> >
> > It looks like the script line that is not working properly is:
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >
> > grid is set to None here for your build. Trying something simpler, in
> > pvpython can you try the following and let us know if it works:
> > =
> > from paraview.simple import *
> > a = Wavelet()
> > a.UpdatePipeline()
> > b = a.GetClientSideObject()
> > c = b.GetOutputDataObject(0)
> > print c
> > =
> >
> >
> >
> > It should give output like the following if it works:
> > vtkImageData (0x4586a00)
> >   Debug: Off
> >   Modified Time: 204809
> >   Reference Count: 2
> >   Registered Events: (none)
> >   Information: 0x4586450
> >   Data Released: False
> >   Global Release Data: Off
> >   UpdateTime: 204810
> >   Field Data:
> > Debug: Off
> > Modified Time: 204775
> > Reference Count: 1
> > Registered Events: (none)
> > Number Of Arrays: 0
> > Number Of Components: 0
> > Number Of Tuples: 0
> >   Number Of Points: 9261
> >   Number Of Cells: 8000
> >   Cell Data:
> > Debug: Off
> > Modified Time: 204783
> > Reference Count: 1
> > Registered Events:
> >   Registered Observers:
> > vtkObserver (0x4586550)
> >   Event: 33
> >   EventName: ModifiedEvent
> >   Command: 0x45864a0
> >   Priority: 0
> >   Tag: 1
> > Number Of Arrays: 0
> > Number Of Components: 0
> > Number Of Tuples: 0
> > Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
> > Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
> > Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
> > Scalars: (none)
> > Vectors: (none)
> > Normals: (none)
> > TCoords: (none)
> > Tensors: (none)
> > GlobalIds: (none)
> > PedigreeIds: (none)
> > EdgeFlag: (none)
> >   Point Data:
> > Debug: Off
> > Modified Time: 204809
> > Reference Count: 1
> > Registered Events:
> >   Registered Observers:
> > vtkObserver (0x45864f0)
> >   Event: 33
> >   EventName: ModifiedEvent
> >   Command: 0x45864a0
> >   Priority: 0
> >   Tag: 1
> > Number Of Arrays: 1
> > Array 0 name = RTData
> > Number Of Components: 1
> > Number Of Tuples: 9261
> > Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
> > Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
> > Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
> > Scalars:
> >   Debug: Off
> >   Modified Time: 204809
> >   Reference Count: 2
> >   Registered Events: (none)
> >   Name: RTData
> >   Data type: float
> >   Size: 9261
> >   MaxId: 9260
> >   NumberOfComponents: 1
> >   Information: 0
> >   Name: RTData
> >   Number Of Components: 1
> >   Number Of Tuples: 9261
> >   Size: 9261
> >   MaxId: 9260
> >   LookupTable: (none)
> > Vectors: (none)
> > Normals: (none)
> > TCoords: (none)
> > Tensors: (none)
> > GlobalIds: (none)
> > PedigreeIds: (none)
> > EdgeFlag: (none)
> >   Bounds:
> > Xmin,Xmax: (-10, 10)
> > Ymin,Ymax: (-10, 10)
> > Zmin,Zmax: (-10, 10)
> >   Compute Time: 204875
> >   Spacing: (1, 1, 1)
> >   Origin: (0, 0, 0)
> >   Dimensions: (21, 21, 21)
> >   Increments: (0, 0, 0)
> >   Extent: (-10, 10, -10, 10, -10, 10)
> >
> >
> >
> > On Tue, Aug 15, 2017 at 2:27 PM, 
> wrote:
> >
> >> Hi Andy,
> >>
> >> Thanks for your help and the script. Actually, I was adding input names
> >> to
> >> the script by hand. Anyway, I tested your script and it gives similar
> >> error as follows,
> >>
> >>   File
> >> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> >> egl/lib/site-packages/paraview/coprocessing.py",
> >> line 305, in CreateProducer
> >> if grid.IsA("vtkImageData") == True or \
> >> AttributeError: 'NoneType' object has no attribute 'IsA'
> >> grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >>   File
> >> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> >> egl/lib/site-packages/paraview/coprocessing.py",
> >> line 305, in CreateProducer
> >> if grid.IsA("vtkImageData") == True or \
> >> AttributeError: 'NoneType' object has no attribute 'IsA'
> >> grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >>   File
> >> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> >> egl/lib/site-packages/paraview/coprocessing.py",
> >> line 

Re: [Paraview] Segmentation fault in protobuf

[Andy Bauer]

Hi Ufuk,

It looks like the script line that is not working properly is:
grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)

grid is set to None here for your build. Trying something simpler, in
pvpython can you try the following and let us know if it works:
=
from paraview.simple import *
a = Wavelet()
a.UpdatePipeline()
b = a.GetClientSideObject()
c = b.GetOutputDataObject(0)
print c
=



It should give output like the following if it works:
vtkImageData (0x4586a00)
  Debug: Off
  Modified Time: 204809
  Reference Count: 2
  Registered Events: (none)
  Information: 0x4586450
  Data Released: False
  Global Release Data: Off
  UpdateTime: 204810
  Field Data:
Debug: Off
Modified Time: 204775
Reference Count: 1
Registered Events: (none)
Number Of Arrays: 0
Number Of Components: 0
Number Of Tuples: 0
  Number Of Points: 9261
  Number Of Cells: 8000
  Cell Data:
Debug: Off
Modified Time: 204783
Reference Count: 1
Registered Events:
  Registered Observers:
vtkObserver (0x4586550)
  Event: 33
  EventName: ModifiedEvent
  Command: 0x45864a0
  Priority: 0
  Tag: 1
Number Of Arrays: 0
Number Of Components: 0
Number Of Tuples: 0
Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
Scalars: (none)
Vectors: (none)
Normals: (none)
TCoords: (none)
Tensors: (none)
GlobalIds: (none)
PedigreeIds: (none)
EdgeFlag: (none)
  Point Data:
Debug: Off
Modified Time: 204809
Reference Count: 1
Registered Events:
  Registered Observers:
vtkObserver (0x45864f0)
  Event: 33
  EventName: ModifiedEvent
  Command: 0x45864a0
  Priority: 0
  Tag: 1
Number Of Arrays: 1
Array 0 name = RTData
Number Of Components: 1
Number Of Tuples: 9261
Copy Tuple Flags: ( 1 1 1 1 1 0 1 1 )
Interpolate Flags: ( 1 1 1 1 1 0 0 1 )
Pass Through Flags: ( 1 1 1 1 1 1 1 1 )
Scalars:
  Debug: Off
  Modified Time: 204809
  Reference Count: 2
  Registered Events: (none)
  Name: RTData
  Data type: float
  Size: 9261
  MaxId: 9260
  NumberOfComponents: 1
  Information: 0
  Name: RTData
  Number Of Components: 1
  Number Of Tuples: 9261
  Size: 9261
  MaxId: 9260
  LookupTable: (none)
Vectors: (none)
Normals: (none)
TCoords: (none)
Tensors: (none)
GlobalIds: (none)
PedigreeIds: (none)
EdgeFlag: (none)
  Bounds:
Xmin,Xmax: (-10, 10)
Ymin,Ymax: (-10, 10)
Zmin,Zmax: (-10, 10)
  Compute Time: 204875
  Spacing: (1, 1, 1)
  Origin: (0, 0, 0)
  Dimensions: (21, 21, 21)
  Increments: (0, 0, 0)
  Extent: (-10, 10, -10, 10, -10, 10)



On Tue, Aug 15, 2017 at 2:27 PM,  wrote:

> Hi Andy,
>
> Thanks for your help and the script. Actually, I was adding input names to
> the script by hand. Anyway, I tested your script and it gives similar
> error as follows,
>
>   File
> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> egl/lib/site-packages/paraview/coprocessing.py",
> line 305, in CreateProducer
> if grid.IsA("vtkImageData") == True or \
> AttributeError: 'NoneType' object has no attribute 'IsA'
> grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>   File
> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> egl/lib/site-packages/paraview/coprocessing.py",
> line 305, in CreateProducer
> if grid.IsA("vtkImageData") == True or \
> AttributeError: 'NoneType' object has no attribute 'IsA'
> grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
>   File
> "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/
> egl/lib/site-packages/paraview/coprocessing.py",
> line 305, in CreateProducer
> if grid.IsA("vtkImageData") == True or \
> AttributeError: 'NoneType' object has no attribute 'IsA'
>
> I'll tested whole environment once again with Intel compiler to see it
> helps or not. Let me know if you have any other idea.
>
> Regards,
>
> --ufuk
>
>
> > Hi Ufuk,
> >
> > For the allinputsgridwriter.py you currently need to manually add in the
> > inputs yourself (i.e. replace the "namedinputs = ['input']" line with the
> > name of your inputs. That has caught me in the past as well so I decided
> > to
> > fix that. Attached is my new version of that script where it doesn't
> > require you to specify the input names in case you want to try this new
> > one
> > instead. If you do, please let us know if that solves your problem or
> not.
> >
> > Best,
> > Andy
> >
> >
> > On Tue, Aug 15, 2017 at 12:40 PM, Ben Boeckel 
> > wrote:
> >
> >> On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@be.itu.edu.tr
> >> wrote:
> >> > I solved the problem and i am able to run the simulation code with
> >> > Catalyst 

Re: [Paraview] Segmentation fault in protobuf

[Andy Bauer]

Hi Ufuk,

For the allinputsgridwriter.py you currently need to manually add in the
inputs yourself (i.e. replace the "namedinputs = ['input']" line with the
name of your inputs. That has caught me in the past as well so I decided to
fix that. Attached is my new version of that script where it doesn't
require you to specify the input names in case you want to try this new one
instead. If you do, please let us know if that solves your problem or not.

Best,
Andy


On Tue, Aug 15, 2017 at 12:40 PM, Ben Boeckel 
wrote:

> On Tue, Aug 15, 2017 at 17:59:47 +0300, u.utku.turunco...@be.itu.edu.tr
> wrote:
> > I solved the problem and i am able to run the simulation code with
> > Catalyst support by installing PV (5.4.0 rc4 and 5.3.0) with newer
> version
> > of protobuf library (3.3.0) and compiling the model code with this
> version
> > of PV (using gcc).
> >
> > Now, the problem is that the code gives following warnings and do nothing
> > with standard allinputsgridwriter.py script. Do you think that it is
> > related with protobuf library. The same setup is working without any
> > problem in an other system using Intel compiler.
>
> It'd be better to try with one MPI process rather than…I count 10 to get
> the error? Not sure what's up though, Andy?
>
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> > if grid.IsA("vtkImageData") == True or \
> >   File
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> >   File
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > if grid.IsA("vtkImageData") == True or \
> > if grid.IsA("vtkImageData") == True or \
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >   File
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> > if grid.IsA("vtkImageData") == True or \
> > if grid.IsA("vtkImageData") == True or \
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> > if grid.IsA("vtkImageData") == True or \
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> >   File
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > if grid.IsA("vtkImageData") == True or \
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> > [PERFLOG] :: COPROC  2 0.01404021SEC.
> >  Running COP Component: 2005-08-27T00:12:00 --> 2005-08-27T00:18:00 Time
> > Step: 2 [ 720.00]
> > ATM-TO-COP: redist mask [CROSS] to mask [CROSS]
> > ATM-TO-COP: redist topo [CROSS] to topo [CROSS]
> > AttributeError: 'NoneType' object has no attribute 'IsA'
> > grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
> >   File
> > "/home/ext-dell-guest1/rds/hpc-work/progs/paraview-5.3.0/egl
> /lib/site-packages/paraview/coprocessing.py",
> > line 305, in CreateProducer
> > if grid.IsA("vtkImageData") == True or \
>
> --Ben
>
from paraview.simple import *

from paraview import coprocessing

# the frequency to output everything
outputfrequency = 5

# --- CoProcessor definition ---

def CreateCoProcessor():
  def _CreatePipeline(coprocessor, datadescription):
class Pipeline:
  for i in range(datadescription.GetNumberOfInputDescriptions()):
inputdescription = datadescription.GetInputDescription(i)
name = datadescription.GetInputDescriptionName(i)
adaptorinput = coprocessor.CreateProducer( datadescription, name )
grid = adaptorinput.GetClientSideObject().GetOutputDataObject(0)
extension = None
if  grid.IsA('vtkImageData') or grid.IsA('vtkUniformGrid'):
  writer = servermanager.writers.XMLPImageDataWriter(Input=adaptorinput)
  extension = '.pvti'
elif  grid.IsA('vtkRectilinearGrid'):
  writer = servermanager.writers.XMLPRectilinearGridWriter(Input=adaptorinput)
  extension = '.pvtr'
elif  grid.IsA('vtkStructuredGrid'):
  writer = servermanager.writers.XMLPStructuredGridWriter(Input=adaptorinput)
  extension = '.pvts'
elif  grid.IsA('vtkPolyData'):
  writer = servermanager.writers.XMLPPolyDataWriter(Input=adaptorinput)
  extension = '.pvtp'
  

Re: [Paraview] Paraview Catalyst offscreen rendering

[Andy Bauer]

Hi,

I'd recommend trying to run pvserver or pvbatch in parallel and see if you
get the same error. My guess is that it's a connection or firewall issue.

On Thu, Aug 3, 2017 at 7:46 AM, Lukáš Kresta <lukas.kre...@gmail.com> wrote:

> Thank you. With new build from support I got new error: ERROR: In
> /apps/easybuild/build/ParaView/5.4.0/intel-2017a-
> mpi-OSPRay-TEST/ParaView-v5.4.0/ParaViewCore/ClientServerCore/Core/
> vtkTCPNetworkAccessManager.cxx, line 413
> vtkTCPNetworkAccessManager (0x6edc60):
> Should I try to rebuild ParaView or now it is problem with firewall or
> something like that?
>
> 2017-07-27 20:13 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> I think what you're missing is -DVTK_USE_X=OFF and probably
>> -DVTK_USE_OFFSCREEN=ON. If that doesn't work, please send your
>> CMakeCache.txt from your build directory.
>>
>> On Thu, Jul 27, 2017 at 5:48 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>> wrote:
>>
>>> it was build with easybuild with these parametrs:
>>>
>>> cmake 
>>> /apps/easybuild/build/ParaView/5.4.0/intel-2017a-mpi-OSPRay/ParaView-v5.4.0/
>>>
>>> -DCMAKE_INSTALL_PREFIX=/apps/all/ParaView/5.4.0-intel-2017a-mpi-OSPRay
>>>
>>> -DCMAKE_C_COMPILER='mpiicc' -DCMAKE_Fortran_FLAGS='-O2 -xHost -ftz 
>>> -fp-speculation=safe -fp-model source -fPIC'
>>>
>>> -DCMAKE_CXX_FLAGS='-O2 -xHost -ftz -fp-speculation=safe -fp-model source 
>>> -fPIC' -DCMAKE_CXX_COMPILER='mpiicpc'
>>>
>>> DCMAKE_Fortran_COMPILER='mpiifort' -DCMAKE_C_FLAGS='-O2 -xHost -ftz 
>>> -fp-speculation=safe -fp-model source -fPIC'
>>>
>>> -DCMAKE_VERBOSE_MAKEFILE=ON -DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON 
>>> -DVTK_OPENGL_HAS_OSMESA=ON
>>>
>>> -DPARAVIEW_USE_MPI=ON -DOPENGL_INCLUDE_DIR=$EBROOTMESA/include 
>>> -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so
>>>
>>> -DOSMESA_INCLUDE_DIR=$EBROOTMESA/include 
>>> -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so
>>>
>>> -DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so -DVTK_USE_SYSTEM_HDF5=ON 
>>> -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON
>>>
>>> -DVTK_RENDERING_BACKEND=OpenGL2 -DPARAVIEW_USE_OSPRAY=ON 
>>> -DOSPRAY_INSTALL_DIR=$EBROOT
>>>  OSPRAY -DPARAVIEW_QT_VERSION=5 -DBUILD_TESTING=OFF
>>>
>>>
>>> I hope, it will help solve my problem. If you need, i can send you complete 
>>> log.
>>>
>>>
>>> 2017-07-26 17:37 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>>>
>>>> Hi,
>>>>
>>>> It sounds like you didn't properly build with OSMesa. If you share your
>>>> CMakeCache.txt from your ParaView build I can see if I can track down the
>>>> problem.
>>>>
>>>> Best,
>>>> Andy
>>>>
>>>> On Wed, Jul 26, 2017 at 11:20 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>>>> wrote:
>>>>
>>>>> Thank you, but I have ParaView build with OSMesa without X. If I run
>>>>> program with Catalyst(genereted script from ParaView, with render views) 
>>>>> on
>>>>> cluster with mpi, ussually one render view will show, but on anothers
>>>>> process it crash with this error: ERROR: In .../ParaView-v5.4.0/VTK/Render
>>>>> ing/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
>>>>> vtkXOpenGLRenderWindow (0x3f7cbf0): GLEW could not be initialized. I
>>>>> have the same error with pvserver with or without 
>>>>> --use-offscreen-rendering
>>>>> or without pvserver.
>>>>>
>>>>> If i run Catalyst with script only for live visualization then the
>>>>> program go without problem but i dont get pictures which i want. Is there
>>>>> some posibility how fix the error or how to get pictures(with offscreen
>>>>> rendering)?
>>>>>
>>>>> 2017-07-14 16:24 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> If you're not memory constrained I suggest just doing a full ParaView
>>>>>> build with OSMesa and X11 disabled. There are quite a few discussions on
>>>>>> the PV mailing list on how to do that.
>>>>>>
>>>>>> If you're memory constrained then I would suggest building with all
>>>>>> of the Catalyst editions enabled and see if that works for you.

Re: [Paraview] [EXTERNAL] Building Catalyst for Albany

[Andy Bauer]

Hi Dan,

In order to work with an install directory you need to enable
PARAVIEW_INSTALL_DEVELOPMENT_FILES during your CMake configuration. I
personally just use my build directory for linking simulations with
Catalyst though.

Best,
Andy

On Wed, Aug 2, 2017 at 11:19 AM, Ibanez, Daniel Alejandro <
daib...@sandia.gov> wrote:

> It seems I can point Albany at my *build* directory of Catalyst, although
> I wonder why these things aren’t available in the *install* directory.
>
>
>
> *From: *ParaView  on behalf of "Ibanez,
> Daniel Alejandro" 
> *Date: *Wednesday, August 2, 2017 at 9:14 AM
> *To: *"paraview@paraview.org" 
> *Subject: *[EXTERNAL] [Paraview] Building Catalyst for Albany
>
>
>
> Hello,
>
>
>
> I’m trying to revive the integration of Catalyst into the Albany
> application.
>
> I’ve grabbed the Catalyst-v5.4.1-RC2-Base-Enable-Python tarball and
> configured like this:
>
>
>
> #!/bin/bash -ex
>
> $HOME/src/Catalyst-v5.4.1-RC2-Base-Enable-Python/cmake.sh
> $HOME/src/Catalyst-v5.4.1-RC2-Base-Enable-Python \
>
> -DCMAKE_INSTALL_PREFIX:PATH=$HOME/install/gcc/catalyst \
>
> -DCMAKE_CXX_COMPILER:FILEPATH=$HOME/install/gcc/mpich/bin/mpicxx \
>
> -DCMAKE_C_COMPILER:FILEPATH=$HOME/install/gcc/mpich/bin/mpicc \
>
> 2>&1 | tee config_log
>
>
>
> But the install directory doesn’t contain any headers or
> ParaViewConfig.cmake files.
>
> In Albany, the following is done:
>
>
>
> find_package(ParaView REQUIRED COMPONENTS vtkPVPythonCatalyst)
>
> include("${PARAVIEW_USE_FILE}")
>
>
>
> target_link_libraries(albanyCatalyst LINK_PRIVATE vtkPVPythonCatalyst)
>
>
>
>
>
> Where am I going wrong? What is it I should be installing?
>
>
>
> Thanks!
>
>
>
> Dan Ibanez
>
> ___
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>
> Please keep messages on-topic and check the ParaView Wiki at:
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Re: [Paraview] Paraview Catalyst offscreen rendering

[Andy Bauer]

I think what you're missing is -DVTK_USE_X=OFF and probably
-DVTK_USE_OFFSCREEN=ON. If that doesn't work, please send your
CMakeCache.txt from your build directory.

On Thu, Jul 27, 2017 at 5:48 AM, Lukáš Kresta <lukas.kre...@gmail.com>
wrote:

> it was build with easybuild with these parametrs:
>
> cmake 
> /apps/easybuild/build/ParaView/5.4.0/intel-2017a-mpi-OSPRay/ParaView-v5.4.0/
>
> -DCMAKE_INSTALL_PREFIX=/apps/all/ParaView/5.4.0-intel-2017a-mpi-OSPRay
>
> -DCMAKE_C_COMPILER='mpiicc' -DCMAKE_Fortran_FLAGS='-O2 -xHost -ftz 
> -fp-speculation=safe -fp-model source -fPIC'
>
> -DCMAKE_CXX_FLAGS='-O2 -xHost -ftz -fp-speculation=safe -fp-model source 
> -fPIC' -DCMAKE_CXX_COMPILER='mpiicpc'
>
> DCMAKE_Fortran_COMPILER='mpiifort' -DCMAKE_C_FLAGS='-O2 -xHost -ftz 
> -fp-speculation=safe -fp-model source -fPIC'
>
> -DCMAKE_VERBOSE_MAKEFILE=ON -DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON 
> -DVTK_OPENGL_HAS_OSMESA=ON
>
> -DPARAVIEW_USE_MPI=ON -DOPENGL_INCLUDE_DIR=$EBROOTMESA/include 
> -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.so
>
> -DOSMESA_INCLUDE_DIR=$EBROOTMESA/include 
> -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.so
>
> -DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.so -DVTK_USE_SYSTEM_HDF5=ON 
> -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON
>
> -DVTK_RENDERING_BACKEND=OpenGL2 -DPARAVIEW_USE_OSPRAY=ON 
> -DOSPRAY_INSTALL_DIR=$EBROOT
>  OSPRAY -DPARAVIEW_QT_VERSION=5 -DBUILD_TESTING=OFF
>
>
> I hope, it will help solve my problem. If you need, i can send you complete 
> log.
>
>
> 2017-07-26 17:37 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> It sounds like you didn't properly build with OSMesa. If you share your
>> CMakeCache.txt from your ParaView build I can see if I can track down the
>> problem.
>>
>> Best,
>> Andy
>>
>> On Wed, Jul 26, 2017 at 11:20 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>> wrote:
>>
>>> Thank you, but I have ParaView build with OSMesa without X. If I run
>>> program with Catalyst(genereted script from ParaView, with render views) on
>>> cluster with mpi, ussually one render view will show, but on anothers
>>> process it crash with this error: ERROR: In .../ParaView-v5.4.0/VTK/Render
>>> ing/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
>>> vtkXOpenGLRenderWindow (0x3f7cbf0): GLEW could not be initialized. I
>>> have the same error with pvserver with or without --use-offscreen-rendering
>>> or without pvserver.
>>>
>>> If i run Catalyst with script only for live visualization then the
>>> program go without problem but i dont get pictures which i want. Is there
>>> some posibility how fix the error or how to get pictures(with offscreen
>>> rendering)?
>>>
>>> 2017-07-14 16:24 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>>>
>>>> Hi,
>>>>
>>>> If you're not memory constrained I suggest just doing a full ParaView
>>>> build with OSMesa and X11 disabled. There are quite a few discussions on
>>>> the PV mailing list on how to do that.
>>>>
>>>> If you're memory constrained then I would suggest building with all of
>>>> the Catalyst editions enabled and see if that works for you.
>>>>
>>>> Best,
>>>> Andy
>>>>
>>>> On Fri, Jul 14, 2017 at 3:31 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to ask, which Paraview Catalyst (python) script use(with
>>>>> render view or live visualization). If i want save images with offscreen
>>>>> rendering on HPC.  On cluster is no gpu. And how to properly use it?
>>>>>
>>>>> Thank you for your help.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ___
>>>>> 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
>>>>>
>>>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>>
>>>>> Follow this link to subscribe/unsubscribe:
>>>>> http://public.kitware.com/mailman/listinfo/paraview
>>>>>
>>>>>
>>>>
>>>
>>
>
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Re: [Paraview] Paraview Catalyst offscreen rendering

[Andy Bauer]

Hi,

It sounds like you didn't properly build with OSMesa. If you share your
CMakeCache.txt from your ParaView build I can see if I can track down the
problem.

Best,
Andy

On Wed, Jul 26, 2017 at 11:20 AM, Lukáš Kresta <lukas.kre...@gmail.com>
wrote:

> Thank you, but I have ParaView build with OSMesa without X. If I run
> program with Catalyst(genereted script from ParaView, with render views) on
> cluster with mpi, ussually one render view will show, but on anothers
> process it crash with this error: ERROR: In .../ParaView-v5.4.0/VTK/
> Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
> vtkXOpenGLRenderWindow (0x3f7cbf0): GLEW could not be initialized. I have
> the same error with pvserver with or without --use-offscreen-rendering or
> without pvserver.
>
> If i run Catalyst with script only for live visualization then the program
> go without problem but i dont get pictures which i want. Is there some
> posibility how fix the error or how to get pictures(with offscreen
> rendering)?
>
> 2017-07-14 16:24 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> If you're not memory constrained I suggest just doing a full ParaView
>> build with OSMesa and X11 disabled. There are quite a few discussions on
>> the PV mailing list on how to do that.
>>
>> If you're memory constrained then I would suggest building with all of
>> the Catalyst editions enabled and see if that works for you.
>>
>> Best,
>> Andy
>>
>> On Fri, Jul 14, 2017 at 3:31 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> I would like to ask, which Paraview Catalyst (python) script use(with
>>> render view or live visualization). If i want save images with offscreen
>>> rendering on HPC.  On cluster is no gpu. And how to properly use it?
>>>
>>> Thank you for your help.
>>>
>>>
>>>
>>>
>>> ___
>>> 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
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/paraview
>>>
>>>
>>
>
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Re: [Paraview] Paraview Catalyst offscreen rendering

[Andy Bauer]

Hi,

If you're not memory constrained I suggest just doing a full ParaView build
with OSMesa and X11 disabled. There are quite a few discussions on the PV
mailing list on how to do that.

If you're memory constrained then I would suggest building with all of the
Catalyst editions enabled and see if that works for you.

Best,
Andy

On Fri, Jul 14, 2017 at 3:31 AM, Lukáš Kresta 
wrote:

> Hi,
>
> I would like to ask, which Paraview Catalyst (python) script use(with
> render view or live visualization). If i want save images with offscreen
> rendering on HPC.  On cluster is no gpu. And how to properly use it?
>
> Thank you for your help.
>
>
>
>
> ___
> 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
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
___
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Search the list archives at: http://markmail.org/search/?q=ParaView

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Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop on Windows

[Andy Bauer]

Hi,

I tested on Linux (Ubuntu 16.04).

Best,
Andy

On Tue, Jul 11, 2017 at 1:58 PM, <klarm...@mechanik.tu-darmstadt.de> wrote:

> Hi Andy,
>
> I just tried my example on arch linux and it works as expected. (ParaView
> 5.4.0-RC1)
>
> Somehow I got the feeling it is an issue related to Windows. Just to be
> sure, which OS did you choose to test the example code?
>
> Thank you very much for your time and support,
> Simon
>
>
>
>
> Am 2017-07-11 17:02, schrieb Andy Bauer:
>
>> Hi Simon,
>>
>> I tried with PV master (84f6e514) and couldn't replicate the crash. I
>> was able to get the connection between the GUI and the CatalystTest
>> executable though since I saw the PVTrivialProducer come up in the
>> GUI.
>>
>> Maybe you could try PV master and see if it works for you. Beyond that
>> I think figuring out your issue would take a non-trivial amount of
>> effort to figure out.
>>
>> Cheers,
>> Andy
>>
>> On Tue, Jul 11, 2017 at 8:04 AM, Simon Klarmann
>> <klarm...@mechanik.tu-darmstadt.de> wrote:
>>
>> Hi Andy,
>>>
>>> I want to be able to close the connection from both sides. Closing
>>> the connection from the Insitu side works by calling
>>> vtkLiveInsituLink::DropLiveInsituConnection().
>>>
>>> Closing the connection from the Live side, e.g. by closing the GUI,
>>> causes my application to hang in the vtkSocket::Receive() method.
>>>
>>> After enabling the Debug mode I get the following Error on the
>>> Insitu side:
>>>
>>> “ERROR: In
>>> D:\build\ParaView-v5.4.0\VTK\Common\System\vtkSocket.cxx, line 572
>>>
>>> vtkClientSocket (08BFFC00): Socket error in call to send.
>>> Eine bestehende Verbindung wurde softwaregesteuert durch den
>>> Hostcomputer abgebrochen.”
>>>
>>> „Eine bestehende Verbindung wurde softwaregesteuert durch den
>>> Hostcomputer abgebrochen“
>>>
>>> This seems to be a windows specific message notifying about a
>>> software controlled termination of the connection. So the
>>> information of the termination of the connection is somewhere
>>> available. The method throwing this error is the vtkSocket::Send()
>>> method.
>>>
>>> This error shows up as soon as I close the connection from the Live
>>> side (GUI) and then perform an InsituUpdate on the Insitu side.
>>> Still after this message, my Insitu side runs into
>>> vtkSocket::Receive() and get stuck there, trying to receive data.
>>>
>>> Additional Info:
>>>
>>> Performing the live visualization with the vtkCPPythonAdapter leads
>>> to the same error message and a crash of the Insitu application.
>>>
>>> Attached is a minimalistic working example. In both cases the error
>>> happens.
>>>
>>> Steps to reproduce:
>>>
>>> 1.   Start Paraview ->Catalyst->Connect
>>>
>>> 2.   Start the application, choose either 0 for python or 1 for
>>> cpp, then the PVTrivialproducer should show up in Paraview
>>>
>>> 3.   Close Paraview
>>>
>>> 4.   Continue the application ->crash
>>>
>>> I hope this helps a little bit to get an insight on what I did.
>>>
>>> Thanks,
>>>
>>> Simon
>>>
>>> VON: Andy Bauer [mailto:andy.ba...@kitware.com [1]]
>>> GESENDET: Montag, 10. Juli 2017 22:21
>>>
>>> AN: Simon Klarmann
>>> CC: paraview@paraview.org
>>> BETREFF: Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in
>>>
>>> loop on Windows
>>>
>>> Hi,
>>>
>>> Are you trying to close the connection from the in situ side? The
>>> design was for the connection to be close through the GUI.
>>>
>>> It's difficult to say what exactly is going on here without getting
>>> fairly deep into the problem. Theoretically though it should be
>>> possible to do the Live link in C++ as most of the Python routines
>>> call wrapped C++ routines.
>>>
>>> There should be some way to figure out the status of the connection
>>> on the PV server (the builtin server if you're not connected to a
>>> separate pvserver process) either the NotifyClientDisconnected()
>>> method, or vtkLiveInsituLink::OnConnectionClosedEvent() or
>>> vtkLiveInsituLink::DropLiveInsituConnection() member functions.
>>>
>>> Cheers,
>>>
>>> Andy
>>>
>>

Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop on Windows

[Andy Bauer]

Hi Simon,

I tried with PV master (84f6e514) and couldn't replicate the crash. I was
able to get the connection between the GUI and the CatalystTest executable
though since I saw the PVTrivialProducer come up in the GUI.

Maybe you could try PV master and see if it works for you. Beyond that I
think figuring out your issue would take a non-trivial amount of effort to
figure out.

Cheers,
Andy

On Tue, Jul 11, 2017 at 8:04 AM, Simon Klarmann <
klarm...@mechanik.tu-darmstadt.de> wrote:

> Hi Andy,
>
>
>
> I want to be able to close the connection from both sides. Closing the
> connection from the Insitu side works by calling vtkLiveInsituLink::
> DropLiveInsituConnection().
>
> Closing the connection from the Live side, e.g. by closing the GUI, causes
> my application to hang in the vtkSocket::Receive() method.
>
>
>
> After enabling the Debug mode I get the following Error on the Insitu side:
>
> “ERROR: In D:\build\ParaView-v5.4.0\VTK\Common\System\vtkSocket.cxx, line
> 572
>
> vtkClientSocket (08BFFC00): Socket error in call to send. Eine
> bestehende Verbindung wurde softwaregesteuert durch den Hostcomputer
> abgebrochen.”
>
>
>
> „Eine bestehende Verbindung wurde softwaregesteuert durch den Hostcomputer
> abgebrochen“
>
> This seems to be a windows specific message notifying about a software
> controlled termination of the connection. So the information of the
> termination of the connection is somewhere available. The method throwing
> this error is the vtkSocket::Send() method.
>
>
>
> This error shows up as soon as I close the connection from the Live side
> (GUI) and then perform an InsituUpdate on the Insitu side. Still after this
> message, my Insitu side runs into vtkSocket::Receive() and get stuck there,
> trying to receive data.
>
>
>
>
>
> Additional Info:
>
> Performing the live visualization with the vtkCPPythonAdapter leads to the
> same error message and a crash of the Insitu application.
>
>
>
> Attached is a minimalistic working example. In both cases the error
> happens.
>
>
>
> Steps to reproduce:
>
> 1.   Start Paraview ->Catalyst->Connect
>
> 2.   Start the application, choose either 0 for python or 1 for cpp,
> then the PVTrivialproducer should show up in Paraview
>
> 3.   Close Paraview
>
> 4.   Continue the application ->crash
>
>
>
>
>
> I hope this helps a little bit to get an insight on what I did.
>
>
>
> Thanks,
>
> Simon
>
>
>
>
>
>
>
>
>
> *Von:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Gesendet:* Montag, 10. Juli 2017 22:21
>
> *An:* Simon Klarmann
> *Cc:* paraview@paraview.org
> *Betreff:* Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop
> on Windows
>
>
>
> Hi,
>
>
>
> Are you trying to close the connection from the in situ side? The design
> was for the connection to be close through the GUI.
>
>
>
> It's difficult to say what exactly is going on here without getting fairly
> deep into the problem. Theoretically though it should be possible to do the
> Live link in C++ as most of the Python routines call wrapped C++ routines.
>
>
>
> There should be some way to figure out the status of the connection on the
> PV server (the builtin server if you're not connected to a separate
> pvserver process) either the NotifyClientDisconnected() method,
> or vtkLiveInsituLink::OnConnectionClosedEvent() or 
> vtkLiveInsituLink::DropLiveInsituConnection()
> member functions.
>
>
>
> Cheers,
>
> Andy
>
>
>
> On Mon, Jul 10, 2017 at 10:34 AM, Simon Klarmann <klarm...@mechanik.tu-
> darmstadt.de> wrote:
>
> Sorry I think I have chosen the wrong reply method.
>
>
>
> Hi Andy,
>
>
>
> I already got rid of Python on both sides. CoProcessing with Live
> connection is working by directly using the vtkLiveInsituLink (pure C++
> implementation).
>
>
>
> Working with both Paraview 5.2  and 5.4.
>
>
>
> My problem is closing the connection on the Live side (e.g. closing
> Paraview). Doing so, my Insitu side hangs (when trying again to send data,
> m_link->InsituUpdate, see below) in the receive method of the vtkSocket
> class until at some point an integer underflow happens.
>
>
>
> Closing the connection from the Insitu side everything works as expected.
>
>
>
> Are there any methods to directly check if the connection is still alive?
>
> Or is it a Windows specific problem?
>
>
>
>
>
>
>
> Additionally the steps for the live connection in C++, for sure there may
> be more elegant ways:
>
>
>
> // Initializati

Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop on Windows

[Andy Bauer]

Hi,

Are you trying to close the connection from the in situ side? The design
was for the connection to be close through the GUI.

It's difficult to say what exactly is going on here without getting fairly
deep into the problem. Theoretically though it should be possible to do the
Live link in C++ as most of the Python routines call wrapped C++ routines.

There should be some way to figure out the status of the connection on the
PV server (the builtin server if you're not connected to a separate
pvserver process) either the NotifyClientDisconnected() method,
or vtkLiveInsituLink::OnConnectionClosedEvent()
or vtkLiveInsituLink::DropLiveInsituConnection() member functions.

Cheers,
Andy

On Mon, Jul 10, 2017 at 10:34 AM, Simon Klarmann <
klarm...@mechanik.tu-darmstadt.de> wrote:

> Sorry I think I have chosen the wrong reply method.
>
>
>
> Hi Andy,
>
>
>
> I already got rid of Python on both sides. CoProcessing with Live
> connection is working by directly using the vtkLiveInsituLink (pure C++
> implementation).
>
>
>
> Working with both Paraview 5.2  and 5.4.
>
>
>
> My problem is closing the connection on the Live side (e.g. closing
> Paraview). Doing so, my Insitu side hangs (when trying again to send data,
> m_link->InsituUpdate, see below) in the receive method of the vtkSocket
> class until at some point an integer underflow happens.
>
>
>
> Closing the connection from the Insitu side everything works as expected.
>
>
>
> Are there any methods to directly check if the connection is still alive?
>
> Or is it a Windows specific problem?
>
>
>
>
>
>
>
> Additionally the steps for the live connection in C++, for sure there may
> be more elegant ways:
>
>
>
> // Initialization
>
>
>
> vtkCPProcessor  *m_proc = vtkCPProcessor::New();
>
> m_proc->Initialize();
>
>
>
> vtkLiveInsituLink  *m_link = vtkLiveInsituLink::New();
>
> m_link->SetInsituPort(2);
>
> m_link->SetHostname("localhost");
>
> m_link->SetProcessType(vtkLiveInsituLink::INSITU);
>
>
>
> vtkSMProxyManager  *m_spxm = vtkSMProxyManager::
> GetProxyManager()->GetActiveSessionProxyManager();
>
> vtkSMProxy *m_px = m_spxm->NewProxy("sources",
> "PVTrivialProducer");
>
> vtkSMSourceProxy *m_spx = vtkSMSourceProxy::
> SafeDownCast(m_px);
>
> m_spxm->RegisterProxy("sources", m_spx);
>
>
>
> vtkObjectBase *obase = m_spx->GetClientSideObject();
>
> vtkPVTrivialProducer *prod =
>
>vtkPVTrivialProducer::SafeDownCast(obase);
>
> prod->SetOutput(m_toplot, m_time);// m_toplot is a
> vtkMultiBlockDataSet
>
>
>
> m_link->Initialize(m_spxm);
>
>
>
>
>
> //Update the live side
>
> m_link->InsituUpdate(m_time, m_tstep);
>
> m_spx->UpdatePipeline(m_time);
>
> m_link->InsituPostProcess(m_time,m_tstep);
>
>
>
>
>
> Thanks,
>
> Simon
>
>
>
>
>
>
>
>
>
>
>
> *Von:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Gesendet:* Donnerstag, 6. Juli 2017 17:14
> *An:* Simon Klarmann
> *Cc:* paraview@paraview.org
> *Betreff:* Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop
> on Windows
>
>
>
> Hi Simon,
>
>
>
> Is the Python dependency that you're trying to get rid of on the Catalyst
> side or on the pvserver/GUI side? If I remember correctly on the Catalyst
> side Python was required for the Live connection.
>
>
>
> Cheers,
>
> Andy
>
>
>
> On Wed, Jul 5, 2017 at 10:11 AM, Simon Klarmann <klarm...@mechanik.tu-
> darmstadt.de> wrote:
>
> Dear Members,
>
>
>
> I wanted to get rid of the dependency on Python. The connection by pure
> C++ works just fine.
>
>
>
> The problem occurs when establishing the live connection to Paraview,
> closing Paraview and then try to send some data again.
>
> I tracked it down to the vtkSocket class inside the method Receive. After
> the connection is terminated on the Paraview side, e.g. by closing
> Paraview, the call of vtkLiveInsituLink::InsituUpdate gets stuck in the
> vtkSocket::Receive method. Even though I get a message that the connection
> was terminated.
>
>
>
> A temporary fix for my case was to replace in Line 609 of the
> vtkSocket.cxx if (nRecvd == 0) with if (nRecvd <= 0), because on
> disconnection the return value of nRecvd is -1. Then everyth

Re: [Paraview] multiple visualization pipeline at a time with co-processing

[Andy Bauer]

time ', 9.8, ' time step ', 98L)
> ('SCRIPT1 DCP time ', 9.8, ' time step ', 98L)
> ('SCRIPT2 RDD time ', 9.8, ' time step ', 98L)
> ('SCRIPT2 DCP time ', 9.8, ' time step ', 98L)
> ('SCRIPT1 DCP time ', 9.9, ' time step ', 99L)
> ('SCRIPT2 DCP time ', 9.9, ' time step ', 99L)
>
>
> > Hi Ufuk,
> >
> > It's looking to me like the issue is in the adaptor some place. I tried
> > running your scripts (modified slightly) with the CxxFullExample
> > (./CxxFullExample script_1.py script_2.py) and was able to get image_s1*
> > and image_s2* files out of it and did not see the warning you mention. I
> > also modified that example to use atm_input2d instead of input for the
> > input/grid identifier to make sure that wasn't the case. I've attached
> > this
> > example with the scripts modified to print out some debug information.
> >
> > Some questions (these are pretty basic things that you've probably
> already
> > gotten working properly but maybe there's some small thing that was
> > forgotten):
> >
> >- Does your g_coprocessor only get created in your initialization
> >routine and deleted in the finalization step? That should not be
> > created
> >and deleted during each in situ processing step.
> >- Do the vtkCPPythonScriptPipelines only get added during
> >initialization? They should not be added and removed from
> g_coprocessor
> >every time step.
> >
> > Also, could you try running with the scripts that I included in the
> > cat.tgz
> > tarball? The print statements there will print out the time and time
> steps
> > during the simulation run to help me diagnose (both need to be increasing
> > between calls to Catalyst). Also, if you share your adaptor code with me
> I
> > can take a quick look.
> >
> > Cheers,
> > Andy
> >
> >
> >
> > On Fri, Jul 7, 2017 at 7:30 AM, Ufuk Utku Turuncoglu (BE) <
> > u.utku.turunco...@be.itu.edu.tr> wrote:
> >
> >> Hi Andy,
> >>
> >> Strange! To test the idea and eliminate other problems i am using same
> >> script twice with little mods (i just changed the name of the output png
> >> file). So, if i pass script_1.py and script_2.py to the model, it gives
> >> warning like before and creates output just for second script
> >> (script_2.py). If i pass only one of them then the code is working
> >> without
> >> any problem and produces desired output.
> >>
> >> Thanks,
> >> Regards,
> >>
> >> --ufuk
> >>
> >>
> >>
> >> On 06/07/2017 18:09, Andy Bauer wrote:
> >>
> >> Hi Ufuk,
> >>
> >> I'm guessing the issue is that the calls to Catalyst are not consistent.
> >> Could you share your Python scripts? Also, did you modify them manually?
> >>
> >> I tried with PV 5.3. with the
> >> ../ParaView-v5.3.0/Examples/Catalyst/CxxFullExample/
> >> example with the attached scripts simultaneously by running with
> >> "./CxxFullExample doubleoutputs.py output3.py image11.py" and got the
> >> correct output and no warnings.
> >>
> >> Cheers,
> >> Andy
> >>
> >> On Tue, Jul 4, 2017 at 7:04 AM, Ufuk Utku Turuncoglu (BE) <
> >> u.utku.turunco...@be.itu.edu.tr> wrote:
> >>
> >>> Hi Andy,
> >>>
> >>> I tested you suggestion about using multiple script in co-processing.
> >>> In
> >>> this case, i used following code in the adaptor side to add multiple
> >>> pipeline
> >>>
> >>>   for (int i = 0; i < *nscript; i++) {
> >>> pipeline->Initialize(pythonScriptNames[i]);
> >>> g_coprocessor->AddPipeline(pipeline);
> >>>   }
> >>>
> >>> When i run the simulation, i am getting following warning
> >>>
> >>> Warning: In
> >>> /okyanus/users/uturuncoglu/progs/paraview-5.3.0/src/ParaView
> >>> Core/VTKExtensions/Core/vtkPVTrivialProducer.cxx, line 66
> >>> vtkPVTrivialProducer (0x13816760): New time step is not after last time
> >>> step.
> >>>
> >>> the output seems not correct and it is zoom out version of second
> >>> pipeline (png file). The first pipeline is not even triggered. Do i
> >>> missing
> >>> something in here? BTW, i am using PV 5.3.
> >>>
> >>> Thanks,
> >>>
> >>> --ufuk
> >>>
> >>>
&g

Re: [Paraview] multiple visualization pipeline at a time with co-processing

[Andy Bauer]

Hi Ufuk,

It's looking to me like the issue is in the adaptor some place. I tried
running your scripts (modified slightly) with the CxxFullExample
(./CxxFullExample script_1.py script_2.py) and was able to get image_s1*
and image_s2* files out of it and did not see the warning you mention. I
also modified that example to use atm_input2d instead of input for the
input/grid identifier to make sure that wasn't the case. I've attached this
example with the scripts modified to print out some debug information.

Some questions (these are pretty basic things that you've probably already
gotten working properly but maybe there's some small thing that was
forgotten):

   - Does your g_coprocessor only get created in your initialization
   routine and deleted in the finalization step? That should not be created
   and deleted during each in situ processing step.
   - Do the vtkCPPythonScriptPipelines only get added during
   initialization? They should not be added and removed from g_coprocessor
   every time step.

Also, could you try running with the scripts that I included in the cat.tgz
tarball? The print statements there will print out the time and time steps
during the simulation run to help me diagnose (both need to be increasing
between calls to Catalyst). Also, if you share your adaptor code with me I
can take a quick look.

Cheers,
Andy



On Fri, Jul 7, 2017 at 7:30 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi Andy,
>
> Strange! To test the idea and eliminate other problems i am using same
> script twice with little mods (i just changed the name of the output png
> file). So, if i pass script_1.py and script_2.py to the model, it gives
> warning like before and creates output just for second script
> (script_2.py). If i pass only one of them then the code is working without
> any problem and produces desired output.
>
> Thanks,
> Regards,
>
> --ufuk
>
>
>
> On 06/07/2017 18:09, Andy Bauer wrote:
>
> Hi Ufuk,
>
> I'm guessing the issue is that the calls to Catalyst are not consistent.
> Could you share your Python scripts? Also, did you modify them manually?
>
> I tried with PV 5.3. with the 
> ../ParaView-v5.3.0/Examples/Catalyst/CxxFullExample/
> example with the attached scripts simultaneously by running with
> "./CxxFullExample doubleoutputs.py output3.py image11.py" and got the
> correct output and no warnings.
>
> Cheers,
> Andy
>
> On Tue, Jul 4, 2017 at 7:04 AM, Ufuk Utku Turuncoglu (BE) <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Hi Andy,
>>
>> I tested you suggestion about using multiple script in co-processing. In
>> this case, i used following code in the adaptor side to add multiple
>> pipeline
>>
>>   for (int i = 0; i < *nscript; i++) {
>> pipeline->Initialize(pythonScriptNames[i]);
>> g_coprocessor->AddPipeline(pipeline);
>>   }
>>
>> When i run the simulation, i am getting following warning
>>
>> Warning: In /okyanus/users/uturuncoglu/progs/paraview-5.3.0/src/ParaView
>> Core/VTKExtensions/Core/vtkPVTrivialProducer.cxx, line 66
>> vtkPVTrivialProducer (0x13816760): New time step is not after last time
>> step.
>>
>> the output seems not correct and it is zoom out version of second
>> pipeline (png file). The first pipeline is not even triggered. Do i missing
>> something in here? BTW, i am using PV 5.3.
>>
>> Thanks,
>>
>> --ufuk
>>
>>
>> On 16/05/2017 16:08, Andy Bauer wrote:
>>
>> Hi Ufuk,
>>
>> If you create a vtkCPythonScriptPipeline, when you initialize it with the
>> script file name (which has to be done on each process) everything will be
>> taken care of with respect to broadcasting the file contents from process 0
>> to the others. We aren't sophisticated enough to parse the Python script to
>> see if it imports other scripts that are not part of ParaView (e.g.
>> paraview.simple) or Python (e.g. sys). That is why I recommended the first
>> approach as opposed to the second approach above. Depending on the compute
>> platform and how many MPI processes are in the run the difference may be
>> negligible but having 100K processes or more trying to access the same file
>> can seriously slow down an HPC machine.
>>
>> Cheers,
>> Andy
>>
>> On Tue, May 16, 2017 at 8:24 AM, Ufuk Utku Turuncoglu (BE) <
>> u.utku.turunco...@be.itu.edu.tr> wrote:
>>
>>> Thanks Andy. That is exactly what i am looking for. The broadcasting
>>> mechanism is not clear to me yet. Do i need to broadcast only the file
>>> names? Anyway, i will try to implement it and see what is going on there.
>>

Re: [Paraview] Integrating precompiled Catalyst into external projects

[Andy Bauer]

Hi Jimmy,

If you're building Catalyst and want to install for others to link against
you will want to enable the PARAVIEW_INSTALL_DEVELOPMENT_FILES CMake option
when configuring.

It may be possible to have precompiled Catalyst installs with development
files available but there hasn't been a strong call for that to be done.

Cheers,
Andy

On Wed, Jul 5, 2017 at 8:08 AM, A .  wrote:

> Dear members,
>
>
> I would like to have Catalyst precompiled and ready for use for developers
> that want to work on my project. In this way they don't need to go through
> the procedure of installing dependencies and building Catalyst themselves
> (which currently takes longer than building my project...).
>
>
> The problem is the absolute paths that are used in all the .cmake files,
> such as ParaViewConfig.cmake and UseParaView.cmake (and all .cmake files
> they call on).
>
>
> I thought a "make install" would do the trick as normally it will copy all
> the essential files (system independent) to the CMAKE_INSTALL_PREFIX
> directory. But I cannot use the contents of the installation folder as the
> directory to point to when linking to Catalyst in my project (since there
> are no configuration files copied).
>
>
> I was doubtful to ask this question, because if it were possible, I would
> expect a precompiled Catalyst to be hosted on the ParaView download page.
> But out of curiosity I ask nonetheless; is it possible?
>
>
> Best,
>
> Jimmy
>
> ___
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>
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Re: [Paraview] C++ Catalyst vtkSocket::Receive stuck in loop on Windows

[Andy Bauer]

Hi Simon,

Is the Python dependency that you're trying to get rid of on the Catalyst
side or on the pvserver/GUI side? If I remember correctly on the Catalyst
side Python was required for the Live connection.

Cheers,
Andy

On Wed, Jul 5, 2017 at 10:11 AM, Simon Klarmann <
klarm...@mechanik.tu-darmstadt.de> wrote:

> Dear Members,
>
>
>
> I wanted to get rid of the dependency on Python. The connection by pure
> C++ works just fine.
>
>
>
> The problem occurs when establishing the live connection to Paraview,
> closing Paraview and then try to send some data again.
>
> I tracked it down to the vtkSocket class inside the method Receive. After
> the connection is terminated on the Paraview side, e.g. by closing
> Paraview, the call of vtkLiveInsituLink::InsituUpdate gets stuck in the
> vtkSocket::Receive method. Even though I get a message that the connection
> was terminated.
>
>
>
> A temporary fix for my case was to replace in Line 609 of the
> vtkSocket.cxx if (nRecvd == 0) with if (nRecvd <= 0), because on
> disconnection the return value of nRecvd is -1. Then everything works well.
>
>
>
> I only used the following methods in the given order to transfer the data:
>
>
>
> vtkLiveInsituLink::InsituUpdate
>
> vtkSMSourceProxy::UpdatePipeline
>
> vtkLiveInsituLink::InsituPostProcess
>
>
>
>
>
> Are there further steps to perform or is there a way to check if the
> connection is still alive?
>
>
>
>
>
> Operating System: Windows 7, Visual Studio 2017
>
>
>
> Thanks,
>
> Simon
>
>
>
>
>
>
>
>
>
> Dipl.-Ing. Simon Klarmann
>
>
>
> *Bau- und Umweltingenieurwissenschaften*
> Technische Universität Darmstadt
>
> Fachgebiet Festkörpermechanik
>
>
>
> Tel.: +49 6151 16 – 22642 <+49%206151%201622642>
>
> Mail: klarm...@mechanik.tu-darmstadt.de
>
> Franziska-Braun-Straße 7
>
> Gebäude L5|01, Raum 542
>
> 64287 Darmstadt
>
>
>
> ___
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>
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> opensource/opensource.html
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Re: [Paraview] multiple visualization pipeline at a time with co-processing

[Andy Bauer]

Hi Ufuk,

I'm guessing the issue is that the calls to Catalyst are not consistent.
Could you share your Python scripts? Also, did you modify them manually?

I tried with PV 5.3. with
the ../ParaView-v5.3.0/Examples/Catalyst/CxxFullExample/ example with the
attached scripts simultaneously by running with "./CxxFullExample
doubleoutputs.py output3.py image11.py" and got the correct output and no
warnings.

Cheers,
Andy

On Tue, Jul 4, 2017 at 7:04 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi Andy,
>
> I tested you suggestion about using multiple script in co-processing. In
> this case, i used following code in the adaptor side to add multiple
> pipeline
>
>   for (int i = 0; i < *nscript; i++) {
> pipeline->Initialize(pythonScriptNames[i]);
> g_coprocessor->AddPipeline(pipeline);
>   }
>
> When i run the simulation, i am getting following warning
>
> Warning: In /okyanus/users/uturuncoglu/progs/paraview-5.3.0/src/
> ParaViewCore/VTKExtensions/Core/vtkPVTrivialProducer.cxx, line 66
> vtkPVTrivialProducer (0x13816760): New time step is not after last time
> step.
>
> the output seems not correct and it is zoom out version of second pipeline
> (png file). The first pipeline is not even triggered. Do i missing
> something in here? BTW, i am using PV 5.3.
>
> Thanks,
>
> --ufuk
>
>
> On 16/05/2017 16:08, Andy Bauer wrote:
>
> Hi Ufuk,
>
> If you create a vtkCPythonScriptPipeline, when you initialize it with the
> script file name (which has to be done on each process) everything will be
> taken care of with respect to broadcasting the file contents from process 0
> to the others. We aren't sophisticated enough to parse the Python script to
> see if it imports other scripts that are not part of ParaView (e.g.
> paraview.simple) or Python (e.g. sys). That is why I recommended the first
> approach as opposed to the second approach above. Depending on the compute
> platform and how many MPI processes are in the run the difference may be
> negligible but having 100K processes or more trying to access the same file
> can seriously slow down an HPC machine.
>
> Cheers,
> Andy
>
> On Tue, May 16, 2017 at 8:24 AM, Ufuk Utku Turuncoglu (BE) <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Thanks Andy. That is exactly what i am looking for. The broadcasting
>> mechanism is not clear to me yet. Do i need to broadcast only the file
>> names? Anyway, i will try to implement it and see what is going on there.
>>
>> Thanks again,
>> Regards,
>>
>> --ufuk
>>
>>
>> On 16/05/2017 14:58, Andy Bauer wrote:
>>
>> Hi Ufuk,
>>
>> Unless I'm not understanding your question correctly, I think you can get
>> what you want by adding in multiple vtkCPPythonScriptPipelines to your
>> vtkCPProcessor object in your adaptor. Alternatively if you want to have a
>> single, master Catalyst script handling other Catalyst scripts you can do
>> something like the following:
>> 
>> import script_a
>> import script_b
>> import script_c
>>
>> def RequestDataDescription(datadescription):
>>   script_a.RequestDataDescription(datadescription)
>>   script_b.RequestDataDescription(datadescription)
>>   script_c.RequestDataDescription(datadescription)
>>
>> def DoCoProcessing(datadescription):
>>   script_a.DoCoProcessing(datadescription)
>>   script_b.DoCoProcessing(datadescription)
>>   script_c.DoCoProcessing(datadescription)
>> ===
>>
>> The first way is the recommended way though as that should be more
>> efficient by having process 0 read the scripts and broadcasting the script
>> contents to the other  processes for use. The second method will only do
>> that for the master script.
>>
>> Please let me know if this doesn't answer your question.
>>
>> Cheers,
>> Andy
>>
>> On Tue, May 16, 2017 at 5:46 AM, Ufuk Utku Turuncoglu (BE) <
>> u.utku.turunco...@be.itu.edu.tr> wrote:
>>
>>> Hi All,
>>>
>>> I just wonder that is it possible to trigger multiple visualization
>>> pipeline in the same time with co-processing. The co-processing script
>>> generator plugin mainly outputs only single pipeline at a time and that is
>>> fine but what about combining multiple Python script (generated by plugin)
>>> using higher level Python script to trigger multiple pipelines. So, i think
>>> that this will be much efficient way to look at different part of the data
>>> without writing to the disk. I am not sure but somebody else might do it

Re: [Paraview] Saving png images in Catalyst-live

[Andy Bauer]

Hi,

Currently you will need to save the images in the PV GUI during the Live
connection. If you need images at specific time steps you will need to set
Live breakpoints. I hope to be able to modify Catalyst image output through
the Live connection but there are a lot of options that aren't always easy
to capture so it will take quite a bit of design work to get right.

Cheers,
Andy

On Mon, Jul 3, 2017 at 5:39 AM, Lukáš Kresta  wrote:

> Hi,
>
> i would like to save image with my ParaView Catalyst. But I use live
> visualization(no render view) and I send to Catalyst unstructured grid. Can
> I somehow generate png image?
>
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Re: [Paraview] Pipe back data from ParaView to simulation program through Catalyst

[Andy Bauer]

Hi Jimmy,

There is no current way to do this in Catalyst without custom code. I know
others have done it already but haven't seen the actual implementation for
that. We hope to have funding in the next year to get more sophisticated
with this in Catalyst but there are not specific projects yet that will
fund us to work on this.

If I were to try to do a simple implementation of this now what I would do
is add in a filter with the options you want and add that in as a plugin to
PV. Then in your Python script you can interrogate those values and pass
the data back to the simulation through the vtkCPDataDescription::UserData.

Cheers,
Andy

On Thu, Jun 29, 2017 at 11:47 AM, A .  wrote:

> Dear members,
>
>
> I have successfully been able to use ParaView Catalyst to do in-situ
> visualization. The data that is generated from my simulation program is
> forwarded to ParaView with the use of these so-called 'adaptors'. The API
> is very straightforward and it was done easily. However I was wondering if
> feeding back data from ParaView into my simulation program through Catalyst
> is also possible. In other words can ParaView serve as a (semi) graphical
> user interface?
>
>
> For instance, at some point in the simulation in ParaView I want to change
> the size of one of my simulation objects, which in my simulation program is
> represented as a private data member of the object's class. So I want to
> pause the simulation, select the object and change the value of the
> object's size. Is there a way to pipe this data back into the simulation
> (in-situ) and continue the simulation?
>
>
> If the above description is too specific, I would just like to ask if the
> user can be interactive with simulation program through ParaView in any
> way. I can think of a way of exporting the changed ParaView state to file,
> parse that in my simulation program and update the simulation state, but I
> was wondering if there is a neater / faster way of doing this.
>
>
> Best,
>
> Jimmy
>
>
> ___
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Re: [Paraview] Sliding time window statistics

[Andy Bauer]

Hi Ross,

The easiest way I can think of to do this would be to create a ParaView
Python script to loop over the windows/chunks that you want. What I would
do is use the trace capability to load the files in your first chunk that
you want and create your full pipeline. Then save that state and edit it to
loop over the set chunks that you want with the given files corresponding
to that chunk. Note that I'm assuming here that the data time steps fall
nicely into your time chunks. If your data sets have multiple time steps in
a single file (e.g. time series ExodusII files) then you can use the
Extract Time Steps filter to get what time steps you want from your reader.

Cheers,
Andy

On Wed, Jun 28, 2017 at 7:56 AM, Ross Gardiner <
ross.gardi...@ultrahaptics.com> wrote:

> Hi all,
>
> I have a time series of scalar fields (imageData) and want to use ParaView
> to compute a moving average of the values in the field with respect to time.
>
> For example (just looking at a single point in the field for this example):
>
> Time -->
>
> 02462
>
> |-|
>  2
>  |-|
>   4
>   |-|
>4
>
> In my research so far, I’ve found the Temporal Statistics filter, but this
> doesn’t appear to support ‘chunking’ the time series or using a sliding
> window.
>
> Is there any way to do something like this in ParaView? Would I have to
> write a custom filter? If so, where should I start?
>
> I’m trying to do this as part of a numerical approximation to an integral
> dt.
>
> Thanks,
>
> Ross
>
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Re: [Paraview] Calculation of Lambda2 using ParaView...

[Andy Bauer]

Hi,

The best way to do this would be in a programmable filter. I'm guessing
numpy has some method to compute eigenvalues for non-symmetric matrices.
Beyond that adding the capability to the Python calculator or some other
filter would be needed.



On Tue, Jun 13, 2017 at 3:35 AM, Stefan Melber  wrote:

> Hi Andy,
>
> i think i found the reason: i need the computation of (unsymmetrical)
> eigenvalues for lambda2 - however it seems that the function "eingenvalue"
> calculates only symmetric ones (see https://www.paraview.org/
> ParaView/Doc/Nightly/www/py-doc/paraview.vtk.numpy_
> interface.algorithms.html). How can i calculate the unsymmetric ones with
> ParaView?
>
> Best regards,
>
>  Stefan
>
>
> Hi,
>
> Maybe compute each portion manually and check that against the correct
> values. Also, verifying the gradient calculation is correct is another
> thing to look at. If the grid isn't specified properly then the gradient
> operation will likely be wrong.
>
> On Fri, Jun 9, 2017 at 8:46 AM, Stefan Melber 
> wrote:
>
>> Hi,
>>
>>
>> for vortex-detection i (tried) to calculate the lambda2-criterion (see
>> e.g. https://en.wikipedia.org/wiki/Lambda2_method) with ParaView. The
>> way of calculation is based on this link http://www.iesensor.com/blog/2
>> 016/01/24/using-paraview-to-visualise-vorticity-lambda2-vort
>> icity-q-criterion/.
>>
>> However - the results are a kind of "wrong" - see attached pictures:
>> l2_solver.png shows what the flow solver writes out for lambda2,
>> l2_paraview.png shows what calculated with the algorithm below.
>>
>> Calculation of lambda2:
>>
>> D = Gradients = [d_ij]
>> S = strain(Vel)
>>
>> S = (D + D^T)/2
>> Omega = (D - D^T)/2
>>
>> lambda = EigenValue_of(S^2 + Omega^2)
>>= EigenValue_of(S^2 + (D - S)^2)
>>= EigenValue_of(S^2 + (Gradients - strain(vel))^2)
>>
>> lambda2 = lambda_Y
>>
>> and in ParaView this mean
>>
>> o Vector of velocity with "Calculator".: Vel =
>> iHat*x_velocity+jHat*y_velocity+kHat*z_velocity
>> o Gradients of Vel with "GradientOfUnstructuredDataSet": switch on
>> "compute gradient" and name it "Gradients"
>> o Calculate lambda with "PythonCalculator".: lambda =
>> eigenvalue(strain(Vel)**2+(Gradients - strain(Vel))**2)
>> o Caluclate lambda2 with Calculator: lambda2 =
>> lambda_Y
>>
>>
>>
>> Does anyone see the error why the calculation of lambda2 with ParaView
>> does not work?
>>
>> Remark: i contacted the author of the blog above already - seems he never
>> tested his calculation and has no idea what is "wrong".
>>
>> Stefan
>>
>>
>>
>> 
>>
>>  _/ *Dr. Stefan Melber-Wilkending*
>>_/_/
>>  _/  _/ Deutsches Zentrum für Luft-
>>  _/_/_/_/_/_/_/_/_/_/ und Raumfahrt e.V. (DLR)
>>_/_/_/_/
>>  _/_/_/_/ German Aerospace Center
>>_/_/_/_/_/_/_/_/_/_/  Institute of Aerodynamics
>>  _/  _/  _  _   and Flow Technology
>>  _/_/   | \ |  |_|   Transport Aircraft Branch
>>  _/ |_/ |_ | \
>>  Lilienthalplatz 7
>>  Fields of activities:  38108 Braunschweig
>>  Germany
>>  o Numerical Windtunnel Simulation
>>  o Aero-Acoustic Windtunnel DesignPhone : +49 531/295-2836
>> <%28531%29%20295-2836>
>>  o Numerical Optimization Fax. .: +49 531/295-2914
>> <%28531%29%20295-2914>
>>  o Visualization Techniques
>>  o High-Lift Aerodynamics   Email : stefan.mel...@dlr.de
>>  o Glider-Aerodynamics  Web ..: http://www.dlr.de/AS
>>
>>
>> 
>>
>>
>> ___
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Re: [Paraview] Calculation of Lambda2 using ParaView...

[Andy Bauer]

Hi,

Maybe compute each portion manually and check that against the correct
values. Also, verifying the gradient calculation is correct is another
thing to look at. If the grid isn't specified properly then the gradient
operation will likely be wrong.

On Fri, Jun 9, 2017 at 8:46 AM, Stefan Melber  wrote:

> Hi,
>
>
> for vortex-detection i (tried) to calculate the lambda2-criterion (see
> e.g. https://en.wikipedia.org/wiki/Lambda2_method) with ParaView. The way
> of calculation is based on this link http://www.iesensor.com/blog/
> 2016/01/24/using-paraview-to-visualise-vorticity-lambda2-
> vorticity-q-criterion/.
>
> However - the results are a kind of "wrong" - see attached pictures:
> l2_solver.png shows what the flow solver writes out for lambda2,
> l2_paraview.png shows what calculated with the algorithm below.
>
> Calculation of lambda2:
>
> D = Gradients = [d_ij]
> S = strain(Vel)
>
> S = (D + D^T)/2
> Omega = (D - D^T)/2
>
> lambda = EigenValue_of(S^2 + Omega^2)
>= EigenValue_of(S^2 + (D - S)^2)
>= EigenValue_of(S^2 + (Gradients - strain(vel))^2)
>
> lambda2 = lambda_Y
>
> and in ParaView this mean
>
> o Vector of velocity with "Calculator".: Vel =
> iHat*x_velocity+jHat*y_velocity+kHat*z_velocity
> o Gradients of Vel with "GradientOfUnstructuredDataSet": switch on
> "compute gradient" and name it "Gradients"
> o Calculate lambda with "PythonCalculator".: lambda =
> eigenvalue(strain(Vel)**2+(Gradients - strain(Vel))**2)
> o Caluclate lambda2 with Calculator: lambda2 =
> lambda_Y
>
>
>
> Does anyone see the error why the calculation of lambda2 with ParaView
> does not work?
>
> Remark: i contacted the author of the blog above already - seems he never
> tested his calculation and has no idea what is "wrong".
>
> Stefan
>
>
>
> 
>
>  _/ *Dr. Stefan Melber-Wilkending*
>_/_/
>  _/  _/ Deutsches Zentrum für Luft-
>  _/_/_/_/_/_/_/_/_/_/ und Raumfahrt e.V. (DLR)
>_/_/_/_/
>  _/_/_/_/ German Aerospace Center
>_/_/_/_/_/_/_/_/_/_/  Institute of Aerodynamics
>  _/  _/  _  _   and Flow Technology
>  _/_/   | \ |  |_|   Transport Aircraft Branch
>  _/ |_/ |_ | \
>  Lilienthalplatz 7
>  Fields of activities:  38108 Braunschweig
>  Germany
>  o Numerical Windtunnel Simulation
>  o Aero-Acoustic Windtunnel DesignPhone : +49 531/295-2836
> <(531)%20295-2836>
>  o Numerical Optimization Fax. .: +49 531/295-2914
> <(531)%20295-2914>
>  o Visualization Techniques
>  o High-Lift Aerodynamics   Email : stefan.mel...@dlr.de
>  o Glider-Aerodynamics  Web ..: http://www.dlr.de/AS
>
>
> 
>
>
> ___
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Re: [Paraview] pvpython vtkMPIController usage? rank is always 0

[Andy Bauer]

Note that you can run both the ParaView GUI and  pvpython with MPI in order
to initialize, finalize and use MPI functions but as Dave said, they
should/will always be run with a single MPI process. The argument to run
MPI with either is "--mpi".

On Tue, May 16, 2017 at 1:11 PM, David E DeMarle 
wrote:

> Try your script within pvbatch.
>
> pvpython is analogous to the Qt client application, it (usually) is not
> part of an MPI execution environment. Either one can connect to an MPI
> parallel pvserver.
> pvbatch is a python interface that is meant to be run on the server. It is
> directly connected to the pvserver.
>
>
>
>
>
>
> David E DeMarle
> Kitware, Inc.
> Principal Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909 <(518)%20881-4909>
>
> On Tue, May 16, 2017 at 1:07 PM, Ephraim Obermaier <
> ephraimoberma...@gmail.com> wrote:
>
>> Hello,
>> I am trying to use VTK's MPI communication from pvpython, running with
>> OpenMPI's mpirun. It seems like ParaView hasn't enabled the MPI
>> capabilities for VTK, although it was compiled from source with
>> PARAVIEW_USE_MPI=ON and correctly found the system OpenMPI-2.0.0 libraries
>> and includes.
>>
>> I am running the short example below with the command "mpirun -n 2
>> pvpython test.py". The full output is also attached.
>> In short, both MPI processes report rank=0 and size=1 and their
>> controller is a vtkDummyController although I expected rank=0..1, size=2
>> and a vtkMPIController.
>>
>> Is it possible to determine the problem with the given information? Do I
>> need extra CMake settings besides "PARAVIEW_USE_MPI=ON" to enable MPI for
>> VTK?
>> ParaView by itself runs fine in parallel, and I can start several
>> parallel pvservers using "mpirun -n 16 pvserver".
>>
>> --- test.py: ---
>> import vtk
>>
>> c = vtk.vtkMultiProcessController.GetGlobalController()
>>
>> print "comm:",type(c)
>> rank = c.GetLocalProcessId()
>> print "rank:",rank
>> size = c.GetNumberOfProcesses()
>> print "size:",size
>>
>> if rank == 0:
>> ssource = vtk.vtkSphereSource()
>> ssource.Update()
>> print " 0 sending."
>> c.Send(ssource.GetOutput(), 1, 1234)
>> else:
>> sphere = vtk.vtkPolyData()
>> print " 1 receiving."
>> c.Receive(sphere, 0, 1234)
>> print sphere
>>
>> --- Test run: ---
>> $ mpirun -n 2 pvpython test.py
>> comm: 
>> rank: 0
>> size: 1
>>  0 sending.
>> Warning: In /home/user/.local/easybuild/build/ParaView/5.3.0/foss-2016b-
>> mpi/ParaView-v5.3.0/VTK/Parallel/Core/vtkDummyCommunicator.h, line 47
>> vtkDummyCommunicator (0x1ff74e0): There is no one to send to.
>> [... 7 more times the same Warning...]
>>
>> comm: 
>> rank: 0
>> size: 1
>>  0 sending.
>> Warning: In /home/user/.local/easybuild/build/ParaView/5.3.0/foss-2016b-
>> mpi/ParaView-v5.3.0/VTK/Parallel/Core/vtkDummyCommunicator.h, line 47
>> vtkDummyCommunicator (0x22c14e0): There is no one to send to.
>> [... 7 more times the same Warning...]
>> --- end of output ---
>>
>> Thank you!
>> Ephraim
>>
>>
>> 
>>  Virenfrei.
>> www.avast.com
>> 
>> <#m_-1876715506680916602_m_7351775176557461903_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>>
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Re: [Paraview] multiple visualization pipeline at a time with co-processing

[Andy Bauer]

Hi Ufuk,

If you create a vtkCPythonScriptPipeline, when you initialize it with the
script file name (which has to be done on each process) everything will be
taken care of with respect to broadcasting the file contents from process 0
to the others. We aren't sophisticated enough to parse the Python script to
see if it imports other scripts that are not part of ParaView (e.g.
paraview.simple) or Python (e.g. sys). That is why I recommended the first
approach as opposed to the second approach above. Depending on the compute
platform and how many MPI processes are in the run the difference may be
negligible but having 100K processes or more trying to access the same file
can seriously slow down an HPC machine.

Cheers,
Andy

On Tue, May 16, 2017 at 8:24 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Thanks Andy. That is exactly what i am looking for. The broadcasting
> mechanism is not clear to me yet. Do i need to broadcast only the file
> names? Anyway, i will try to implement it and see what is going on there.
>
> Thanks again,
> Regards,
>
> --ufuk
>
>
> On 16/05/2017 14:58, Andy Bauer wrote:
>
> Hi Ufuk,
>
> Unless I'm not understanding your question correctly, I think you can get
> what you want by adding in multiple vtkCPPythonScriptPipelines to your
> vtkCPProcessor object in your adaptor. Alternatively if you want to have a
> single, master Catalyst script handling other Catalyst scripts you can do
> something like the following:
> 
> import script_a
> import script_b
> import script_c
>
> def RequestDataDescription(datadescription):
>   script_a.RequestDataDescription(datadescription)
>   script_b.RequestDataDescription(datadescription)
>   script_c.RequestDataDescription(datadescription)
>
> def DoCoProcessing(datadescription):
>   script_a.DoCoProcessing(datadescription)
>   script_b.DoCoProcessing(datadescription)
>   script_c.DoCoProcessing(datadescription)
> ===
>
> The first way is the recommended way though as that should be more
> efficient by having process 0 read the scripts and broadcasting the script
> contents to the other  processes for use. The second method will only do
> that for the master script.
>
> Please let me know if this doesn't answer your question.
>
> Cheers,
> Andy
>
> On Tue, May 16, 2017 at 5:46 AM, Ufuk Utku Turuncoglu (BE) <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Hi All,
>>
>> I just wonder that is it possible to trigger multiple visualization
>> pipeline in the same time with co-processing. The co-processing script
>> generator plugin mainly outputs only single pipeline at a time and that is
>> fine but what about combining multiple Python script (generated by plugin)
>> using higher level Python script to trigger multiple pipelines. So, i think
>> that this will be much efficient way to look at different part of the data
>> without writing to the disk. I am not sure but somebody else might do it
>> before.
>>
>> Regards,
>>
>> --ufuk
>>
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Re: [Paraview] multiple visualization pipeline at a time with co-processing

[Andy Bauer]

Hi Ufuk,

Unless I'm not understanding your question correctly, I think you can get
what you want by adding in multiple vtkCPPythonScriptPipelines to your
vtkCPProcessor object in your adaptor. Alternatively if you want to have a
single, master Catalyst script handling other Catalyst scripts you can do
something like the following:

import script_a
import script_b
import script_c

def RequestDataDescription(datadescription):
  script_a.RequestDataDescription(datadescription)
  script_b.RequestDataDescription(datadescription)
  script_c.RequestDataDescription(datadescription)

def DoCoProcessing(datadescription):
  script_a.DoCoProcessing(datadescription)
  script_b.DoCoProcessing(datadescription)
  script_c.DoCoProcessing(datadescription)
===

The first way is the recommended way though as that should be more
efficient by having process 0 read the scripts and broadcasting the script
contents to the other  processes for use. The second method will only do
that for the master script.

Please let me know if this doesn't answer your question.

Cheers,
Andy

On Tue, May 16, 2017 at 5:46 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi All,
>
> I just wonder that is it possible to trigger multiple visualization
> pipeline in the same time with co-processing. The co-processing script
> generator plugin mainly outputs only single pipeline at a time and that is
> fine but what about combining multiple Python script (generated by plugin)
> using higher level Python script to trigger multiple pipelines. So, i think
> that this will be much efficient way to look at different part of the data
> without writing to the disk. I am not sure but somebody else might do it
> before.
>
> Regards,
>
> --ufuk
>
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Re: [Paraview] Bug or feature?

[Andy Bauer]

Hi,

Please keep the discussions on the mailing list so that everyone that wants
to can follow along.

I'm able to volume render by components as well as magnitude. It may be
that you need to play around with the Color Map Editor to get things as
you'd like them to look.

I'm not an expert on volume rendering but it seems to me like something is
wrong with your cell connectivity when I use the Extract Surface filter.
It's possible that this is also causing issues with the volume rendering
but I couldn't say for sure.

Andy

On Sun, May 7, 2017 at 5:20 AM, Cornelis Bockemühl <
cornelis.bockemu...@gmail.com> wrote:

> This is my example, mostly stripped down to the core of the problem: see
> the Col2comp data array that has 2 components (see attached zipped vtu
> file). The model has something more than 600 cells, and in both components
> (comp1 and comp2) many of them are 0. In comp2 it is even all except 18 -
> and this can easily be seen in a "surface" view: almost everything is blue
> == 0. It can also be analyzed with cut and slice filters, so it is also the
> case "inside" the model.
>
> Now with a volume view this is completely different: comp2 looks as if
> indeed many cells have values "above blue"!
>
> But I must admit that initially I did not look well enough: also the
> volume view changes a little if I change between "magnitude", "comp1" and
> "comp2" - only that it does not look like matching the surface views at
> all: all cells except one actually have a 0 in one of the two components -
> which should be clearly visible also in the volume view I suppose!
>
> I could reproduce this behaviour not only on my self-compiled version 5.3
> paraview, but also in a downloaded and installed binary version 5.1.2
> (64-bit).
>
> In other words: I am a bit confused now! ;-)
>
> Regards,
> Cornelis
>
>
>
> 2017-05-07 0:49 GMT+02:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> I am able to do a volume visualization for each component of a 3
>> component array (i.e. a vector) of both point and cell data in PV 5.3. This
>> was done with a both a vtkImageData and a vtkUnstructuredGrid. Once I
>> choose my 3 component array for volume rendering in the upper left corner
>> of the GUI, the default is the Magnitude but I can switch to each component
>> as well with the drop down dialog that is just to the right of where I
>> choose which array I want to pseudo-color by.
>>
>> Any chance you could share your dataset and specific instructions on how
>> you're doing things? Alternatively, you can use the Calculator filter to
>> extract one component of your multi-component array but this is a bit
>> computationally wasteful.
>>
>> Cheers,
>> Andy
>>
>> On Sat, May 6, 2017 at 12:15 PM, Cornelis Bockemühl <
>> cornelis.bockemu...@gmail.com> wrote:
>>
>>> Dear Paraview users and experts,
>>>
>>> In some project I am generating a dataset that has a multi-component
>>> column as a result, with a variable number of columns depending on the
>>> problem. These data are "cell data" of some "unstructured grid", and I can
>>> nicely visualize it in Paraview, component by component.
>>>
>>> Only with the visualization as a "volume" I have problems: It seems that
>>> with this you can only visualize the "magnitude", while switching between
>>> the components does not work! This works only in other viewing modes, but
>>> the "volume" is sometimes very useful because you can look "inside" the
>>> volume.
>>>
>>> Now I am asking myself if this is a bug (with a certain chance to have
>>> it fixed or even fix it myself...) or a feature?
>>>
>>> I mean: the fact that "magnitude" is the default for displaying
>>> multi-component arrays already gives some hint in the direction: this type
>>> of columns is mostly intended to be used as coordinates! Which is actually
>>> not my case.
>>>
>>> Technically I could of course switch to just generating a set of
>>> single-component arrays instead of one multi-component array. I only did it
>>> otherwise because the columns are very closely related, so it looked like a
>>> good idea initially...
>>>
>>> Any hint or experience?
>>>
>>> Regards,
>>> Cornelis
>>>
>>> PS: I am using Paraview 5.3 on Windows 64bit
>>>
>>> --
>>> Cornelis Bockemühl
>>> Basel, Schweiz
>>>
>>> __

Re: [Paraview] Bug or feature?

[Andy Bauer]

Hi,

I am able to do a volume visualization for each component of a 3 component
array (i.e. a vector) of both point and cell data in PV 5.3. This was done
with a both a vtkImageData and a vtkUnstructuredGrid. Once I choose my 3
component array for volume rendering in the upper left corner of the GUI,
the default is the Magnitude but I can switch to each component as well
with the drop down dialog that is just to the right of where I choose which
array I want to pseudo-color by.

Any chance you could share your dataset and specific instructions on how
you're doing things? Alternatively, you can use the Calculator filter to
extract one component of your multi-component array but this is a bit
computationally wasteful.

Cheers,
Andy

On Sat, May 6, 2017 at 12:15 PM, Cornelis Bockemühl <
cornelis.bockemu...@gmail.com> wrote:

> Dear Paraview users and experts,
>
> In some project I am generating a dataset that has a multi-component
> column as a result, with a variable number of columns depending on the
> problem. These data are "cell data" of some "unstructured grid", and I can
> nicely visualize it in Paraview, component by component.
>
> Only with the visualization as a "volume" I have problems: It seems that
> with this you can only visualize the "magnitude", while switching between
> the components does not work! This works only in other viewing modes, but
> the "volume" is sometimes very useful because you can look "inside" the
> volume.
>
> Now I am asking myself if this is a bug (with a certain chance to have it
> fixed or even fix it myself...) or a feature?
>
> I mean: the fact that "magnitude" is the default for displaying
> multi-component arrays already gives some hint in the direction: this type
> of columns is mostly intended to be used as coordinates! Which is actually
> not my case.
>
> Technically I could of course switch to just generating a set of
> single-component arrays instead of one multi-component array. I only did it
> otherwise because the columns are very closely related, so it looked like a
> good idea initially...
>
> Any hint or experience?
>
> Regards,
> Cornelis
>
> PS: I am using Paraview 5.3 on Windows 64bit
>
> --
> Cornelis Bockemühl
> Basel, Schweiz
>
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Re: [Paraview] How to run a simulation with Catalyst and display the result using tiled display?

[Andy Bauer]

Hi,

I believe that this should be possible but I haven't done it myself so I
can't guarantee that it would work. There may be some needed development
involved in order to get it working properly.

Andy

On Tue, Apr 18, 2017 at 9:31 AM, 张驭洲  wrote:

>
>
> Hello,
>
> I want to visualize a simulation program in situ and display it using a
> tiled screen. I can run the simulation with Catalyst and MPI, and I can
> also configure ParaView for a 3x2 tiled screen. However, if I run paraview
> with tiled display, the control of the servers' window will be taken by
> paraview so I can't start the simulation program. I tried to start the
> simulation through ssh, but after connecting to the simulation using
> Catalyst, the simulation program crashed with these errors:
>
> ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkSocket.cxx,
> line 481
> vtkClientSocket (0x1f0bbb0): Socket error in call to connect. Connection
> refused.
>
> ERROR: In /root/Desktop/ParaView-v5.2.0/VTK/Common/System/vtkClientSocket.cxx,
> line 53
> vtkClientSocket (0x1f0bbb0): Failed to connect to server localhost:4
>
> ERROR: In 
> /root/Desktop/ParaView-v5.2.0/VTK/Parallel/Core/vtkSocketCommunicator.cxx,
> line 714
> vtkSocketCommunicator (0x3798ec0): Ca n not connect to localhost on port
> 4
>
> APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
>
> Actually the Catalyst connecting port should be 2 and when I click
> "Catalyst>connect" in  the GUI, it is indeed 2. I don't know why
> the port in the error message is 4. I noticed that if I let Catalyst to
> output images, there will be windows of the same number of mpi simulation
> processes on the server, but the windows is of the same size of the view in
> the GUI on the client, which sames not for tiled display.
>
> So, is it possible to display the result of in situ visualization with
> tiled display?
>
> Thanks a lot!
> -Zhang
>
>
>
>
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Re: [Paraview] [paraview][catalyst]

[Andy Bauer]

Hi,

It is using the default settings for a vtkImageGrid which is to set the
spacing to 1 in each direction and the origin to (0,0,0). vtkImageData has
SetOrigin() and SetSpacing() methods. You can see the class documentation
at http://www.vtk.org/doc/nightly/html/classvtkImageData.html.

Cheers,
Andy

On Fri, Apr 14, 2017 at 7:54 AM, 刘楚高  wrote:

> hi, all
>
> In Catalyst example "Fortran90FullExample" -> "FECxxAdaptor.cxx"->"
> createcpimagedata_", the grid is new and has no coordinates. So, how to
> transfer the simulation grid coordinates to this vtkImageData grid?
>
> Thank you!
>
> extern "C" void createcpimagedata_(int* nxstart, int* nxend, int* nx,
>
>int* ny, int* nz)
>
> {
>
>   if (!vtkCPPythonAdaptorAPI::GetCoProcessorData())
>
> {
>
> vtkGenericWarningMacro("Unable to access CoProcessorData.");
>
> return;
>
> }
>
>
>   // The simulation grid is a 3-dimensional topologically and
> geometrically
>
>   // regular grid. In VTK/ParaView, this is considered an image data set.
>
>   vtkSmartPointer grid = vtkSmartPointer:
> :New();
>
>
>   grid->SetExtent(*nxstart-1, *nxend-1, 0, *ny-1, 0, *nz-1);
>
>
>   // Name should be consistent between here, Fortran and Python client
> script.
>
>   vtkCPPythonAdaptorAPI::GetCoProcessorData()->GetInputDescriptionByName("
> input")->SetGrid(grid);
>
>   vtkCPPythonAdaptorAPI::GetCoProcessorData()->GetInputDescriptionByName("
> input")->SetWholeExtent(0, *nx-1, 0, *ny-1, 0, *nz-1);
>
> }
>
> --
> 中国空气动力研究与发展中心 计算空气动力研究所
> Blog: http://blog.donews.com/frank777
> MSN: frank1985...@hotmail.com
>
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Re: [Paraview] [EXTERNAL] Extracting min/max values of current data range as a variable in python

[Andy Bauer]

Hi Ryan,

You should also be able to get the number of tuples, number of components,
the range for each component, the name (though that is likely already
known) and the data type that is being stored (e.g. double, float, int,
etc.). I don't know how to get all of those of the top of my head but can
poke around if needed.

Best,
Andy

On Wed, Apr 12, 2017 at 1:01 PM, Jamison, Ryan Dale <rdja...@sandia.gov>
wrote:

> Andy,
>
> I combined the Extract Filter Block with the example you outlined below
> and it worked! I was able to use GetRange() to get the minimum and maximum
> of the array for the current time.
>
> On a side note, other than GetRange(), what else can be done with data
> from GetArray()?
>
> Best, Ryan
>
> On Apr 11, 2017, at 7:46 PM, Andy Bauer <andy.ba...@kitware.com> wrote:
>
> Hi,
>
> Besides Yoshimi's way, you should be able to do something like the
> following from pvpython, pvbatch or Python shell.
> yourfilter.PointData.GetArray().GetRange() # or CellData
>
> For example, for a Python script for a Wavelet source you would do the
> following:
> w = Wavelet()
> w.UpdatePipeline() # needed to execute the pipeline to create the output
> w.PointData.GetArray("RTData").GetRange()
>
> This will work for the output of a filter that returns a regular VTK data
> set or a multiblock data set. If you want the range for only a single block
> of a multiblock I'd recommend using the Extract Block filter to get that
> block. It should be a shallow copy of the data set to do that so it should
> be very fast, even if you don't need the output of the Extract Block filter
> for anything else.
>
> Best,
> Andy
>
> On Tue, Apr 11, 2017 at 9:29 PM, kenichiro yoshimi <
> rccm.kyosh...@gmail.com> wrote:
>
>> Hi,
>>
>> I also want to know if there is a simple way to do, since I only have
>> the somewhat redundant code:
>> ---
>> source = GetActiveSource()
>>
>> #options for component: -1, 0, 1 and 2 => Mag, X, Y, Z
>> component = -1
>>
>> cdi = source.GetDataInformation().GetCompositeDataInformation()
>>
>> for i in range(cdi.GetNumberOfChildren()):
>>   print 'Block Name: ', cdi.GetName(i)
>>
>>   data = cdi.GetDataInformation(i).GetCellDataInformation()
>>   for j in range(data.GetNumberOfArrays()):
>> array = data.GetArrayInformation(j)
>> arrayName = array.GetName()
>> dataRange = array.GetComponentRange(component)
>> print arrayName, dataRange
>> ---
>>
>> Thanks,
>> yoshimi
>>
>> 2017-04-12 6:10 GMT+09:00 Jamison, Ryan Dale <rdja...@sandia.gov>:
>> > Hello Everyone,
>> >
>> > I’m wanting to gain more control over automation with my paraview python
>> > scripts. This time around, I’d like to be able to extract information
>> from
>> > the model and use it in my python script.
>> >
>> > For example, I’d like to extract the minimum and maximum values of a
>> cell
>> > variable from a specific block and use those values in the python
>> script.
>> > Once I extract this information, I’d use it for some additional
>> processing.
>> > Something like:
>> >
>> > minValue, maxValue = someCoolParaviewFunction(blockName, variableName)
>> >
>> > Is this possible? If so, any suggestions on how to do it?
>> >
>> > Thanks,
>> >
>> > Ryan
>> >
>> > ___
>> > 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
>> >
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>> >
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>> >
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Re: [Paraview] [EXTERNAL] NaN coloring on non-NaN component

[Andy Bauer]

Hi Cory,

What's the behavior supposed to be in PV 5.3 when pseudo-coloring by a
variable which has 0 variation? When I look at this in PV 5.3 the lookup
table range goes from 0 to 3.4e38. Is that what it's supposed to be?

Thanks,
Andy

On Tue, Apr 11, 2017 at 10:39 AM, Cory Quammen 
wrote:

> Hi Dan,
>
> I believe you are encountering this bug in 5.2:
> https://gitlab.kitware.com/paraview/paraview/issues/17127
>
> It has been fixed in ParaView 5.3.0 and I verified that it works with
> the dataset you provided.
>
> Best regards,
> Cory
>
> On Tue, Apr 11, 2017 at 10:30 AM, Ibanez, Daniel Alejandro
>  wrote:
> > Installing the ParaView 5.0.1 binary made this go away.
> >
> > 
> > From: ParaView  on behalf of Ibanez,
> Daniel
> > Alejandro 
> > Sent: Tuesday, April 11, 2017 8:15 AM
> > To: paraview@paraview.org
> > Cc: Granzow, Brian N (External Contacts)
> > Subject: [EXTERNAL] [Paraview] NaN coloring on non-NaN component
> >
> >
> > Hello,
> >
> >
> > I'm using the ParaView 5.2.0 binary download for Mac.
> >
> > I've attached an unstructured grid VTK file, using binary encoding.
> >
> > When I open this file, and try to color by the Y component
> >
> > of nodal velocity, I get the NaN color.
> >
> > I've checked the data right before it goes into the file
> >
> > and am pretty certain there are no NaN or infinity values
> >
> > (by std::isnan, std::isinf, and writing to std::cerr in C++).
> >
> >
> > Could someone take a look at this and confirm whether
> >
> > its a bug or something is actually wrong with my data ?
> >
> >
> > Much appreciated,
> >
> >
> > Dan Ibanez
> >
> >
> > ___
> > Powered by www.kitware.com
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> >
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> > http://paraview.org/Wiki/ParaView
> >
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> >
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> >
>
>
>
> --
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> Staff R Engineer
> Kitware, Inc.
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Re: [Paraview] Switching time steps when running parallel

[Andy Bauer]

Hi,

I was able to reproduce this issue with a data set that Alex shared
privately with me (but is ok to share publicly). I've created a bug report (
https://gitlab.kitware.com/paraview/paraview/issues/17333).

Cheers,
Andy

ps. Alex: I've cc'ed the list so that others can follow the issue.

On Tue, Mar 28, 2017 at 12:02 PM, Andy Bauer <andy.ba...@kitware.com> wrote:

> Hi,
>
> Any chance you could share the data set? I cannot determine the problem
> from the error message and am not sure I can reproduce it otherwise.
>
> Thanks,
> Andy
>
> On Tue, Mar 28, 2017 at 11:31 AM, Stief, Alexander <
> alexander.st...@hs-aalen.de> wrote:
>
>> I am using the ensight gold file format for transient results.
>>
>> When running Paraview in parallel mode (Auto MPI), I am unable to load
>> any time step except the first one.
>>
>> Trying to load a different time step results in the error message:
>>
>>
>>
>>
>>
>> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-lin
>> ux-shared-release_opengl2_qt4_superbuild/source-paraview/
>> ParaViewCore/VTKExtensions/Default/vtkPEnSightReader.cxx, line 343
>>
>> vtkPEnSightGoldBinaryReader (0x30d9510): error reading geometry file
>> ../ModelEnsight/LB_results.geo 0
>>
>>
>>
>> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-lin
>> ux-shared-release_opengl2_qt4_superbuild/source-paraview/
>> VTK/Common/ExecutionModel/vtkExecutive.cxx, line 784
>>
>> vtkCompositeDataPipeline (0x30d8f40): Algorithm
>> vtkPEnSightGoldBinaryReader(0x30d9510) returned failure for request:
>> vtkInformation (0x31fc9a0)
>>
>>   Debug: Off
>>
>>   Modified Time: 96520
>>
>>   Reference Count: 1
>>
>>   Registered Events: (none)
>>
>>   Request: REQUEST_DATA
>>
>>   ALGORITHM_AFTER_FORWARD: 1
>>
>>   FORWARD_DIRECTION: 0
>>
>>   FROM_OUTPUT_PORT: 0
>>
>>
>>
>>
>>
>> When I try the same without Auto MPI enabled it works perfectly. It is
>> just that I would like to use Auto MPI because it speeds up the filters a
>> lot.
>>
>> I tried with versions 5.2.0 and 5.3.0.
>>
>>
>>
>> Regards
>>
>> Alex
>>
>> ___
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>>
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Re: [Paraview] Switching time steps when running parallel

[Andy Bauer]

Hi,

Any chance you could share the data set? I cannot determine the problem
from the error message and am not sure I can reproduce it otherwise.

Thanks,
Andy

On Tue, Mar 28, 2017 at 11:31 AM, Stief, Alexander <
alexander.st...@hs-aalen.de> wrote:

> I am using the ensight gold file format for transient results.
>
> When running Paraview in parallel mode (Auto MPI), I am unable to load any
> time step except the first one.
>
> Trying to load a different time step results in the error message:
>
>
>
>
>
> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-
> linux-shared-release_opengl2_qt4_superbuild/source-paraview/ParaViewCore/
> VTKExtensions/Default/vtkPEnSightReader.cxx, line 343
>
> vtkPEnSightGoldBinaryReader (0x30d9510): error reading geometry file
> ../ModelEnsight/LB_results.geo 0
>
>
>
> ERROR: In /home/buildslave/dashboards/buildbot/paraview-pvbinsdash-
> linux-shared-release_opengl2_qt4_superbuild/source-paraview/VTK/Common/
> ExecutionModel/vtkExecutive.cxx, line 784
>
> vtkCompositeDataPipeline (0x30d8f40): Algorithm
> vtkPEnSightGoldBinaryReader(0x30d9510) returned failure for request:
> vtkInformation (0x31fc9a0)
>
>   Debug: Off
>
>   Modified Time: 96520
>
>   Reference Count: 1
>
>   Registered Events: (none)
>
>   Request: REQUEST_DATA
>
>   ALGORITHM_AFTER_FORWARD: 1
>
>   FORWARD_DIRECTION: 0
>
>   FROM_OUTPUT_PORT: 0
>
>
>
>
>
> When I try the same without Auto MPI enabled it works perfectly. It is
> just that I would like to use Auto MPI because it speeds up the filters a
> lot.
>
> I tried with versions 5.2.0 and 5.3.0.
>
>
>
> Regards
>
> Alex
>
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Re: [Paraview] Attach arrows onto streamlines/stream tubes more smoothly

[Andy Bauer]

I think it is because you have set the Shaft radius to 0. The start of the
arrow doesn't appear because of this and I'm suspecting that the start of
the arrow is centered along the streamline. Maybe try using using either a
non-zero value for the Shaft radius that is bigger than the Tube radius or
use the Cone glyph type instead.

On Wed, Mar 15, 2017 at 5:59 PM, Liang Wang <frank0...@gmail.com> wrote:

> Hi Andy,
>
> The results are similar if I apply glyph on streamlines directly (see the
> attached image).
>
> I guess the difficulty part is that arrow heads are not easily centered on
> lines/tubes?
>
> On Wed, Mar 15, 2017 at 5:50 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> Hi,
>>
>> How does it look if you Glyph the streamlines themselves instead of the
>> tubes?
>>
>> On Wed, Mar 15, 2017 at 5:40 PM, Liang Wang <frank0...@gmail.com> wrote:
>>
>>> By using the arrow glyph filter on the lines/tubes, the arrows are often
>>> slightly dislocated (and thus slightly misaligned) from the tubes
>>> themselves (see the attached image).
>>>
>>> In comparison, I am trying to get images like
>>> http://www.tecplot.com/wp-content/uploads/2016/01/fstream.jpg or
>>> https://i.stack.imgur.com/z8nkm.png
>>>
>>> Logically, the arrows could have been an attribute of the
>>> streamlines/stream tubes?
>>>
>>> ___
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>>>
>>
>
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Re: [Paraview] Attach arrows onto streamlines/stream tubes more smoothly

[Andy Bauer]

Hi,

How does it look if you Glyph the streamlines themselves instead of the
tubes?

On Wed, Mar 15, 2017 at 5:40 PM, Liang Wang  wrote:

> By using the arrow glyph filter on the lines/tubes, the arrows are often
> slightly dislocated (and thus slightly misaligned) from the tubes
> themselves (see the attached image).
>
> In comparison, I am trying to get images like http://www.tecplot.com/wp-
> content/uploads/2016/01/fstream.jpg or https://i.stack.imgur.com/z8nkm.png
>
> Logically, the arrows could have been an attribute of the
> streamlines/stream tubes?
>
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Re: [Paraview] StreamTracer: Combined ReasonForTermination or select individual polylines?

[Andy Bauer]

In Python you can do something like create a Threshold filter to

# create a new 'Threshold'

threshold1 = Threshold(Input=streamTracer1)

threshold1.Scalars = ['CELLS', 'SeedIds']

threshold1.ThresholdRange = [1.0, 2.0]
threshold1.CellData['ReasonForTermination'].GetRange()

This will give you the range of values in the threshold output for the
ReasonForTermination array. You can query the number of seeds for the
high resolution line source with .SeedType.Resolution



On Tue, Mar 14, 2017 at 4:31 PM, Liang Wang <frank0...@gmail.com> wrote:

> A follow-up question: How to perform the `Find Data` by `criteria` in
> Python? I tried to record a macro but only got
>
> extractSelection1 = ExtractSelection(Input=tube1,
> Selection=None)
>
> On Tue, Mar 14, 2017 at 3:47 PM, Liang Wang <frank0...@gmail.com> wrote:
>
>> Thank you, Andy.
>>
>>
>> I):
>>
>> I'm using 5.3 and your example is what I would get. But what I want is a
>> way to tell if the two streamlines from the same seed point are terminated
>> for different reasons. It might be more clear from the image I attached. I
>> would like to tell
>>
>> 1) closed field lines that have both ends terminated on the sphere
>> surface (the red tubes)
>> 2) semi-open field lines that have on the ends terminated on the sphere
>> surface, the other goes out-of-domain (the red and blue tubes)
>> 3) open field lines that have both ends out-of-bound (not shown in the
>> image, would be blue tubes)
>>
>> (Or, ideal, I would be happier to be able to tell if the open end of the
>> semi-open field lines goes out of the southern or northern bound)
>>
>> Indeed, I saw people doing this in Mayavi-based python (see
>> https://github.com/KristoforMaynard/Viscid/blob/dev/viscid/
>> cython/streamline.pyx and http://kristoformaynard.github
>> .io/Viscid/docs/master/examples/mayavi.html). One obstacle I can see is
>> that ParaView (or vtk?) probably treats the two streamlines from the same
>> seed point independently, thus it won't be easy to tag them together.
>>
>> II):
>>
>> I realize that I am demanding too much. I tried your way of `Find Data`,
>> and now I am able to manually choose individual streamlines, which is
>> already helpful.
>>
>>
>>
>> On Tue, Mar 14, 2017 at 3:17 PM, Andy Bauer <andy.ba...@kitware.com>
>> wrote:
>>
>>> Hi,
>>>
>>> What version of ParaView are you using?
>>>
>>> From my testing it looks like each direction for the stream tracer seeds
>>> has a separate reason for termination in PV 5.3 -- see the attached image.
>>> The domain is a box with length 20 on each side, the velocity is [1, 0, 0],
>>> the seeds are a line source going from min to max of the bounding box
>>> ([-10, -10, -10] to [10,10,10]).  The red is for when the maximum
>>> streamline length has exceeded my specified max length of 5 and the blue is
>>> for when the streamline exited the domain.
>>>
>>> Is there a case where the same reason for termination value is being
>>> used for multiple termination criteria?
>>>
>>> You can use the SeedIds cell data array in the Threshold filter or use
>>> the Edit->Find Data option to select a given streamline from the seed id.
>>>
>>> Cheers,
>>> Andy
>>>
>>>
>>>
>>> On Tue, Mar 14, 2017 at 2:24 PM, Liang Wang <frank0...@gmail.com> wrote:
>>>
>>>> If the IntegrationDirection is set to BOTH, the two segments of the
>>>> streamlines from the seed might terminate for different reasons. For
>>>> example, one end might end due to STAGNATION, the other due
>>>> to OUT_OF_DOMAIN. When coloring by ReasonForTermination, then the two
>>>> segments are colored differently.
>>>>
>>>> My question is: Can a user create more cases of ReasonForTermination so
>>>> that we can tell examples like above? Or, how can I select individual
>>>> streamlines by its SeedIds (I tried IdsSelection, but that appears to work
>>>> for cell/point data only, not for polydata?)
>>>>
>>>> My current solution is to use threshold filter to select lines in the
>>>> different regions and apply different solid colors. But it would be nice if
>>>> I can handle a few different cases more directly, even if that involves
>>>> some coding in C++ or Python.
>>>>
>>>> Thanks.
>>>>
>>>> ___
>>>> Powered by ww

Re: [Paraview] CellCenters filter produces non-deterministic result

[Andy Bauer]

You can try doing the following in the GUI's Python shell (starting out
with the reader as the active source):
ii = ImageDataToUniformGrid()
ii.SelectInputScalars = ['CELLS', 'vtkGhostType']
Show()
Render()

This still shows the ghost cells but if you do operations like slice or cut
it will not include these cells. Note that the ImageDataToUniformGrid
filter has an option to Reverse whether zero/non-zero is to be interpreted
as a blanked cell.






On Wed, Mar 8, 2017 at 9:20 AM, David Doria <daviddo...@gmail.com> wrote:

> On Tue, Mar 7, 2017 at 8:10 PM, Andy Bauer <andy.ba...@kitware.com> wrote:
>
>> Hi David,
>>
>> I'm not sure how it works with structured grids but with vtkUniformGrids
>> (i.e. vtkImageData with blanking) the VTK readers and writers really just
>> produce vtkImageData and the blanking is ignored. It may be the same with
>> the XML structured grid files. My suggestion would be to look at the
>> vtkImageDataToUniformGrid class in VTK and try doing a similar thing in
>> ParaView using the Python Programmable filter.
>>
>> Cheers,
>> Andy
>>
>> On Tue, Mar 7, 2017 at 10:22 AM, David Doria <daviddo...@gmail.com>
>> wrote:
>>
>>> On Mon, Mar 6, 2017 at 11:14 AM, Andy Bauer <andy.ba...@kitware.com>
>>> wrote:
>>>
>>>> Thanks for the bug report!
>>>>
>>>> I think the stackoverflow issue is probably also related to blanking. I
>>>> added to your bug report with two other (likely) related issues.
>>>>
>>>> As a side note, I think if blanking was used instead of ghost cells
>>>> this may work properly.
>>>>
>>>> Thanks,
>>>> Andy
>>>>
>>>> On Mon, Mar 6, 2017 at 8:45 AM, David Doria <daviddo...@gmail.com>
>>>> wrote:
>>>>
>>>>> On Sun, Mar 5, 2017 at 7:05 PM, Andy Bauer <andy.ba...@kitware.com>
>>>>> wrote:
>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> This looks like it has to do with blanking (i.e. in PV 5.2 if I don't
>>>>>> load the vtkGhostType array it has the proper bounds). Would you mind
>>>>>> putting in a bug report on Gitlab (https://gitlab.kitware.com/pa
>>>>>> raview/paraview)?
>>>>>>
>>>>>> Thanks,
>>>>>> Andy
>>>>>>
>>>>>
>>>>> Done:
>>>>> https://gitlab.kitware.com/paraview/paraview/issues/17244
>>>>>
>>>>> Here is another presumed bug that seems to also have to do with
>>>>> blanking: http://stackoverflow.com/questions/42543340/cell-l
>>>>> abels-in-selection-display-inspector-dont-work-when-any-cell
>>>>> s-are-ghosted - not trying to pollute this thread but do you think
>>>>> that behavior could be helpful to understand the Cell Centers issue?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> David
>>>>>
>>>>
>>>>
>>> Hi Andy,
>>>
>>> The file was created with something like this:
>>>
>>> https://gist.github.com/daviddoria/8bf981aa593b7cefcd9114588e4766db
>>>
>>> Does calling
>>>
>>> structuredGrid->BlankPoint(0);
>>>
>>> not count as "using blanking"? Can you point me to the "right way" to do
>>> this if this is not the current best practice?
>>>
>>> Thanks!
>>>
>>> David
>>>
>>
>>
> I created a uniform grid:
>
> https://gist.github.com/daviddoria/99fa99c52aa07ee78b7e7412e74d592f
> https://drive.google.com/open?id=0B8yIfGqnlfSoNTNKWWtua1pEUTA
>
> Using the vtkXMLImageDataWriter seemed to write the same type of
> vtkGhostType array (shown in the cell data in Paraview), but Paraview
> doesn't seem to respect the blanking - all 8 voxels are drawn.
>
> Any other ideas?
>
> David
>
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Re: [Paraview] CellCenters filter produces non-deterministic result

[Andy Bauer]

Hi David,

I'm not sure how it works with structured grids but with vtkUniformGrids
(i.e. vtkImageData with blanking) the VTK readers and writers really just
produce vtkImageData and the blanking is ignored. It may be the same with
the XML structured grid files. My suggestion would be to look at the
vtkImageDataToUniformGrid class in VTK and try doing a similar thing in
ParaView using the Python Programmable filter.

Cheers,
Andy

On Tue, Mar 7, 2017 at 10:22 AM, David Doria <daviddo...@gmail.com> wrote:

> On Mon, Mar 6, 2017 at 11:14 AM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> Thanks for the bug report!
>>
>> I think the stackoverflow issue is probably also related to blanking. I
>> added to your bug report with two other (likely) related issues.
>>
>> As a side note, I think if blanking was used instead of ghost cells this
>> may work properly.
>>
>> Thanks,
>> Andy
>>
>> On Mon, Mar 6, 2017 at 8:45 AM, David Doria <daviddo...@gmail.com> wrote:
>>
>>> On Sun, Mar 5, 2017 at 7:05 PM, Andy Bauer <andy.ba...@kitware.com>
>>> wrote:
>>>
>>>> Hi David,
>>>>
>>>> This looks like it has to do with blanking (i.e. in PV 5.2 if I don't
>>>> load the vtkGhostType array it has the proper bounds). Would you mind
>>>> putting in a bug report on Gitlab (https://gitlab.kitware.com/pa
>>>> raview/paraview)?
>>>>
>>>> Thanks,
>>>> Andy
>>>>
>>>
>>> Done:
>>> https://gitlab.kitware.com/paraview/paraview/issues/17244
>>>
>>> Here is another presumed bug that seems to also have to do with
>>> blanking: http://stackoverflow.com/questions/42543340/cell-l
>>> abels-in-selection-display-inspector-dont-work-when-any-cell
>>> s-are-ghosted - not trying to pollute this thread but do you think that
>>> behavior could be helpful to understand the Cell Centers issue?
>>>
>>> Thanks,
>>>
>>> David
>>>
>>
>>
> Hi Andy,
>
> The file was created with something like this:
>
> https://gist.github.com/daviddoria/8bf981aa593b7cefcd9114588e4766db
>
> Does calling
>
> structuredGrid->BlankPoint(0);
>
> not count as "using blanking"? Can you point me to the "right way" to do
> this if this is not the current best practice?
>
> Thanks!
>
> David
>
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Re: [Paraview] CellCenters filter produces non-deterministic result

[Andy Bauer]

Thanks for the bug report!

I think the stackoverflow issue is probably also related to blanking. I
added to your bug report with two other (likely) related issues.

As a side note, I think if blanking was used instead of ghost cells this
may work properly.

Thanks,
Andy

On Mon, Mar 6, 2017 at 8:45 AM, David Doria <daviddo...@gmail.com> wrote:

> On Sun, Mar 5, 2017 at 7:05 PM, Andy Bauer <andy.ba...@kitware.com> wrote:
>
>> Hi David,
>>
>> This looks like it has to do with blanking (i.e. in PV 5.2 if I don't
>> load the vtkGhostType array it has the proper bounds). Would you mind
>> putting in a bug report on Gitlab (https://gitlab.kitware.com/pa
>> raview/paraview)?
>>
>> Thanks,
>> Andy
>>
>
> Done:
> https://gitlab.kitware.com/paraview/paraview/issues/17244
>
> Here is another presumed bug that seems to also have to do with blanking:
> http://stackoverflow.com/questions/42543340/cell-labels-in-
> selection-display-inspector-dont-work-when-any-cells-are-ghosted - not
> trying to pollute this thread but do you think that behavior could be
> helpful to understand the Cell Centers issue?
>
> Thanks,
>
> David
>
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Re: [Paraview] CellCenters filter produces non-deterministic result

[Andy Bauer]

Hi David,

This looks like it has to do with blanking (i.e. in PV 5.2 if I don't load
the vtkGhostType array it has the proper bounds). Would you mind putting in
a bug report on Gitlab (https://gitlab.kitware.com/paraview/paraview)?

Thanks,
Andy

On Sun, Mar 5, 2017 at 11:31 AM, David Doria  wrote:

> With this file
> , when I
> apply a Cell Centers filter sometimes it works (see attached works.jpg) and
> sometimes it produces garbage output (note the Y-range) (see attached
> broken.jpg)
>
> Can anyone explain why this is?
>
> Thanks,
>
> David
>
> (See the same question here for inline images: http://stackoverflow.com/
> questions/42543496/cellcenters-filter-non-deterministic-result)
>
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Re: [Paraview] Query on EGL libs for Paraview 5.0.1

[Andy Bauer]

Hi,

Maybe look in:
 /usr/lib/nvidia-

for the drivers -- that's where  it is for my r367 NVIDIA drivers on Ubuntu
16.04. Otherwise you may need to check with NVIDIA on where it gets
installed for your set of drivers and system.

On Sat, Mar 4, 2017 at 10:19 PM, Bishwajit Dutta  wrote:

> Hi All,
>
> I am trying to compile Paraview 5.0.1 with EGL support as I want to use
> NVIDIA Tesla K20c
> for rendering in Ubuntu 14.04. This is without any windowing system as
> K20c is designed for
> server based rendering (without any VGA port and OpenGL support (I think!))
>
> I went through
>
> https://blog.kitware.com/off-screen-rendering-through-the-
> native-platform-interface-egl/
>
> and as I understand, for this I need to set the below Paraview flags
> before compilation:
>
> VTK_EGL_DEVICE_INDEX=set to graphics driver index
> VTK_USE_OFFSCREEN_EGL =on
> EGL_INCLUDE_DIR
> EGL_LIBRARY /usr/lib/x86_64-linux-gnu/libEGL.so
> EGL_gldispatch_LIBRARY /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0
> EGL_opengl_LIBRARY /usr/lib/x86_64-linux-gnu/libOpenGL.so
>
> My query is on gettting the correct libs i.e. libEGL.so,
> libGLdispatch.so.0 and libOpenGL.so.
>
> When I installed "NVIDIA-Linux-x86_64-375.26.run" these libs were not
> installed.
>
> Which is the right place to get them. I can see several links on internet
> search:
>
> https://github.com/NVIDIA/libglvnd/blob/master/README.md
>
> https://www.mesa3d.org/egl.html
>
> Which is the correct one
>
> Thanks in advance for help.
>
> BR,
> Bishwajit
> Virginia Tech
>
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Re: [Paraview] 3 arguments to _CreatePipeline for Catalyst

[Andy Bauer]

Hi,

Please keep the conversations on the mailing list so that all can
participate.

The best way currently to pass information back and forth between the
adaptor (i.e. C++ code) and the Catalyst pipelines is to use the
vtkCPDataDescription's UserData member which is a vtkFieldData object (
http://www.paraview.org/ParaView/Doc/Nightly/www/cxx-doc/classvtkCPDataDescription.html).
It is Python wrapped so you can access it in the Python scripts as well.

Cheers,
Andy

On Tue, Feb 21, 2017 at 2:54 AM, Lukáš Kresta <lukas.kre...@gmail.com>
wrote:

> Thank you. How can I send that argument from adaptor? (I use C++)
>
> 2017-02-20 16:08 GMT+01:00 Andy Bauer <andy.ba...@kitware.com>:
>
>> Hi,
>>
>> If you edit the coprocessing.py script in the ParaView build/install
>> directory you can do that.
>>
>> Maybe an easier way though is to just create global variable that is used
>> in your _CreatePipeline() method. An example is:
>> from paraview.simple import *
>> from paraview import coprocessing
>>
>> myvalue = 0
>> #--
>> # Code generated from cpstate.py to create the CoProcessor.
>> # ParaView 5.1.2-411-gf717569 64 bits
>>
>>
>> # --- CoProcessor definition ---
>>
>> def CreateCoProcessor():
>>   def _CreatePipeline(coprocessor, datadescription):
>> class Pipeline:
>>   global myvalue
>>   print 'myvalue is ', myvalue
>> ...
>>
>>
>>
>> On Mon, Feb 20, 2017 at 3:26 AM, Lukáš Kresta <lukas.kre...@gmail.com>
>> wrote:
>>
>>> Is somehow possible to send 3. argument to CreatePipeline or it is fixed
>>> to have only 2 arguments?
>>>
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>>>
>>
>
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Re: [Paraview] Different visualization result using serial or parallel ParaView ...

[Andy Bauer]

Hi Stefan,

Thanks for the bug issue report. There is a potential fix in VTK at
https://gitlab.kitware.com/vtk/vtk/merge_requests/2504

I am optimistic that this will  make it into the upcomgin ParaView 5.3
release.

Thanks,
Andy

On Fri, Feb 10, 2017 at 7:35 AM, Stefan Melber  wrote:

> Hi,
>
> amendment: the test case i send to you also crashes using the D31-filter:
>
> Executing with: Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> Executing with: 0
> 0
>
> 
> ===
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 23833 RUNNING AT bsastf670os
> =   EXIT CODE: 139
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> 
> ===
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
> (signal 11)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
> This now looks like a bug ;-)
>
>  Stefan
>
> Stefan,
>
> Attached is a fixed state file. Since the file didn't have ghost-cell
> information, the filters like "Compute Derivatives" didn't produce correct
> result at the process boundary cells. By putting a "Ghost Cell Generator"
> filter in the pipeline, one can address that issue.
>
> Utkarsh
>
> On Thu, Feb 9, 2017 at 8:18 AM, Utkarsh Ayachit <
> utkarsh.ayac...@kitware.com> wrote:
>
>> That's odd. Stefan, can you send me the dataset please? I'll have it
>> looked into.
>>
>> Thanks
>> Utkarsh
>>
>> On Thu, Feb 9, 2017 at 4:04 AM, Stefan Melber 
>> wrote:
>>
>>> Hi,
>>>
>>>
>>> during visualization of vortices i found a bug (or feature?) of
>>> ParaView: running the case in serial mode the results look fine. However,
>>> doing the same in parallel mode (e.g. 8 cores) the picture looks "ugly".
>>> Has anyone seen such an effect running in parallel? I am using the current
>>> version (v5.2.0) on a Linux 64bit machine with a Quadro 4000 graphics card.
>>>
>>> Attached there are two pics showing the effect, a picture of the used
>>> pipeline and the restart file...
>>>
>>> The test-data can be send to you for testing - i just need a
>>> email-address to send it to.
>>>
>>> Best regards,
>>>
>>>  Stefan
>>>
>>>
>>>
>>>
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>>>
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>>>
>>>
>>
>
>
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Re: [Paraview] 3 arguments to _CreatePipeline for Catalyst

[Andy Bauer]

Hi,

If you edit the coprocessing.py script in the ParaView build/install
directory you can do that.

Maybe an easier way though is to just create global variable that is used
in your _CreatePipeline() method. An example is:
from paraview.simple import *
from paraview import coprocessing

myvalue = 0
#--
# Code generated from cpstate.py to create the CoProcessor.
# ParaView 5.1.2-411-gf717569 64 bits


# --- CoProcessor definition ---

def CreateCoProcessor():
  def _CreatePipeline(coprocessor, datadescription):
class Pipeline:
  global myvalue
  print 'myvalue is ', myvalue
...



On Mon, Feb 20, 2017 at 3:26 AM, Lukáš Kresta 
wrote:

> Is somehow possible to send 3. argument to CreatePipeline or it is fixed
> to have only 2 arguments?
>
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Re: [Paraview] Error writing Paraview on MPI

[Andy Bauer]

Hi,

You will need to be more specific about what you are exactly doing. Are you
writing out your data in VTK or ParaView with 32 processes or some other
way?

Can you share your data set? That would help diagnose the issue.

Andy

On Mon, Feb 20, 2017 at 6:27 AM, José Luis López López <
jlopezfis...@ciencias.unam.mx> wrote:

> Hi! All,
>
> I am writing my VTK files through the server in MPI 32 processors. It
> seems that it is not writing right my files, does someone has a clue or how
> to track the bug?
>
> for small domains it seems to work fine,
>
> Jose
>
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Re: [Paraview] issue about deformed and misplaced color bars ...

[Andy Bauer]

Hi Ufuk,

I'm not sure if this fix will make it into the 5.3 release. We'll try but
we have a pretty hard deadline for the release.

As a workaround, while Trace is not capturing the movement the Python state
does. You can use that information to set the desired values in your
Catalyst Python script. The example from my Python state is:
rTDataLUTColorBar = GetScalarBar(rTDataLUT, renderView1)
rTDataLUTColorBar.Position = [0.30443396226415076, 0.7281124807395994]
rTDataLUTColorBar.Position2 = [0.43027, 0.1201]
rTDataLUTColorBar.Orientation = 'Horizontal'
rTDataLUTColorBar.Title = 'RTData'
rTDataLUTColorBar.ComponentTitle = ''
rTDataLUTColorBar.TitleFontSize = 16
rTDataLUTColorBar.LabelBold = 1
rTDataLUTColorBar.LabelItalic = 1
rTDataLUTColorBar.LabelFontSize = 16

Currently there's an issue with the LabelFontSize. I've entered a gitlab
issue at https://gitlab.kitware.com/paraview/paraview/issues/17194

Thanks for checking on this.

Best,
Andy


On Fri, Feb 17, 2017 at 4:39 AM,  wrote:

> Hi,
>
> I was using Catalyst with 5.2 and the color bars are shown as tiny and
> also misplaced when it is compared with ParaView output. I also checked it
> with 5.3RC1 and the issue is still in there. So, is there any plan to fix
> it in 5.3. There ware also discussion about it in the mail list and it
> seems that it is related with following issue but aim not sure.
>
> https://gitlab.kitware.com/paraview/paraview/issues/17113
>
> Regards,
>
> --ufuk
>
>
>
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Re: [Paraview] Automating contour isosurface values in parallel Catalyst Python script

[Andy Bauer]

Glad to hear!

Also, thanks for replying to the list.

On Fri, Feb 17, 2017 at 4:50 AM, <yvan.fourn...@free.fr> wrote:

>
> Hi Andy and Joachim,
>
> I adapted Andy's suggestions, and my script is now both slightly simpler
> (no mpi4py or numpy dependencies) and works on both machines.
>
> PS. I cc'd the ParaView mailing list, since I started this thread on it,
> and forgot "reply to all" in one of my own responses...
>
> Thanks again for the help, and best regards,
>
>   Yvan
>
> - Mail original -
> De: "Andy Bauer" <andy.ba...@kitware.com>
> À: "Yvan Fournier" <yvan.fourn...@free.fr>, "Joachim Pouderoux" <
> joachim.pouder...@kitware.com>
> Envoyé: Jeudi 16 Février 2017 16:15:03
> Objet: Re: [Paraview] Automating contour isosurface values in parallel
> Catalyst Python script
>
>
>
> Hi Yvan,
>
> I inlined some answers below...
>
> Best,
> Andy
>
> ps. I cc'ed Joachim since it looks like you meant to cc him but did not.
>
>
>
>
>
>
>
> On Thu, Feb 16, 2017 at 6:25 AM, < yvan.fourn...@free.fr > wrote:
>
>
> Hi Andy and Joachim,
>
> Thanks for your answers. I suspected I would need a solution of this sort.
>
> I prefer computing the min and max myself rather than adapting a Catalyst
> edition, as I often use full/default ParaView with OSMesa instead of
> Catalyst Editions (I only got a "standard" base + Python + extensions...
> edition working very recently; with older versions of the editions, some
> filter was always missing and I could not use Python scripts generated by
> the Coprocessing Generator plugin).
>
>
>
> I generally just use the full PV version also. It is only when I need to
> be very light on memory that I switch to the Catalyst editions. Others have
> noted that the Catalyst editions are easier to build on HPC systems though
> and prefer that route.
>
>
>
>
> I made good progress, and now have a solution which works with a 1 or
> 2-week-old build from the master branch, using numpy, but does not work on
> a build with ParaView 5.1.2 on an older machine due to missing features:
>
> - "from paraview.vtk.numpy_interface.algorithms import *" fails,
> complaining it does not find numpy and tells me to check it was installed
> properly (it is installed, though might have been installed after the
> ParaView build)
>
>
>
> I do not know about this issue as I have not seen it before and was not
> involved with the integration. Maybe Joachim knows. Otherwise I would
> suggest going back to the PV mailing list.
>
>
>
>
> - using:
> controller = coprocessing.vtkCompositeMultiProcessContro
> ller.GetGlobalController()
> if controller and controller.IsA("vtkMPIController") and 
> controller.GetNumberOfProcesses()
> > 1:
> from mpi4py import MPI
> comm = vtkMPI4PyCommunicator.ConvertToPython(controller.GetCommunicator())
>
>
>
>
> In cases like this I just use:
>
> import vtk
>
> controller = vtk.vtkMultiProcessController.GetGlobalController()
>
> c.AllReduce(, , , vtk.vtkCommunicator.MAX_OP)
>
>
> to get the max values. vtkCommunicator has the named constants for
> operations. The "global" communicator will be the one that Catalyst uses
> which may be a subcommunicator of MPI_COMM_WORLD. I'm not sure if mpi4py
> will be over the Catalyst MPI processes or all of them. Also, you may want
> to try "from paraview import vtk" instead of just "import vtk". Less VTK
> Python stuff should be imported then but it may be missing something you
> want. I don't use vtkMPI4PYCommunicator so I cannot say how well that
> should work for your needs.
>
>
>
>
> I have a "NameError: global name 'vtkMPI4PyCommunicator' is not defined"
> message
>
> In my earlier tests, I tried simply using the AllReduce() method from the
> controller, with vtkArrays, but I was stuck on finding the correct value
> for the last argument, which seems to be an integer describing the
> collective reduction operation (I need min and max). But I was unable to
> find any examples for this in Python, (whether Googling for examples or
> printing dict() and (help() of various Python objects).
> The documentation only specifies some methods may not be available in
> Python...
>
> Are there named constants describing those operations in the Python
> wrappers of vtkMPIController ?
> I assume I could find the integer values in the C++ documentation/sources,
> but I would rather have named constants for readability and in case of
> future changes.
> I guess using the vtkMPIController would slightly simplify the 

Re: [Paraview] volume vs volume

[Andy Bauer]

As a side note, the Mesh Quality filter does not work on all 3D cell types.
I think prisms and pyramids are not supported.

On Wed, Feb 15, 2017 at 9:07 AM, Dennis Conklin  wrote:

> Oops – meant Mesh Quality filter
>
>
>
> *From:* Dennis Conklin
> *Sent:* Wednesday, February 15, 2017 7:56 AM
> *To:* Paraview (paraview@paraview.org) 
> *Subject:* Re: [Paraview] volume vs volume
>
>
>
> Alan,
>
>
>
> A quick and dirty way to get individual element volumes is to use the mesh
> refinement filter and set the Quality measure to volume.   Then the
> “Quality” variable in the elements is actually volume.
>
>
>
> Dennis
>
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Re: [Paraview] One render view on Paraview Catalyst

[Andy Bauer]

Hi,

In the ParaView GUI you can set the Remote Render Threshold (under
Edit->Settings...->Render View) to a very large number to ensure that all
rendered data gets delivered to the client for rendering. In general this
is a bad way to do things though since that can use a lot of bandwidth and
memory.

If you are trying to just have a single render view in Catalyst with a
parallel run, I don't think it's possible to get just a single window. You
either need to have a window for each MPI process or no windows at all. For
no windows at all you will need to use either OSMesa or EGL for offscreen
rendering.

--Andy


On Wed, Feb 15, 2017 at 3:49 AM, Lukáš Kresta 
wrote:

> I generated python script for Catalyst from Paraview. When I run my code
> with MPI, I get render window for every MPI process. But i want to have
> only one window for all MPI processes.
>
> I already tried have script for view only on root and on another only
> script for live visualization (without view), but I still get view for
> every MPI process.
>
> Have someone some idea how to "fix" my problem?
>
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Re: [Paraview] Automating contour isosurface values in parallel Catalyst Python script

[Andy Bauer]

Hi Yvan,

Another option is just to compute it yourself. The reason that the global
min and max aren't know in Catalyst is that it requires communication but
many times the value isn't needed so in order to make Catalyst more
efficient it doesn't compute that value for you automatically. In the
Python scripts you can import mpi4py or import vtk and use the
vtkMultiProcessController to do the global operation. Note that for my way
you'll need to call UpdatePipeline(datadescription.GetTime()) before
getting the output and globally determining the value. Then you can set the
isosurfaces values array with that information.

If you try this out and have issues, please let us know and we can go from
there.

Cheers,
Andy

On Tue, Feb 14, 2017 at 3:02 PM, Joachim Pouderoux <
joachim.pouder...@kitware.com> wrote:

> Hi Yvan,
>
> Regarding MinMax: this filter is indeed not exposed by any standard
> Catalyst edition but it is
> easy to add. See for instance in 
> ParaView/Catalyst/Editions/Extras/manifest.json
> how the
> PVExtractSelection filter is exposed (line 50 and 247).
> Just do the same with the MinMax filter (see proxy's declaration at
> filters.xml:~11725).
>
> Best,
> Joachim
>
>
> *Joachim Pouderoux*, PhD
>
> *Technical Expert - Scientific Computing Team*
> *Kitware SAS *
>
>
> 2017-02-13 17:31 GMT-04:00 Yvan Fournier :
>
>> Hello,
>>
>> I'm in the process of migrating some VTK scripts in the Code_Saturne
>> (code-
>> saturne.org) test suite to Catalyst Python scripts, and am having some
>> difficulty automating some cases using contour plots:
>>
>> For time-dependent data, I do not know the value ranges in advance, and
>> would
>> like to query them so as to build an Isosurface values array spanning that
>> range.
>>
>> I can manage to access the point and cell data arrays and ther ranges, but
>> printing the ranges in parallel, it seems I have local values only, while
>> I need
>> a global range.
>>
>> I searched for examples in the documentation, on the Wiki, ..., and found
>> an
>> example for MinMax, but don't seem to ba able to access the correct type
>> of
>> Proxy under Catalyst (the default servermanager is not connected in the
>> usual
>> way.
>>
>> For scalar bar color look-up tables, I can manage with
>> "coprocessor.WriteImages(datadescription, rescale_lookuptable=True)" in
>> the
>> coprocessing script, but for a more general case such as thar needed for
>> contour
>> plots, I've been running around in circles in the last hours trying to
>> find and
>> adapt a relevant example.
>>
>> Does anyone have a suggestion ? Thanks in advance,
>>
>> Yvan Fournier
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Re: [Paraview] Cataylst pipeline not updating

[Andy Bauer]

Hi Tim,

I'm glad this fixed the issue. You'll want to always pass in the time to
UpdatePipeline() for Catalyst. The issue was that the pipeline thought that
everything it had was current since the time didn't change and none if the
filters' parameters changed and therefore it skipped recomputing what it
thought would be the same result. I do wonder if the start of the pipeline
should mark that it is modified. I'll have to think about that some more.
Even if that were true though you'd still want to pass in the time value to
UpdatePipeline(). This is true as well for ParaView Python pipelines in
general for time dependent sources.

No problem about the delay in reporting -- I was more than happy to let
your computers do the proof rather than verifying it myself :)

Cheers,
Andy

On Tue, Feb 14, 2017 at 11:00 AM, Gallagher, Timothy P <
tim.gallag...@gatech.edu> wrote:

> Hi Andy,
>
>
> Looks like passing the current time step into the UpdatePipeline calls
> made it work as expected. Sorry for the delay in reporting, it took a long
> time for the job to move through the queue!
>
>
> Anyway, looks like it's working properly and I am getting the data as
> expected.
>
>
> For future reference, should I always just pass the time in? Or are the
> possibly other, unintended side effects from that as well to watch out for?
>
>
> Thanks again,
>
>
> Tim
>
>
> --
> *From:* Andy Bauer <andy.ba...@kitware.com>
> *Sent:* Monday, February 13, 2017 11:30 AM
>
> *To:* Gallagher, Timothy P
> *Cc:* paraview@paraview.org
> *Subject:* Re: [Paraview] Cataylst pipeline not updating
>
> Hi Tim,
>
> It's possible that there's something funky going on when the data set
> being passed through parts of the pipeline are empty. I'm hoping for the
> easy fix with passing in the time since I've know that has caused
> unexpected behavior before. If that doesn't solve your issue then I'll
> probably have to do something similar and run it locally to see what's
> going on.
>
> Cheers,
> Andy
>
> On Mon, Feb 13, 2017 at 11:06 AM, Gallagher, Timothy P <
> tim.gallag...@gatech.edu> wrote:
>
>> The RequestDataDescription is the same as the default output from the
>> script generator, so I didn't include it. The DoCoProcessing gets called
>> every time step and the volumeIntegrals data is updated and written
>> correctly every delta_t, so I'm confident in that part.
>>
>>
>> I will add the calls you suggested and re-run. It takes some time for it
>> to evolve to the point something will happen -- I don't have it saving data
>> frequently enough to run a quick test, I was expecting the pipeline to save
>> it for me!
>>
>>
>> The other thing that occurred to me -- is there something about the
>> Contour filter that turns it off/disables it when the pipeline is built and
>> there is no surface at that contour level?
>>
>>
>> Thanks,
>>
>>
>> Tim
>>
>>
>> --
>> *From:* Andy Bauer <andy.ba...@kitware.com>
>> *Sent:* Monday, February 13, 2017 10:56 AM
>> *To:* Gallagher, Timothy P
>> *Cc:* paraview@paraview.org
>> *Subject:* Re: [Paraview] Cataylst pipeline not updating
>>
>> Hi Tim,
>>
>> Try adding in the current time to the UpdatePipeline() calls, e.g.
>> *.UpdatePipeline(datadescription.GetCurrentTime())
>>
>> It's tough to tell with RequestDataDescription() missing but I assume
>> that DoCoProcessing() is getting called when you want, correct?
>>
>> Let me know if that doesn't solve the problem.
>>
>> Best,
>> Andy
>>
>> On Mon, Feb 13, 2017 at 5:45 AM, Gallagher, Timothy P <
>> tim.gallag...@gatech.edu> wrote:
>>
>>> Back with another question!
>>>
>>>
>>> I have a pipeline that has 1 input and 4 outputs. The simplest is a
>>> IntegrateVariables filter hooked up to the input. Another branch of the
>>> pipeline goes through several PythonCalculator filters and a
>>> CellDataToPointData filter and then arrives at the three outputs:
>>>
>>>
>>> 1. The CD2PD filter is connected to a Contour filter with a single
>>> level, X. This is then connected to an IntegrateVariables filter (used to
>>> compute the area of the Contour) and a Writer.
>>>
>>> 2. The CD2PD filter is also connected to another Contour filter with a
>>> single level Y. This is connected to an IntegrateVariables and Writer just
>>> as in 1.
>>>
>>> 3. The CD2PD filter is sliced two times with each slice in a different
>>> ren

Re: [Paraview] Cataylst pipeline not updating

[Andy Bauer]

Hi Tim,

It's possible that there's something funky going on when the data set being
passed through parts of the pipeline are empty. I'm hoping for the easy fix
with passing in the time since I've know that has caused unexpected
behavior before. If that doesn't solve your issue then I'll probably have
to do something similar and run it locally to see what's going on.

Cheers,
Andy

On Mon, Feb 13, 2017 at 11:06 AM, Gallagher, Timothy P <
tim.gallag...@gatech.edu> wrote:

> The RequestDataDescription is the same as the default output from the
> script generator, so I didn't include it. The DoCoProcessing gets called
> every time step and the volumeIntegrals data is updated and written
> correctly every delta_t, so I'm confident in that part.
>
>
> I will add the calls you suggested and re-run. It takes some time for it
> to evolve to the point something will happen -- I don't have it saving data
> frequently enough to run a quick test, I was expecting the pipeline to save
> it for me!
>
>
> The other thing that occurred to me -- is there something about the
> Contour filter that turns it off/disables it when the pipeline is built and
> there is no surface at that contour level?
>
>
> Thanks,
>
>
> Tim
>
>
> --
> *From:* Andy Bauer <andy.ba...@kitware.com>
> *Sent:* Monday, February 13, 2017 10:56 AM
> *To:* Gallagher, Timothy P
> *Cc:* paraview@paraview.org
> *Subject:* Re: [Paraview] Cataylst pipeline not updating
>
> Hi Tim,
>
> Try adding in the current time to the UpdatePipeline() calls, e.g.
> *.UpdatePipeline(datadescription.GetCurrentTime())
>
> It's tough to tell with RequestDataDescription() missing but I assume that
> DoCoProcessing() is getting called when you want, correct?
>
> Let me know if that doesn't solve the problem.
>
> Best,
> Andy
>
> On Mon, Feb 13, 2017 at 5:45 AM, Gallagher, Timothy P <
> tim.gallag...@gatech.edu> wrote:
>
>> Back with another question!
>>
>>
>> I have a pipeline that has 1 input and 4 outputs. The simplest is a
>> IntegrateVariables filter hooked up to the input. Another branch of the
>> pipeline goes through several PythonCalculator filters and a
>> CellDataToPointData filter and then arrives at the three outputs:
>>
>>
>> 1. The CD2PD filter is connected to a Contour filter with a single level,
>> X. This is then connected to an IntegrateVariables filter (used to compute
>> the area of the Contour) and a Writer.
>>
>> 2. The CD2PD filter is also connected to another Contour filter with a
>> single level Y. This is connected to an IntegrateVariables and Writer just
>> as in 1.
>>
>> 3. The CD2PD filter is sliced two times with each slice in a different
>> render view to save images.
>>
>>
>> I have the coprocessor running every delta_t seconds. The initial
>> IntegrateVariables filter is updated with UpdatePipeline and then the
>> values are saved to disk. This works every step, no issues.
>>
>>
>> I then call UpdatePipeline on both of the Contour and both of the
>> IntegrateVariables filters in 1 and 2. I check if the 'Area' field in the
>> IntegrateVariables exceeds a threshold, and if it does, I save the
>> Contour's to disk as a VTK file. This is not working correctly.
>>
>>
>> If I start the simulation from a point where the Contour's exist in the
>> flow already, then everything works great and the Area field changes in
>> time and it saves the Contour's.
>>
>>
>> However, if the simulation starts without the Contours already in the
>> flow, the Area fields stay zero forever. It's as if the pipeline isn't
>> updating or something. I have attached the DoCoProcessing function used. I
>> don't see anything immediately obvious that would prevent it from updating
>> or getting the correct values for the Area.
>>
>>
>> Am I missing something about how the pipeline or contour filters update?
>>
>>
>> Thanks,
>>
>>
>> Tim
>>
>> ___
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>>
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Re: [Paraview] Cataylst pipeline not updating

[Andy Bauer]

Oops, datadescription.GetTime() instead of datadescription.GetCurrentTime().

On Mon, Feb 13, 2017 at 10:56 AM, Andy Bauer <andy.ba...@kitware.com> wrote:

> Hi Tim,
>
> Try adding in the current time to the UpdatePipeline() calls, e.g.
> *.UpdatePipeline(datadescription.GetCurrentTime())
>
> It's tough to tell with RequestDataDescription() missing but I assume that
> DoCoProcessing() is getting called when you want, correct?
>
> Let me know if that doesn't solve the problem.
>
> Best,
> Andy
>
> On Mon, Feb 13, 2017 at 5:45 AM, Gallagher, Timothy P <
> tim.gallag...@gatech.edu> wrote:
>
>> Back with another question!
>>
>>
>> I have a pipeline that has 1 input and 4 outputs. The simplest is a
>> IntegrateVariables filter hooked up to the input. Another branch of the
>> pipeline goes through several PythonCalculator filters and a
>> CellDataToPointData filter and then arrives at the three outputs:
>>
>>
>> 1. The CD2PD filter is connected to a Contour filter with a single level,
>> X. This is then connected to an IntegrateVariables filter (used to compute
>> the area of the Contour) and a Writer.
>>
>> 2. The CD2PD filter is also connected to another Contour filter with a
>> single level Y. This is connected to an IntegrateVariables and Writer just
>> as in 1.
>>
>> 3. The CD2PD filter is sliced two times with each slice in a different
>> render view to save images.
>>
>>
>> I have the coprocessor running every delta_t seconds. The initial
>> IntegrateVariables filter is updated with UpdatePipeline and then the
>> values are saved to disk. This works every step, no issues.
>>
>>
>> I then call UpdatePipeline on both of the Contour and both of the
>> IntegrateVariables filters in 1 and 2. I check if the 'Area' field in the
>> IntegrateVariables exceeds a threshold, and if it does, I save the
>> Contour's to disk as a VTK file. This is not working correctly.
>>
>>
>> If I start the simulation from a point where the Contour's exist in the
>> flow already, then everything works great and the Area field changes in
>> time and it saves the Contour's.
>>
>>
>> However, if the simulation starts without the Contours already in the
>> flow, the Area fields stay zero forever. It's as if the pipeline isn't
>> updating or something. I have attached the DoCoProcessing function used. I
>> don't see anything immediately obvious that would prevent it from updating
>> or getting the correct values for the Area.
>>
>>
>> Am I missing something about how the pipeline or contour filters update?
>>
>>
>> Thanks,
>>
>>
>> Tim
>>
>> ___
>> 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
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
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>>
>>
>
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Re: [Paraview] Cataylst pipeline not updating

[Andy Bauer]

Hi Tim,

Try adding in the current time to the UpdatePipeline() calls, e.g.
*.UpdatePipeline(datadescription.GetCurrentTime())

It's tough to tell with RequestDataDescription() missing but I assume that
DoCoProcessing() is getting called when you want, correct?

Let me know if that doesn't solve the problem.

Best,
Andy

On Mon, Feb 13, 2017 at 5:45 AM, Gallagher, Timothy P <
tim.gallag...@gatech.edu> wrote:

> Back with another question!
>
>
> I have a pipeline that has 1 input and 4 outputs. The simplest is a
> IntegrateVariables filter hooked up to the input. Another branch of the
> pipeline goes through several PythonCalculator filters and a
> CellDataToPointData filter and then arrives at the three outputs:
>
>
> 1. The CD2PD filter is connected to a Contour filter with a single level,
> X. This is then connected to an IntegrateVariables filter (used to compute
> the area of the Contour) and a Writer.
>
> 2. The CD2PD filter is also connected to another Contour filter with a
> single level Y. This is connected to an IntegrateVariables and Writer just
> as in 1.
>
> 3. The CD2PD filter is sliced two times with each slice in a different
> render view to save images.
>
>
> I have the coprocessor running every delta_t seconds. The initial
> IntegrateVariables filter is updated with UpdatePipeline and then the
> values are saved to disk. This works every step, no issues.
>
>
> I then call UpdatePipeline on both of the Contour and both of the
> IntegrateVariables filters in 1 and 2. I check if the 'Area' field in the
> IntegrateVariables exceeds a threshold, and if it does, I save the
> Contour's to disk as a VTK file. This is not working correctly.
>
>
> If I start the simulation from a point where the Contour's exist in the
> flow already, then everything works great and the Area field changes in
> time and it saves the Contour's.
>
>
> However, if the simulation starts without the Contours already in the
> flow, the Area fields stay zero forever. It's as if the pipeline isn't
> updating or something. I have attached the DoCoProcessing function used. I
> don't see anything immediately obvious that would prevent it from updating
> or getting the correct values for the Area.
>
>
> Am I missing something about how the pipeline or contour filters update?
>
>
> Thanks,
>
>
> Tim
>
> ___
> 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
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
___
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Search the list archives at: http://markmail.org/search/?q=ParaView

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