Re: [Paraview] python mismatch with superbuild on os x

[Cory Quammen]

On Wed, Jan 24, 2018 at 12:57 PM, Sgouros, Thomas
 wrote:
> Hello:
>
> I unpacked a version of the Paraview-v5.4.1 tarball, and then did git clone
> of the superbuild right next to it. So I have this:
>
> $ ls
> ParaView-v5.4.1
> paraview-superbuild
> $ mkdir paraview-superbuild-build
> $ cd paraview-superbuild-build
> $ ccmake ../paraview-superbuild
>
> There is a mismatch between the python it wants and the python on my system
> so the configure step will not run and gives this error:
>
>Python interpreter version (2.7.13) does not match the library version
> (2.7.10)
>
> The /usr/bin/python on my system is 2.7.10. What's it complaining about?
> There are other Pythons on my system. I changed my $PATH so /usr/bin is
> first, and deleted the contents of the paraview-superbuild-build directory
> and that seems to have taken care of it.
>
> This doesn't seem like the right solution to me, posting here either to help
> someone else with the same problem, or so that some developer of the
> superbuild can fix this.

I have encountered the same problem with the interpreter version
differing from the library version while having a homebrew Python
installed on my system. Perhaps there is an opportunity for a bug fix
in CMake's FindPythonInterp.cmake and FindPythonLibs.cmake files.

For now, what you have done is a reasonable workaround.

Thanks,
Cory


> Thank you,
>
>  -Tom
>
>
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Re: [Paraview] [Non-DoD Source] Re: Error when trying to turn on Volume Rendering for large tetrahedral data in ParaView 5.4.1

[Hennessey, Joseph G CTR USARMY RDECOM ARL (US)]

Utkarsh,

Thanks, turning on "Use Data Partitions" helped quite a bit.
The rendering is working for me now. I still suspect there
is a bug somewhere, but with "Use Data Partitions" on
I do not seem to be hitting it, and it is renders faster as well.

Thanks,

Joe

~~~
Joseph G. Hennessey Ph.D., SAIC
Team SAIC
Army Research Lab
DOD Supercomputing Resource Center
Aberdeen Proving Ground, MD 21005
Email:  joseph.g.hennessey2@mail.mil


-Original Message-
From: Utkarsh Ayachit [mailto:utkarsh.ayac...@kitware.com]
Sent: Wednesday, January 24, 2018 4:00 PM
To: Hennessey, Joseph G CTR USARMY RDECOM ARL (US) 

Cc: paraview@paraview.org
Subject: [Non-DoD Source] Re: [Paraview] Error when trying to turn on Volume 
Rendering for large tetrahedral data in ParaView 5.4.1

All active links contained in this email were disabled.  Please verify the 
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Joe,

Sorry, doesn't ring a bell. One thing to try is to turn of "Use Data 
Partitions" (see [1]) if your data is already partitioned between ranks such 
that we can build a sorting order.

Utkarsh


[1] Caution-https://blog.kitware.com/improved-parallel-rendering-in-paraview/

On Wed, Jan 24, 2018 at 3:16 PM, Hennessey, Joseph G CTR USARMY RDECOM ARL 
(US)  wrote:
> Hello,
>
> I am experiencing an error with volume rendering very large
> tetrahedral data with ParaView version  5.4.1.
>
> The data is loaded properly and the surface representation works, but
> when I change the representation to Volume, I get the standard dialog
> below to which I respond "Yes"
>
> 'This will change the representation type to "Volume".
> That may take a while, depending on your dataset. Are you sure?'
>
> I am tested this on two of the HPC supercomputer systems while
> connected to a remote server with multiple compute nodes,
> communicating over MPI. I have verified, I am not running out of
> memory  on the compute nodes or on the client but on large data, (over
> 40 million or so tetrahedrons) the compute nodes will crash without
> any error messages and the remote connection will drop, running out of
> memory would cause a similar failure, but as far as I can tell, that
> is not the case here.
>
> I wanted to see if anyone else had hit this problem, before I try
> building debug versions of the software and using a debugger on them,
> to trace the failure down more thoroughly.
>
> The data has 4 vectors and a scalar defined at each tetrahedron, and
> it renders fine with smaller subsets (less than 20 million or so
> tetrahedron). I would like to be able to scale up to a billion
> tetrahedrons eventually, so a 40 million limit is a problem.
>
> I suspect that there might be an issue in
> vtkOpenGLProjectedTetrahedraMapper.cxx
> where some buffer is maybe 32 bit instead of 64 bit, but I have not
> confirmed this.
>
> Has anyone already solved this problem yet?
>
> Thanks,
>
> Joe
>
> ~~~
> Joseph G. Hennessey Ph.D., SAIC
> Team SAIC
> Army Research Lab
> DOD Supercomputing Resource Center
> Email:  joseph.g.hennessey2@mail.mil
>
>
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> Caution-http://www.kitware.com/opensource/opensource.html
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> Please keep messages on-topic and check the ParaView Wiki at:
> Caution-http://paraview.org/Wiki/ParaView
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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 
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 , 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  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
>>
>>
>> ___
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>>
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>> 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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Re: [Paraview] Error when trying to turn on Volume Rendering for large tetrahedral data in ParaView 5.4.1

[Utkarsh Ayachit]

Joe,

Sorry, doesn't ring a bell. One thing to try is to turn of "Use Data
Partitions" (see [1]) if your data is already partitioned between
ranks such that we can build a sorting order.

Utkarsh


[1] https://blog.kitware.com/improved-parallel-rendering-in-paraview/

On Wed, Jan 24, 2018 at 3:16 PM, Hennessey, Joseph G CTR USARMY RDECOM
ARL (US)  wrote:
> Hello,
>
> I am experiencing an error with volume rendering very large
> tetrahedral data with ParaView version  5.4.1.
>
> The data is loaded properly and the surface representation works,
> but when I change the representation to Volume, I get the standard
> dialog below to which I respond "Yes"
>
> 'This will change the representation type to "Volume".
> That may take a while, depending on your dataset. Are you sure?'
>
> I am tested this on two of the HPC supercomputer systems
> while connected to a remote server with multiple compute nodes,
> communicating over MPI. I have verified, I am not running out of memory
>  on the compute nodes or on the client but on large data,
> (over 40 million or so tetrahedrons) the compute nodes will crash
> without any error messages and the remote connection will drop,
> running out of memory would cause a similar failure, but as far as
> I can tell, that is not the case here.
>
> I wanted to see if anyone else had hit this problem, before I try building
> debug versions of the software and using a debugger on them,
> to trace the failure down more thoroughly.
>
> The data has 4 vectors and a scalar defined at each tetrahedron,
> and it renders fine with smaller subsets (less than 20 million
> or so tetrahedron). I would like to be able to scale up to a billion
> tetrahedrons eventually, so a 40 million limit is a problem.
>
> I suspect that there might be an issue in
> vtkOpenGLProjectedTetrahedraMapper.cxx
> where some buffer is maybe 32 bit instead of 64 bit,
> but I have not confirmed this.
>
> Has anyone already solved this problem yet?
>
> Thanks,
>
> Joe
>
> ~~~
> Joseph G. Hennessey Ph.D., SAIC
> Team SAIC
> Army Research Lab
> DOD Supercomputing Resource Center
> Email:  joseph.g.hennessey2@mail.mil
>
>
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[Paraview] Error when trying to turn on Volume Rendering for large tetrahedral data in ParaView 5.4.1

[Hennessey, Joseph G CTR USARMY RDECOM ARL (US)]

Hello,

I am experiencing an error with volume rendering very large
tetrahedral data with ParaView version  5.4.1.

The data is loaded properly and the surface representation works,
but when I change the representation to Volume, I get the standard 
dialog below to which I respond "Yes" 

'This will change the representation type to "Volume".
That may take a while, depending on your dataset. Are you sure?'

I am tested this on two of the HPC supercomputer systems
while connected to a remote server with multiple compute nodes,
communicating over MPI. I have verified, I am not running out of memory
 on the compute nodes or on the client but on large data,
(over 40 million or so tetrahedrons) the compute nodes will crash
without any error messages and the remote connection will drop,
running out of memory would cause a similar failure, but as far as
I can tell, that is not the case here.

I wanted to see if anyone else had hit this problem, before I try building 
debug versions of the software and using a debugger on them,
to trace the failure down more thoroughly.

The data has 4 vectors and a scalar defined at each tetrahedron,
and it renders fine with smaller subsets (less than 20 million
or so tetrahedron). I would like to be able to scale up to a billion
tetrahedrons eventually, so a 40 million limit is a problem.

I suspect that there might be an issue in 
vtkOpenGLProjectedTetrahedraMapper.cxx
where some buffer is maybe 32 bit instead of 64 bit,
but I have not confirmed this.

Has anyone already solved this problem yet?

Thanks,

Joe

~~~
Joseph G. Hennessey Ph.D., SAIC
Team SAIC
Army Research Lab
DOD Supercomputing Resource Center
Email:  joseph.g.hennessey2@mail.mil



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[Paraview] python mismatch with superbuild on os x

[Sgouros, Thomas]

Hello:

I unpacked a version of the Paraview-v5.4.1 tarball, and then did git clone
of the superbuild right next to it. So I have this:

$ ls
ParaView-v5.4.1
paraview-superbuild
$ mkdir paraview-superbuild-build
$ cd paraview-superbuild-build
$ ccmake ../paraview-superbuild

There is a mismatch between the python it wants and the python on my system
so the configure step will not run and gives this error:

   Python interpreter version (2.7.13) does not match the library
version (2.7.10)

The /usr/bin/python on my system is 2.7.10. What's it complaining about?
There are other Pythons on my system. I changed my $PATH so /usr/bin is
first, and deleted the contents of the paraview-superbuild-build directory
and that seems to have taken care of it.

This doesn't seem like the right solution to me, posting here either to
help someone else with the same problem, or so that some developer of the
superbuild can fix this.

Thank you,

 -Tom
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Re: [Paraview] XDMF file with multiple temporal collections

[Nicolas Cedilnik]

Hello

It's been a while but I'm back to trying to solve this issue. 
Unfortunately this doesn't solve the issue. Using paraview 5.4.1 from 
latest Fedora…


Anything else I should try ?

-- Nicolas


On 11/20/2017 10:46 PM, David E DeMarle wrote:
Try dropping your standalone external geometry and topology and just 
place them in the first timestep's grid. It might make the reader happier.

Like so...

http://www.w3.org/2001/XInclude; Version="3.3">
  
    Name="Collection">

      
        
        
          Precision="4">0 0 0 1 0 0 0 1 0 1 1 0 0 0 1 1 0 1 0 1 1 1 1 1

        
        
          Precision="8">9 0 1 3 2 4 5 7 6

        
        
          Precision="8">0 0 0 0 0 0 0 0

        
        ...
      
      
        
         
         

        
        ...


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Re: [Paraview] Reading group of pvti files: vtkImageData is static over time

[Cory Quammen]

Hi Ahmad,

Please see Mathieu Westphal's comment on the issue you created.

Thanks,
Cory

On Wed, Jan 24, 2018 at 9:02 AM, Ahmad .  wrote:
> Hello again,
>
>
> Could someone please confirm this to be a bug, or otherwise tell me how it
> could be resolved?
>
>
> The problem is that my vtkImageData object changes in size over time, but
> visually it stays the same when I import it in ParaView as a group and play
> it as an animation.
>
> Please see https://gitlab.kitware.com/paraview/paraview/issues/17732 for a
> reproducer and a screenshot of the problem.
>
>
> Best,
> Ahmad
>
>
> 
> Van: Ahmad . 
> Verzonden: dinsdag 9 januari 2018 14:30
>
> Aan: paraview@paraview.org
> Onderwerp: Re: Reading group of pvti files: vtkImageData is static over time
>
>
> Sorry wrong link in my last e-mail. This is the correct one:
> https://gitlab.kitware.com/paraview/paraview/issues/17732
>
>
> 
> Van: Ahmad . 
> Verzonden: dinsdag 9 januari 2018 14:27
> Aan: paraview@paraview.org
> Onderwerp: Re: Reading group of pvti files: vtkImageData is static over time
>
>
> Was about to create a new question about this, but I remembered I had asked
> it already a few months back ;-)
>
> However I didn't receive a reply unfortunately.
>
>
> Does anyone have a clue? I also opened an issue about this on gitlab:
> https://gitlab.kitware.com/paraview/paraview/issues/17698
>
> There are also the files that demonstrate the issue.
>
>
> Cheers!
>
>
> 
> Van: A . 
> Verzonden: donderdag 14 september 2017 17:41
> Aan: paraview@paraview.org
> Onderwerp: Reading group of pvti files: vtkImageData is static over time
>
>
> Hello,
>
>
> I have a vtkImageData object that I write (with a XMLPImageDataWriter) every
> time step to a pvti file.
>
> When I open the group of output_*.pvti files, properties like X, Y, Z extent
> and range do not change as I animate over time.
>
> But when I open the actual files I can see that these values in fact are
> different.
>
>
> And if I open the files individually (for example output_99.pvti) these
> properties are displayed correctly in ParaView.
>
> The problem appears when I open them as a group; it then keeps the
> properties of the first file.
>
>
> Does anyone else has this issue, and is there a way to solve this?
>
>
> Best,
>
> Ahmad
>
>
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Staff R Engineer
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Re: [Paraview] Extracting data on the surface of a block?

[Utkarsh Ayachit]

Louis,

Can you also attach a state file for the vis you're generating
currently, so I get a starting point? I am not sure which block is the
oil drop.

Thanks,
Utkarsh

On Tue, Jan 23, 2018 at 8:12 PM, Steytler, Louis Louw
 wrote:
> Hi Utkarsh,
>
> My data file is rather large, but here is a link to the data:
>
> https://uofi.box.com/s/u4hpipt8kbo0u3oxhz92xeya75kzf6kd
>
> Please let me know if this is too large and I can try to send a smaller 
> version.
>
> I have been using "save data". It seems I have data sets under the "Composite 
> Data Set Index" list in the PlotOnIntersection pipeline.
>
> How is "Chart View" selected again? I didn't find it in the "View" drop down 
> menu at the top, but I was able to open a new layout and select 
> "SpreadSheetView".
>
> Thanks again,
>
> Louis Steytler
> Department of Mechanical Science and Engineering
> University of Illinois at Urbana-Champaign
> 1206 West Green Street
> Urbana, Il 61801
> steyt...@illinois.edu
> 
> From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
> Sent: 23 January 2018 09:32 AM
> To: Steytler, Louis Louw
> Cc: paraview@paraview.org
> Subject: Re: [Paraview] Extracting data on the surface of a block?
>
> By "Export View", I meant "Export Scene" under the "File" menu.
>
> On Tue, Jan 23, 2018 at 10:31 AM, Utkarsh Ayachit
>  wrote:
>> Louis,
>>
>>> This seemed to produce reasonable looking results, but I was not able to
>>> specify the number of points along the arc where data was extracted.
>>
>> PlotOnIntersectionCurves essentially slices the dataset using a
>> implicit plane. The points you get are indeed the insection points
>> between your polydata and the plane and hence there's no control over
>> how many points there can be, besides what's determined by your mesh.
>>
>> If you can share the sample data (feel free to do it off the list,if
>> you'd like), I can see what other options may work.
>>
>>>Also,  upon saving, three files were produced file0.csv, file1.csv, 
>>>file2.csv, and
>>> file3.csv. Not sure why I am not getting just one file?
>>
>> Are you using "save data"? I'd suggest selecting the "Chart View" and
>> then using "Export View" option to export the curves. That will give
>> you a since CSV for the fields you've selected.
>>
>> Utkarsh
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Re: [Paraview] Extracting data on the surface of a block?

[Utkarsh Ayachit]

> How is "Chart View" selected again? I didn't find it in the "View" drop down 
> menu at the top, but I was able to open a new layout and select 
> "SpreadSheetView".

By selecting the "Chart View", I meant simply click on the view that's
showing the plots after you applied the "PlotOnIntersectionCurves"
filter. That will activate the view. Now, when you choose File |
Export View, you'll export the contents of the selected view.

Utkarsh
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Re: [Paraview] Reading group of pvti files: vtkImageData is static over time

[Ahmad .]

Hello again,


Could someone please confirm this to be a bug, or otherwise tell me how it 
could be resolved?


The problem is that my vtkImageData object changes in size over time, but 
visually it stays the same when I import it in ParaView as a group and play it 
as an animation.

Please see https://gitlab.kitware.com/paraview/paraview/issues/17732 for a 
reproducer and a screenshot of the problem.


Best,
Ahmad


Van: Ahmad . 
Verzonden: dinsdag 9 januari 2018 14:30
Aan: paraview@paraview.org
Onderwerp: Re: Reading group of pvti files: vtkImageData is static over time


Sorry wrong link in my last e-mail. This is the correct one: 
https://gitlab.kitware.com/paraview/paraview/issues/17732


Van: Ahmad . 
Verzonden: dinsdag 9 januari 2018 14:27
Aan: paraview@paraview.org
Onderwerp: Re: Reading group of pvti files: vtkImageData is static over time


Was about to create a new question about this, but I remembered I had asked it 
already a few months back ;-)

However I didn't receive a reply unfortunately.


Does anyone have a clue? I also opened an issue about this on gitlab: 
https://gitlab.kitware.com/paraview/paraview/issues/17698

There are also the files that demonstrate the issue.


Cheers!


Van: A . 
Verzonden: donderdag 14 september 2017 17:41
Aan: paraview@paraview.org
Onderwerp: Reading group of pvti files: vtkImageData is static over time


Hello,


I have a vtkImageData object that I write (with a XMLPImageDataWriter) every 
time step to a pvti file.

When I open the group of output_*.pvti files, properties like X, Y, Z extent 
and range do not change as I animate over time.

But when I open the actual files I can see that these values in fact are 
different.


And if I open the files individually (for example output_99.pvti) these 
properties are displayed correctly in ParaView.

The problem appears when I open them as a group; it then keeps the properties 
of the first file.


Does anyone else has this issue, and is there a way to solve this?


Best,

Ahmad
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