[Paraview] deforming sphere-like grid to object

[Christopher Snyder]

Hi all,


Here's what I'd like to do using python scripting.
1) Initialize a set of points and edges that "look like a sphere" using
sphere=Sphere()
2) deform that set of points (and edges) to match a volume whose high
intensity region is also blob-like using an active shape model
3) visualize the evolution of the sphere deformation using paraview.

I only tell you so you can stop me if I'm doing this in a suboptimal way.

My immediate question is simply how can I extract/change the coordinates of
a Sphere() object? Are the points of a "sphere" object constrainted to
forever occupy a sphere shape?

Best,
Chris
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[Paraview] SWKey: Definitions of 'Q-Criterion' and the calculator's mag(*) operator?

[Samuel Key]

  
  
Reference: ParaView Version 4.3.1

I have two technical questions:

(1) In the PV filter 'Gradient Of Unstructured Data Set' is the
"QCriterion" function, the Q-Criterion defined by G. Haller in "An
  objective definition of a vortex," J. Fluid Mech. (2005), vol.
525, pp.1–26?

(2) In the PV filter 'Calculator' what is  the formula used by the
"mag" function to calculate mag(S) where S is a
symmetric 2nd-order tensor? Using matrix notation, the tensor S
would have the following components:

---
| Sxx Sxy Sxz |
| Sxy Syy Syz |
| Sxz Syz Szz |
---

Thanks in advance for the bother,

Samuel W Key
FMA Development, LLC
1005 39th Ave NE
Great Falls, Montana 59404
USA
  

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Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

[srikanth.nagella]

Hi Utkarsh,

Thanks for your reply. I did try using Texture Only and got the same result. 
with paraview 4.3.1 I have done some debugging to see at which point the volume 
rendering fails. On a single machine on k40 with 12GB memory any size above 
2048x1024x1024 float value it fails. When i distribute this across two nodes 
with k40, i can see the data is loaded into the graphic memory but there is no 
display output.

Thanks
Sri

From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
Sent: 20 May 2015 16:33
To: Nagella, Srikanth (STFC,RAL,SC)
Cc: ParaView
Subject: Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

That's odd. Have you tried changing the "Volume Mapper" on the
Properties panel? Try switching between "Texture Only" and "GPU
based".

On Tue, Apr 14, 2015 at 4:07 AM,   wrote:
> Hi
>
>
>
> I am using Paraview 4.1.0 to render a 2k volume using two linux nodes and
> client on windows 7. In slice mode I can see the data but when I switch to
> volume mode it disappears. In the same configuration if I load a 512x512x512
> volume, volume mode rendering is fine.
>
>
>
> Can anyone please help?
>
>
>
> Thanks
>
> Sri
>
> PS: each linux node have 2 x NVIDIA K40 card and 64GB RAM, on client I have
> switched on the Remote Render Threshold and set the value to 0Mbytes.
>
>
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Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

[srikanth.nagella]

Utkarsh,

That would be perfect. 

Thanks
Sri

From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
Sent: 20 May 2015 17:05
To: Nagella, Srikanth (STFC,RAL,SC)
Cc: ParaView
Subject: Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

Sri,

The volume rendering code is being reimplemented. Let's wait to see
how that fares. If you don't mind experimenting, I can ping you once
ParaView git/master has the code ready for experimentation.

Utkarsh

On Wed, May 20, 2015 at 12:02 PM,   wrote:
> Hi Utkarsh,
>
> Thanks for your reply. I did try using Texture Only and got the same result. 
> with paraview 4.3.1 I have done some debugging to see at which point the 
> volume rendering fails. On a single machine on k40 with 12GB memory any size 
> above 2048x1024x1024 float value it fails. When i distribute this across two 
> nodes with k40, i can see the data is loaded into the graphic memory but 
> there is no display output.
>
> Thanks
> Sri
> 
> From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
> Sent: 20 May 2015 16:33
> To: Nagella, Srikanth (STFC,RAL,SC)
> Cc: ParaView
> Subject: Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver
>
> That's odd. Have you tried changing the "Volume Mapper" on the
> Properties panel? Try switching between "Texture Only" and "GPU
> based".
>
> On Tue, Apr 14, 2015 at 4:07 AM,   wrote:
>> Hi
>>
>>
>>
>> I am using Paraview 4.1.0 to render a 2k volume using two linux nodes and
>> client on windows 7. In slice mode I can see the data but when I switch to
>> volume mode it disappears. In the same configuration if I load a 512x512x512
>> volume, volume mode rendering is fine.
>>
>>
>>
>> Can anyone please help?
>>
>>
>>
>> Thanks
>>
>> Sri
>>
>> PS: each linux node have 2 x NVIDIA K40 card and 64GB RAM, on client I have
>> switched on the Remote Render Threshold and set the value to 0Mbytes.
>>
>>
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Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

[Utkarsh Ayachit]

Sri,

The volume rendering code is being reimplemented. Let's wait to see
how that fares. If you don't mind experimenting, I can ping you once
ParaView git/master has the code ready for experimentation.

Utkarsh

On Wed, May 20, 2015 at 12:02 PM,   wrote:
> Hi Utkarsh,
>
> Thanks for your reply. I did try using Texture Only and got the same result. 
> with paraview 4.3.1 I have done some debugging to see at which point the 
> volume rendering fails. On a single machine on k40 with 12GB memory any size 
> above 2048x1024x1024 float value it fails. When i distribute this across two 
> nodes with k40, i can see the data is loaded into the graphic memory but 
> there is no display output.
>
> Thanks
> Sri
> 
> From: Utkarsh Ayachit [utkarsh.ayac...@kitware.com]
> Sent: 20 May 2015 16:33
> To: Nagella, Srikanth (STFC,RAL,SC)
> Cc: ParaView
> Subject: Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver
>
> That's odd. Have you tried changing the "Volume Mapper" on the
> Properties panel? Try switching between "Texture Only" and "GPU
> based".
>
> On Tue, Apr 14, 2015 at 4:07 AM,   wrote:
>> Hi
>>
>>
>>
>> I am using Paraview 4.1.0 to render a 2k volume using two linux nodes and
>> client on windows 7. In slice mode I can see the data but when I switch to
>> volume mode it disappears. In the same configuration if I load a 512x512x512
>> volume, volume mode rendering is fine.
>>
>>
>>
>> Can anyone please help?
>>
>>
>>
>> Thanks
>>
>> Sri
>>
>> PS: each linux node have 2 x NVIDIA K40 card and 64GB RAM, on client I have
>> switched on the Remote Render Threshold and set the value to 0Mbytes.
>>
>>
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>>
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>> http://paraview.org/Wiki/ParaView
>>
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>>
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Re: [Paraview] 2k x 2k x 2k volume rendering using pvserver

[Utkarsh Ayachit]

That's odd. Have you tried changing the "Volume Mapper" on the
Properties panel? Try switching between "Texture Only" and "GPU
based".

On Tue, Apr 14, 2015 at 4:07 AM,   wrote:
> Hi
>
>
>
> I am using Paraview 4.1.0 to render a 2k volume using two linux nodes and
> client on windows 7. In slice mode I can see the data but when I switch to
> volume mode it disappears. In the same configuration if I load a 512x512x512
> volume, volume mode rendering is fine.
>
>
>
> Can anyone please help?
>
>
>
> Thanks
>
> Sri
>
> PS: each linux node have 2 x NVIDIA K40 card and 64GB RAM, on client I have
> switched on the Remote Render Threshold and set the value to 0Mbytes.
>
>
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Re: [Paraview] Loading RAW file

[Utkarsh Ayachit]

This was indeed a bug. See http://www.paraview.org/Bug/view.php?id=15457.

The fix for this is here:
https://gitlab.kitware.com/paraview/paraview/merge_requests/92

Utkarsh

On Wed, Apr 15, 2015 at 7:50 AM,   wrote:
> Hi
>
>
>
> I am using Paraview 4.3.1 in client server mode. After loading RAW file,
> when I switch the mode to slice it throws up these errors and renders half
> of the slice.
>
> ERROR:
> ParaView-v4.3.1-source/VTK/Common/ExecutionModel/vtkStreamingDemandDrivenPipeline.cxx,
> line 857
>
> vtkStreamingDemandDrivenPipeline (0x4e96c70): The update extent specified in
> the information for output port 0 on algorithm vtkTrivialProducer(0x4e965e0)
> is 0 511 0 511 228 228, which is outside the whole extent 0 511 0 255 0 456.
>
>
>
>
>
> ERROR: In
> ParaView-v4.3.1-source/VTK/Common/ExecutionModel/vtkTrivialProducer.cxx,
> line 279
>
> vtkTrivialProducer (0x4e965e0): This data object does not contain the
> requested extent.
>
>
>
> Any solutions?
>
>
>
> Thanks
>
> Sri
>
>
>
>
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Re: [Paraview] Paraview Parallel Data

[Utkarsh Ayachit]

You can use the D3 filter to redistribute the data once its opened in
ParaView that's running in parallel.

On Sun, Apr 26, 2015 at 11:12 PM, 周恒众  wrote:
> Dear:
> I want to do some test to know where the paraview do the data
> distribution and how to controll it.But when I use ply data to do the test
> ,I found that it didn't do data distribution .So I want to get some paraview
> data like in
> http://www.paraview.org/Wiki/ParaView/ParaView_Readers_and_Parallel_Data_Distribution
> .who have some datas like that ? Can you give it to me ?Thank you!
>
> Sincerely
>
> zhou
>
>
>
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Nenad Vujicic]

Utkarsh,

You are right, view is really NULL!! Ok, when I catch signals fired
I'll wait appropriate view is created and then they creating
representation.

Thanks!

On Wed, May 20, 2015 at 5:12 PM, Utkarsh Ayachit
 wrote:
> Step into "createDataRepresentation" in a debugger. You'll see one of
> the arguments is NULL. I suspect its the view. The view isn't setup
> yet. Try making the slot connection to a queued connection that way
> ParaView gets the change to setup the representation object.
>
> On Wed, May 20, 2015 at 11:07 AM, Nenad Vujicic  wrote:
>> Utkarsh,
>>
>> Thank you very much for help, but, it still doesn't work. At Ln 118 it
>> fails and reports in Output Window 'Missing required attribute.' and
>> returns NULL.
>>
>> Thanks for any help!
>>
>> Nenad.
>>
>> On Wed, May 20, 2015 at 4:10 PM, Utkarsh Ayachit
>>  wrote:
 I want to say DataRepresentationCreated is never called! When I create
 instance of my pipeline source with this source code, I get only 3
 messages: "Source Created", and 2 times "Representation Added" after
 pushing Apply button.
>>>
>>> Ah ok. That's because pqObjectBuilder no longer creates the standard
>>> representations for ParaView. A better signal to observe is
>>> pqServerManagerModel::representationAdded(). You're already observer
>>> sourceAdded from the ServerManagerModel. You'll need to qobject_cast<>
>>> to pqDataRepresentation* in your slot, for same effect as before.
>>>
>>> Utkarsh
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Re: [Paraview] error when connecting to pvserver

[Utkarsh Ayachit]

The client and server processes both print out a message with the
handshake strings they compared with. Mind posting both of them?

Thanks

On Sun, Apr 26, 2015 at 8:54 AM,   wrote:
> Hi,
>
> I am trying to connect Paraview server (pvserver) to test the Paraview
> Catalyst example codes from GitHub account. So, i installed Paraview from
> source (under Centos 7.0) without any problem and then test code. The
> problem is that i am getting following error messages when i try to run
> the example,
>
> ERROR: In
> /opt/progs/paraview-4.3.1/src/ParaViewCore/ClientServerCore/Core/vtkTCPNetworkAccessManager.cxx,
> line 424
> vtkTCPNetworkAccessManager (0x1063f00):
> **
> Connection failed during handshake. This can happen for the following
> reasons:
>  1. Connection dropped during the handshake.
>  2. vtkSocketCommunicator::GetVersion() returns different values on the
> two connecting processes (Current value: 100).
>  3. ParaView handshake strings are different on the two connecting
> processes (Current value: paraview.4.3).
> **
>
> In this case, both server and client are using same Paraview installation
> and i disabled both firewall and selinux to eliminate the possible error
> sources that might cause the problem. The server is also started using
> following command,
>
> [turuncu@epsilon-lnx CFullExample2]$ pvserver --server-port=2
> Waiting for client...
> Connection URL: cs://epsilon-lnx:2
> Accepting connection(s): epsilon-lnx:2
>
> and the client code is running as follows,
>
> [turuncu@epsilon-lnx CFullExample2]$ ./CFullExample2
> SampleScripts/feslicescript.py
>
> I enabled live visualization by setting it True and proper server address
> and the port in the Python coprocessor code. I also tried to connect
> server from another machine directly using Paraview and it is working. At
> this point, i just need help to find the problem.
> Best Regards,
>
> --ufuk
>
>
>
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Re: [Paraview] Question about programmable data source

[Utkarsh Ayachit]

You have "Auto Apply" enabled. Hence the APply is happening before you
are able to change the output data type. Disable "Auto Apply" and then
create the Programmable Source. The data type must be set before the
first apply.

Utkarsh

On Wed, May 13, 2015 at 2:38 PM, Wu, James  wrote:
> Hi David
>
>
>
> After remove executive.SetExtentTranslator(outInfo,
> vtk.vtkExtentTranslator()), not the points are rendered.
>
> Why there is no “volume” option available for Representation?
>
>
>
> I want to render as volume
>
>
>
> Thanks,
>
> James
>
>
>
> From: David E DeMarle [mailto:dave.dema...@kitware.com]
> Sent: Wednesday, May 13, 2015 10:52 AM
> To: Wu, James
> Cc: paraview@paraview.org
> Subject: Re: [Paraview] Question about programmable data source
>
>
>
> You have to provide the whole extent in the request information pass.
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
>
>
> On Wed, May 13, 2015 at 1:19 PM, Wu, James  wrote:
>
> I add a programmable data source using vtkImageData. The following is the
> script.
> There is nothing displayed after click "Apply". I am new user to paraview.
> Can any point me what's wrong with the script?
>
> Thanks,
> James
>
> dim = 10
> pdo = self.GetImageDataOutput()
> pdo.SetDimensions(dim, dim, dim)
> pdo.SetOrigin(0, 0, 0)
> pdo.SetSpacing(1, 1, 1)
> pdo.SetExtent(0, dim - 1, 0, dim - 1, 0, dim - 1)
> pdo.AllocateScalars(vtk.VTK_FLOAT, 1)
>
> for x in range(0, dim):
> for y in range(0, dim):
> for z in range(0, dim):
> pdo.SetScalarComponentFromFloat(x, y, z, 0, 0.2)
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Utkarsh Ayachit]

Step into "createDataRepresentation" in a debugger. You'll see one of
the arguments is NULL. I suspect its the view. The view isn't setup
yet. Try making the slot connection to a queued connection that way
ParaView gets the change to setup the representation object.

On Wed, May 20, 2015 at 11:07 AM, Nenad Vujicic  wrote:
> Utkarsh,
>
> Thank you very much for help, but, it still doesn't work. At Ln 118 it
> fails and reports in Output Window 'Missing required attribute.' and
> returns NULL.
>
> Thanks for any help!
>
> Nenad.
>
> On Wed, May 20, 2015 at 4:10 PM, Utkarsh Ayachit
>  wrote:
>>> I want to say DataRepresentationCreated is never called! When I create
>>> instance of my pipeline source with this source code, I get only 3
>>> messages: "Source Created", and 2 times "Representation Added" after
>>> pushing Apply button.
>>
>> Ah ok. That's because pqObjectBuilder no longer creates the standard
>> representations for ParaView. A better signal to observe is
>> pqServerManagerModel::representationAdded(). You're already observer
>> sourceAdded from the ServerManagerModel. You'll need to qobject_cast<>
>> to pqDataRepresentation* in your slot, for same effect as before.
>>
>> Utkarsh
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Re: [Paraview] Saving Stereo Files - Eye Separation Control

[Utkarsh Ayachit]

It's not exposed in the UI, but I believe you can use the Python shell
as follows:

> c = GetActiveCamera()
> c.SetEyeSeparation(...)
> Render()



On Wed, May 13, 2015 at 4:51 PM, Rinehart, Richard D. (GRC-VG00)[DB
Consulting Group, Inc.]  wrote:
> Greetings!
>
> Is there a stereo file saving eye separation control for the binary Win
> version?  Poking around but seems as not with the prebuilt version.
>
> -rich
>
>
>
>
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Re: [Paraview] Question about paraview

[Utkarsh Ayachit]

Here's a snippet that demonstrates how one can do this.

https://gitlab.kitware.com/paraview/paraview/snippets/2

Utkarsh

On Wed, May 13, 2015 at 6:47 PM, Wu, James  wrote:
> I want to run a python scrip when user click on a data source in Pipeline 
> Browser.
> Can anyone tell me how to do this?
>
> Thanks,
> James
>
>
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Re: [Paraview] [paraview] out of memory

[Utkarsh Ayachit]

Not sure what exactly are you seeing. If you have a sample dataset to
share, that'll make it easier.

Thanks
Utkarsh

On Wed, May 20, 2015 at 10:32 AM, dxy  wrote:
> Thanks for your reply. I tried as you said, it doesn't work. I use a
> computer of 16G of memory, it can render out. Then I use 538 ply files, they
> are 11.9MB altogether, but when renderd, it will use 6G memory, either the
> display lists turned on or off. Why it is this?
> Thanks for your help.
>
> dxy
>
> At 2015-05-20 20:22:42, "Utkarsh Ayachit" 
> wrote:
>>Try turning of display lists. In ParaView4.1 it was setting named
>>"Immediate mode rendering" under the Settings dialog. You'll need to
>>enable the checkbox.
>>
>>Utkarsh
>>
>>On Wed, May 20, 2015 at 4:34 AM, 丁晓燕  wrote:
>>> Dear,
>>> I use the paraview of Version4.1, and the memory of my computer
>>> is
>>> 4G. When I load about 190 ply files at the same time, there will be
>>> errors
>>> about out of memory, but it runs normally when the number of the file is
>>> less than 190.
>>>
>>> The error message as shown below:
>>> ERROR: In
>>>
>>> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLCoincidentTopologyResolutionPainter.cxx,
>>> line 176
>>> vtkOpenGLCoincidentTopologyResolutionPainter (7A9A9938): failed after
>>> RenderShiftZBuffer 1 OpenGL errors detected
>>>   0 : (1285) Out of memory
>>> ERROR: In
>>>
>>> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLDisplayListPainter.cxx,
>>> line 188
>>> vtkOpenGLDisplayListPainter (7AAE3358): failed after RenderInternal 1
>>> OpenGL
>>> errors detected
>>>   0 : (1285) Out of memory
>>>
>>> Thanks for your help.
>>> Yours truly,
>>> dxy
>>>
>
>
>
>
>
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Re: [Paraview] Rescale to data range on a field's component in python in Paraview 4.3.1

[Utkarsh Ayachit]

Good point. If I remember correctly, the 4.2 code worked only when
doing the same through Python shell in the UI, not from
pvpython/pvbatch, is that correct?

Here's what you can do for 4.3 case:

lookup_table = GetColorTransferFunction('SIGM')

#change array component used for coloring
id_comp = 2
lookup_table.VectorComponent = id_comp
lookup_table.VectorMode = 'Component'

repr = (the display-properties/repr object from which to get the data ranges).
repr.RescaleTransferFunctionToDataRange()
lookup_table.UpdateScalarBarsComponentTitle(repr.GetArrayInformationForColorArray())

Looking at this, it may make sense to add a new API to the repr to
SetScalarColoring with ability to change the component mode.

Utkarsh


On Mon, May 18, 2015 at 9:31 AM, Christophe Bourcier
 wrote:
> Hi,
>
> In 4.2.0, the following code was enough to display a field's component
> instead of its magnitude and set the right scalar bar:
>
> lookup_table = GetColorTransferFunction('SIGM')
>
> #change array component used for coloring
> id_comp = 2
> lookup_table.VectorComponent = id_comp
> lookup_table.VectorMode = 'Component'
>
>
> In 4.3.1, we have to explicitly get the min and max of the field and
> change the scalar bar name:
>
> # Update the scalar bar range
> source_array = stress.PointData.GetArray("SIGM")
> comp_name = source_array.GetComponentName(id_comp)
> mini, maxi = source_array.GetComponentRange(id_comp)
> lookup_table.RGBPoints = [mini, r, g, b, maxi, r2, g2, b2]
>
> # Update the scalar bar name
> ScalarBar1 = GetScalarBar(lookup_table)
> SetProperties(ScalarBar1, ComponentTitle=comp_name)
>
> Is this a bug, or am I missing something?
>
> In attachment, a script to load in Paraview 4.2.0 and 4.3.1. The
> sample file can be downloaded here: http://bourcier.eu/stress.vtu
>
> Thanks.
>
> Christophe
>
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Re: [Paraview] [paraview] out of memory

[dxy]

Thanks for your reply. I tried as you said, it doesn't work. I use a computer 
of 16G of memory, it can render out. Then I use 538 ply files, they are 11.9MB 
altogether, but when renderd, it will use 6G memory, either the display lists 
turned on or off. Why it is this?
Thanks for your help.


dxy


At 2015-05-20 20:22:42, "Utkarsh Ayachit"  wrote:
>Try turning of display lists. In ParaView4.1 it was setting named
>"Immediate mode rendering" under the Settings dialog. You'll need to
>enable the checkbox.
>
>Utkarsh
>
>On Wed, May 20, 2015 at 4:34 AM, 丁晓燕  wrote:
>> Dear,
>> I use the paraview of Version4.1, and the memory of my computer is
>> 4G. When I load about 190 ply files at the same time, there will be errors
>> about out of memory, but it runs normally when the number of the file is
>> less than 190.
>>
>> The error message as shown below:
>> ERROR: In
>> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLCoincidentTopologyResolutionPainter.cxx,
>> line 176
>> vtkOpenGLCoincidentTopologyResolutionPainter (7A9A9938): failed after
>> RenderShiftZBuffer 1 OpenGL errors detected
>>   0 : (1285) Out of memory
>> ERROR: In
>> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLDisplayListPainter.cxx,
>> line 188
>> vtkOpenGLDisplayListPainter (7AAE3358): failed after RenderInternal 1 OpenGL
>> errors detected
>>   0 : (1285) Out of memory
>>
>> Thanks for your help.
>> Yours truly,
>> dxy
>>



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Re: [Paraview] volume comparison

[Utkarsh Ayachit]

ParaView/VTK really doesn't support mixing two overlapping volumes.
Without going into the details, suffice it to say that the rendering
implementation will result in one of the volumes always on "top" of
the other. An alternative is to to render the volumes in 2 separate
views, side-by-side and then link the camera together to interact
simultaneously with the two views -- enabling similar comparison.
Another option is to extract isosurfaces (contours) from the two
volumes and then render those as surface with opacity < 1. Multiple
overlapping surfaces with translucency should work fine.

Utkarsh

On Tue, May 19, 2015 at 10:22 PM, Christopher Snyder
<22csny...@gmail.com> wrote:
> Hi,
>
> I have two 3D image that I would like to compare to see  if they are "the
> same." I thought it would be illustrative to overlay the two volumes in
> different colors with some opacity.
>
> This presents some difficulty. In my mind I would be able to have 2 volumes
> overlayed, full control of the color map of each volume, and be able to
> control rotation and translation of each volume individually.
>
> If that's not possible directly in the GUI, maybe it's possible through the
> python console?
>
> Best,
> Chris
>
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Utkarsh Ayachit]

> I want to say DataRepresentationCreated is never called! When I create
> instance of my pipeline source with this source code, I get only 3
> messages: "Source Created", and 2 times "Representation Added" after
> pushing Apply button.

Ah ok. That's because pqObjectBuilder no longer creates the standard
representations for ParaView. A better signal to observe is
pqServerManagerModel::representationAdded(). You're already observer
sourceAdded from the ServerManagerModel. You'll need to qobject_cast<>
to pqDataRepresentation* in your slot, for same effect as before.

Utkarsh
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Re: [Paraview] Installing ParaView 4.0.1 on Nodes For Rendering Frames -Slow Rendering w/ Python

[Utkarsh Ayachit]

Are you using x forwarding when you connect to these machines? What is
localhost:10.0 display to? Try running some other X-based application
like gvim, or glxgears etc. and see where that window pops up. If it's
popping up on your laptop, you're using X forwarding. Every render on
the server will then be forwarding X calls to your laptop and that
would explain the slow down.

If there an X server running on the "remote site"? If so, check with
your sysadmin to get access to that X if possible. If not, you'll need
to recoming with OSMesa, I am afraid.

Utkarsh

On Wed, May 20, 2015 at 1:07 AM, Noah Taylor  wrote:
> Hello,
>
> I am using ParaView 4.0.1 since I developed a python script for
> interpretation on this version. I am able to run ParaView fine on my local
> Ubuntu Desktop. I have setup an EC2 AWS instance both a GPU and a CPU
> instance both running Ubuntu but they both are giving me the same problem of
> very very slow rendering for each time step with the offscreen rendering
> option turned on. I also run into this problem on a Unix supercomputer I am
> trying to run my code on. On my local machine it takes less than a second
> for each time step I am rendering to be outputted with the same settings and
> I am not spinning anything  up like pvserver - on the node instances I have,
> it is taking well around a minute or probably more for each frame.
>
> I have read through a lot of similar issues and the documentation for X
> connections but I am not having any luck. The default DISPLAY is set to the
> localhost:10.0 and I have tried changing that to the localhost:0.0 but it
> gives me the bad -X connection error. From there, I followed previous
> mailing list instructions and tried spinning up the pvserver (I don't know
> why since I am not trying to serve anything just render frames) but I get an
> error with the shared libraries that they're too short. I am using the
> default downloadable version of 4.0.1 since I want to try and keep this as
> simple as possible but I don't know if these have the mpi turned on by
> default. Has anybody ran into this Bad X Connection issue and found an easy
> way around it besides messing with the OSMesa and recompiling? I'd really
> appreciate any pointers :)
>
> Thanks,
> Noah
>
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Nenad Vujicic]

Utkarsh,

I'm sorry for confusing:-(.

I want to say DataRepresentationCreated is never called! When I create
instance of my pipeline source with this source code, I get only 3
messages: "Source Created", and 2 times "Representation Added" after
pushing Apply button.

Nenad.

On Wed, May 20, 2015 at 3:50 PM, Utkarsh Ayachit
 wrote:
> Nenad,
>
> Okay I must be missing something very obvious here, but I am totally
> lost here. EventHandlers.cpp confused more than it clarified things
> for me :).
>
> Just focusing on EventHandlers.cpp for now.
>
> Are you saying EventHandlers::DataRepresentationCreated() isn't called
> when a new "DataLabelRepresentation" is created at line #136?
>
> Utkarsh
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Utkarsh Ayachit]

Nenad,

Okay I must be missing something very obvious here, but I am totally
lost here. EventHandlers.cpp confused more than it clarified things
for me :).

Just focusing on EventHandlers.cpp for now.

Are you saying EventHandlers::DataRepresentationCreated() isn't called
when a new "DataLabelRepresentation" is created at line #136?

Utkarsh
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Re: [Paraview] [paraview] out of memory

[Utkarsh Ayachit]

Try turning of display lists. In ParaView4.1 it was setting named
"Immediate mode rendering" under the Settings dialog. You'll need to
enable the checkbox.

Utkarsh

On Wed, May 20, 2015 at 4:34 AM, 丁晓燕  wrote:
> Dear,
> I use the paraview of Version4.1, and the memory of my computer is
> 4G. When I load about 190 ply files at the same time, there will be errors
> about out of memory, but it runs normally when the number of the file is
> less than 190.
>
> The error message as shown below:
> ERROR: In
> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLCoincidentTopologyResolutionPainter.cxx,
> line 176
> vtkOpenGLCoincidentTopologyResolutionPainter (7A9A9938): failed after
> RenderShiftZBuffer 1 OpenGL errors detected
>   0 : (1285) Out of memory
> ERROR: In
> C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLDisplayListPainter.cxx,
> line 188
> vtkOpenGLDisplayListPainter (7AAE3358): failed after RenderInternal 1 OpenGL
> errors detected
>   0 : (1285) Out of memory
>
> Thanks for your help.
> Yours truly,
> dxy
>
>
>
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Re: [Paraview] Troubles with exporting selection labels from current ParaView render view

[Nenad Vujicic]

Utkarsh,

>> - Strange 1: I don't have anymore instance in
>> DataLabelRepresentation for Elevation pipeline source (btw, during
>> this traversing I get only one actor),

> I don't follow. DataLableRepresentation is indeed created for every
> representation shown in the render view.

It seems it is not. When I execute my code snipped (passed down) I get
only 2 sources (good), every source with 1 output port (good) and for
every output port only one GeometryRepresentation (bad). No traces of
DataLabelRepresentation. Btw, my test case is:

1. Create Sphere source with default parameters,
2. Apply Elevation filter on it and turn off its 3d widget line,
3. Select several points on Elevation1 sphere and execute code snippet.

Here is my code snippet:

-- START OF CODE SNIPPET --

// pass through all pipeline sources and pass all its representations
for all output ports
for(i = 0; i < sources.size(); i++)
{
// get pipeline source
pqPipelineSource* source = sources.at(i);

QMessageBox::about(NULL, "1", source->getSMName());

// for every output port, traverse all its representations
for(output_port = 0; output_port <
source->getNumberOfOutputPorts(); output_port++)
{
 QMessageBox::about(NULL, "2", source->getSMName() +
QString("_port_") + QString::number(output_port));

 // traverse all representations for this
 for(j = 0; j < source->getRepresentations(output_port,
active_view).count(); j++)
 {
 // get representation
 // I got active_view with
pqApplicationCore::instance()->getServerManagerModel()->getNumberOfItems
 pqDataRepresentation* current_representation =
source->getRepresentations(output_port, active_view)[j];

 QMessageBox::about(NULL, "3", current_representation->getSMName());
  }
}
}

-- END OF CODE SNIPPET --

Thank you very much for your response!


Nenad.

p.s. sorry for duplicated messages in your inbox:-).





On Mon, May 18, 2015 at 3:49 PM, Utkarsh Ayachit
 wrote:
>> - Strange 1: I don't have anymore instance in
>> DataLabelRepresentation for Elevation pipeline source (btw, during
>> this traversing I get only one actor),
>
> I don't follow. DataLableRepresentation is indeed created for every
> representation shown in the render view.
>
>
>> - Strange 2: When I traverse vtkRenderer's actors, I get 2 actors
>> (sphere mesh and actor with selected points), but, I'm unable to
>> connect selection label properties (which are tied with Elevation
>> pipeline source actor - sphere mesh) and mesh with selected points /
>> cells.
>
> Remember that label actors are added to the 2D / non-composited
> renderer, not the same as the 3D renderer. Which renderer are you
> looking at?
>
>> Q1: How to identify actor from vtkRenderer which contains selection
>> points / cells and get selection properties from this actor or
>>
>> Q2: How to identify actor from pqPipeline source on which are selected
>> points and how from appropriate representations to get actor which
>> contains selected points / cells?
>
> Neither of these are really supported. Look at
> vtkSelectionRepresentation. If you can think of ways of "tagging" the
> actors added by the representations used internally by this class, I
> am all ears.
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[Paraview] [paraview] out of memory

[丁晓燕]

Dear,
I use the paraview of Version4.1, and the memory of my computer is 4G. 
When I load about 190 ply files at the same time, there will be errors about 
out of memory, but it runs normally when the number of the file is less than 
190.


The error message as shown below:
ERROR: In 
C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLCoincidentTopologyResolutionPainter.cxx,
 line 176
vtkOpenGLCoincidentTopologyResolutionPainter (7A9A9938): failed after 
RenderShiftZBuffer 1 OpenGL errors detected
  0 : (1285) Out of memory
ERROR: In 
C:\DBD\pvs-x32\paraview\src\paraview\VTK\Rendering\OpenGL\vtkOpenGLDisplayListPainter.cxx,
 line 188
vtkOpenGLDisplayListPainter (7AAE3358): failed after RenderInternal 1 OpenGL 
errors detected
  0 : (1285) Out of memory


Thanks for your help.
Yours truly,
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Re: [Paraview] Connecting to Catalyst-Enabled Simulation Running on Remote Cluster

[Timo Oster]

I haven't used the examples, so I'm afraid I can't help a lot there.

On 05/20/2015 09:47 AM, Ufuk Utku Turuncoglu (BE) wrote:
> Hi Timo,
> 
> Thanks for your help. Actually, to keep it simple, i am using my laptop
> for both server and client. So, i think there is no need to open ssh
> tunnel in this case and also hash will not be an issue.
> 
> Steps:
> 
> 1 - installed Paraview 4.3.1 source under Mac OS 10.10 by enabling
> Python + OpenMPI + Development files and ParaView works fine.
> 2 - i compiled ParaViewCatalystExampleCode without any problem
> 3 - i run server: mpirun -np 2 ./pvserver (on port 1)
> 4 - i run ParaView and connect to server and Catalyst (on port 2)
> using menus
> 5 - i go to CxxMultiPieceExample directory and i run the code: mpirun
> -np 2 ./CxxMultiPieceExample SampleScripts/feslicescript.py
> 
> in this case, i modified SampleScripts/feslicescript.py as
> coprocessor.EnableLiveVisualization(True) to enable live visualization.
> In this case, the code is running but i am getting
> 
> Invalid output port : pqPipelineSource::getOutputPort( 0 ). Available
> number of output ports: 0
> 
> error under ParaView and also server crashes with following error,
> 
> ERROR: In
> /Users/turuncu/Qsync/progs/paraview-4.3.1/src/VTK/Parallel/Core/vtkSocketCommunicator.cxx,
> line 812
> vtkSocketCommunicator (0x7f993cf20b80): Could not receive tag. 1
> 
> [epsilon:07510] *** Process received signal ***
> [epsilon:07510] Signal: Segmentation fault: 11 (11)
> [epsilon:07510] Signal code: Address not mapped (1)
> [epsilon:07510] Failing at address: 0x30
> [epsilon:07510] [ 0] 0   libsystem_platform.dylib 0x7fff851f1f1a
> _sigtramp + 26
> [epsilon:07510] [ 1] 0   ??? 0x7f993b8578a2 0x0 + 140296105326754
> [epsilon:07510] [ 2] 0   libvtkCommonSystem-pv4.3.1.dylib
> 0x00010fd5c9d9 _ZN9vtkSocket4SendEPKvi + 41
> [epsilon:07510] [ 3] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f313803 _ZN21vtkSocketCommunicator10SendTaggedEPKviiiPKc + 67
> [epsilon:07510] [ 4] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f3131a1 _ZN21vtkSocketCommunicator13SendVoidArrayEPKvxiii + 4625
> [epsilon:07510] [ 5] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d5738e2 _ZN15vtkCommunicator4SendEPKcxii + 98
> [epsilon:07510] [ 6] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d56fa4d _ZN25vtkMultiProcessController4SendEPKcxii + 77
> [epsilon:07510] [ 7] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d56eca7 _ZN20vtkPVProgressHandler14RefreshMessageEPKc + 151
> [epsilon:07510] [ 8] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d56d99b
> _ZN20vtkPVProgressHandler14OnMessageEventEP9vtkObjectmPv + 91
> [epsilon:07510] [ 9] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d5719b8
> _ZN9vtkObject22vtkClassMemberCallbackI20vtkPVProgressHandlerEclEPS_mPv +
> 344
> [epsilon:07510] [10] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x00011056c7d2 _ZN24vtkObjectCommandInternal7ExecuteEP9vtkObjectmPv
> + 98
> [epsilon:07510] [11] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x000110569a7b _ZN16vtkSubjectHelper11InvokeEventEmPvP9vtkObject + 4731
> [epsilon:07510] [12] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x00011056a052 _ZN9vtkObject11InvokeEventEmPv + 66
> [epsilon:07510] [13] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x000110571a7b _ZN15vtkOutputWindow11DisplayTextEPKc + 219
> [epsilon:07510] [14] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x000110571ac6 _ZN15vtkOutputWindow16DisplayErrorTextEPKc + 54
> [epsilon:07510] [15] 0   libvtkCommonCore-pv4.3.1.dylib
> 0x00011057165c _Z31vtkOutputWindowDisplayErrorTextPKc + 44
> [epsilon:07510] [16] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f315619 _ZN21vtkSocketCommunicator13ReceiveTaggedEPviiiPKc + 761
> [epsilon:07510] [17] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f315196 _ZN21vtkSocketCommunicator16ReceiveVoidArrayEPvxiii +
> 4486
> [epsilon:07510] [18] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f2d88a2 _ZN15vtkCommunicator7ReceiveEPhxii + 98
> [epsilon:07510] [19] 0   libvtkParallelCore-pv4.3.1.dylib
> 0x00010f2e91a1 _ZN25vtkMultiProcessController11ProcessRMIsEii + 193
> [epsilon:07510] [20] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d5bb89d
> _ZN26vtkTCPNetworkAccessManager21ProcessEventsInternalEmb + 2717
> [epsilon:07510] [21] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib
> 0x00010d5bba72 _ZN26vtkTCPNetworkAccessManager13ProcessEventsEm + 34
> [epsilon:07510] [22] 0   pvserver 0x00010ba83caa
> _ZL8RealMainiPPcN16vtkProcessModule12ProcessTypesE + 730
> [epsilon:07510] [23] 0   pvserver 0x00010ba839b7 main + 39
> [epsilon:07510] [24] 0   libdyld.dylib 0x7fff8cbe75c9 start + 1
> [epsilon:07510] *** End of error message ***
> --
> mpirun noticed that process rank 0 with PID 7510 on node epsilon exited
> on signal 11 (Segmentation fault: 11).
> 

Re: [Paraview] Connecting to Catalyst-Enabled Simulation Running on Remote Cluster

[Ufuk Utku Turuncoglu (BE)]

Hi Timo,

Thanks for your help. Actually, to keep it simple, i am using my laptop 
for both server and client. So, i think there is no need to open ssh 
tunnel in this case and also hash will not be an issue.


Steps:

1 - installed Paraview 4.3.1 source under Mac OS 10.10 by enabling 
Python + OpenMPI + Development files and ParaView works fine.

2 - i compiled ParaViewCatalystExampleCode without any problem
3 - i run server: mpirun -np 2 ./pvserver (on port 1)
4 - i run ParaView and connect to server and Catalyst (on port 2) 
using menus
5 - i go to CxxMultiPieceExample directory and i run the code: mpirun 
-np 2 ./CxxMultiPieceExample SampleScripts/feslicescript.py


in this case, i modified SampleScripts/feslicescript.py as 
coprocessor.EnableLiveVisualization(True) to enable live visualization. 
In this case, the code is running but i am getting


Invalid output port : pqPipelineSource::getOutputPort( 0 ). Available 
number of output ports: 0


error under ParaView and also server crashes with following error,

ERROR: In 
/Users/turuncu/Qsync/progs/paraview-4.3.1/src/VTK/Parallel/Core/vtkSocketCommunicator.cxx, 
line 812

vtkSocketCommunicator (0x7f993cf20b80): Could not receive tag. 1

[epsilon:07510] *** Process received signal ***
[epsilon:07510] Signal: Segmentation fault: 11 (11)
[epsilon:07510] Signal code: Address not mapped (1)
[epsilon:07510] Failing at address: 0x30
[epsilon:07510] [ 0] 0   libsystem_platform.dylib 0x7fff851f1f1a 
_sigtramp + 26

[epsilon:07510] [ 1] 0   ??? 0x7f993b8578a2 0x0 + 140296105326754
[epsilon:07510] [ 2] 0   libvtkCommonSystem-pv4.3.1.dylib 
0x00010fd5c9d9 _ZN9vtkSocket4SendEPKvi + 41
[epsilon:07510] [ 3] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f313803 _ZN21vtkSocketCommunicator10SendTaggedEPKviiiPKc + 67
[epsilon:07510] [ 4] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f3131a1 _ZN21vtkSocketCommunicator13SendVoidArrayEPKvxiii + 4625
[epsilon:07510] [ 5] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d5738e2 _ZN15vtkCommunicator4SendEPKcxii + 98
[epsilon:07510] [ 6] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d56fa4d _ZN25vtkMultiProcessController4SendEPKcxii + 77
[epsilon:07510] [ 7] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d56eca7 _ZN20vtkPVProgressHandler14RefreshMessageEPKc + 151
[epsilon:07510] [ 8] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d56d99b 
_ZN20vtkPVProgressHandler14OnMessageEventEP9vtkObjectmPv + 91
[epsilon:07510] [ 9] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d5719b8 
_ZN9vtkObject22vtkClassMemberCallbackI20vtkPVProgressHandlerEclEPS_mPv + 344
[epsilon:07510] [10] 0   libvtkCommonCore-pv4.3.1.dylib 
0x00011056c7d2 _ZN24vtkObjectCommandInternal7ExecuteEP9vtkObjectmPv + 98
[epsilon:07510] [11] 0   libvtkCommonCore-pv4.3.1.dylib 
0x000110569a7b _ZN16vtkSubjectHelper11InvokeEventEmPvP9vtkObject + 4731
[epsilon:07510] [12] 0   libvtkCommonCore-pv4.3.1.dylib 
0x00011056a052 _ZN9vtkObject11InvokeEventEmPv + 66
[epsilon:07510] [13] 0   libvtkCommonCore-pv4.3.1.dylib 
0x000110571a7b _ZN15vtkOutputWindow11DisplayTextEPKc + 219
[epsilon:07510] [14] 0   libvtkCommonCore-pv4.3.1.dylib 
0x000110571ac6 _ZN15vtkOutputWindow16DisplayErrorTextEPKc + 54
[epsilon:07510] [15] 0   libvtkCommonCore-pv4.3.1.dylib 
0x00011057165c _Z31vtkOutputWindowDisplayErrorTextPKc + 44
[epsilon:07510] [16] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f315619 _ZN21vtkSocketCommunicator13ReceiveTaggedEPviiiPKc + 761
[epsilon:07510] [17] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f315196 _ZN21vtkSocketCommunicator16ReceiveVoidArrayEPvxiii + 
4486
[epsilon:07510] [18] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f2d88a2 _ZN15vtkCommunicator7ReceiveEPhxii + 98
[epsilon:07510] [19] 0   libvtkParallelCore-pv4.3.1.dylib 
0x00010f2e91a1 _ZN25vtkMultiProcessController11ProcessRMIsEii + 193
[epsilon:07510] [20] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d5bb89d 
_ZN26vtkTCPNetworkAccessManager21ProcessEventsInternalEmb + 2717
[epsilon:07510] [21] 0 libvtkPVClientServerCoreCore-pv4.3.1.dylib 
0x00010d5bba72 _ZN26vtkTCPNetworkAccessManager13ProcessEventsEm + 34
[epsilon:07510] [22] 0   pvserver 0x00010ba83caa 
_ZL8RealMainiPPcN16vtkProcessModule12ProcessTypesE + 730

[epsilon:07510] [23] 0   pvserver 0x00010ba839b7 main + 39
[epsilon:07510] [24] 0   libdyld.dylib 0x7fff8cbe75c9 start + 1
[epsilon:07510] *** End of error message ***
--
mpirun noticed that process rank 0 with PID 7510 on node epsilon exited 
on signal 11 (Segmentation fault: 11).

--

So, i am unable to run Catalyst tests for now. They produces output 
*.vtm files (using writers in the pipeline) if i disable live 
visualization. Please let me know, if you have any suggestion.


Regards,

--ufuk

On 20/05/15 10:31, Timo

Re: [Paraview] xdmf: orders of Origin DXDYDZ arrays in Origin_DXDYDZ

[Armin Wehrfritz]

I encountered the same issue and you can find from the ParaView and XDMF
mailinglist-archives some explanations concerning this topic (search for
"Odd behavior of XDMF files with 3DCORECTMesh").


Concerning the different structured grid types:
3DCoRectMesh (aka vtkImageData):
Axis are perpendicular and spacing is constant (i.e. you only have to
set the mesh dimensions (nx, ny, nz), mesh origin (x0, y0, z0) and cell
dimensions (dx, dy, dz))

3DRectMesh (aka vtkRectilinearGrid):
Axis are perpendicular (i.e. you have to specify the nodes coordinates
along the three axes)

3DSMesh (aka vtkStructuredGrid):
Curvilinear (i.e. you have to specify the coordinates for all mesh nodes)

-Armin




On 05/19/2015 05:08 PM, Liang Wang wrote:

In the first place, I do not understand the difference between
3DRectMesh and 3DCoRectMesh.

I picked the following coordinate for testing:

Nz,Ny,Nx = [80, 90, 100] z0,y0,x0 = [-3.,-2.,-1.] lz,ly,lx =
[Nz*3,Ny*2,Nx] dz,dy,dx = [lz/(Nz-1), ly/(Ny-1), lx/(Nx-1)]

I found I have to use the following lines in the xdmf to get the
correct grid to be shown in Paraview for 3DRectMesh and 3DCoRectMesh,
respectively:

  

-1 -2 -3  1 2 3 

  

-3 -2 -1  3 2 1 

Note that, the Dimensions for Topology in both cases are in zyx
order, while the Origin/DxDyDz arrays have different orders in the
two cases:

3DRectMesh requires Origin=[x0,y0,z0], DX=[dx,dy,dz], i.e., xyz
order 3DCoRectMesh requires Origin=[z0,y0,x0], DX=[dz,dy,dx], i.e.,
zyx order.

Am I writing the correct xdmf codes? How would you specify these
data? Thanks.


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Re: [Paraview] Connecting to Catalyst-Enabled Simulation Running on Remote Cluster

[Timo Oster]

Hi,

I have indeed run into the problem with "Could not receive tag. 1". In
my case I had to make sure that the client and server versions were
exactly the same. When connecting, the vtkSocketCommunicators on client
and server exchange a version hash that must match. This hash is
generated while building ParaView. The file that is generated can be
found in your build directory under
VTK/Parallel/Core/vtkSocketCommunicatorHash.h. Check that your client
and server have the same hash value in this file.

I am assuming that you have correctly set up an ssh tunnel between
client and server to enable the connection (ssh -L 1:localhost:1
user@server). The steps I take to run a in-situ case on a single remote
workstation are listed in my previous mail.

BTW I am using the "trunk" version of ParaView from the git repository,
which is close to version 4.3.1, and I'm running Linux on both client
and server (different distributions).

Regards,

Timo

On 05/19/2015 06:57 PM, u.utku.turunco...@be.itu.edu.tr wrote:
> Hi Timo,
> 
> Have you ever tried to test Catalyst examples in your case.
> 
> https://github.com/Kitware/ParaViewCatalystExampleCode
> 
> I am also trying to run Catalyst examples but i could not. In my case, i
> am able to install Paraview (4.3.1) from source under Mac OS 10.10 and the
> Catalys examples but when i try to run the examples i am getting error
> like,
> 
> ERROR: In
> /Users/turuncu/Qsync/progs/paraview-4.3.1/src/VTK/Parallel/Core/vtkSocketCommunicator.cxx,
> line 812
> vtkSocketCommunicator (0x7f86a52658e0): Could not receive tag. 1
> 
> or
> 
> ERROR: In
> /Users/turuncu/Qsync/progs/paraview-4.3.1/src/VTK/Common/System/vtkSocket.cxx,
> line 572
> vtkClientSocket (0x7fcefc939fe0): Socket error in call to send. Broken pipe.
> 
> So, if you don't mind could you share the details of your work environment
> (OS, Paraview version, etc.) and the steps to run the in-situ example. So,
> that could also help me to find the source of the problem.
> 
> Regards,
> 
> --ufuk
> 
>> Hi all,
>>
>> in an effort to enable live visualization of our simulation code, I have
>> written a Catalyst adaptor for it. The live visualization is working
>> great when the ParaView client runs on the same machine as the
>> simulation, even when the simulation runs in parallel using mpi.
>>
>> Now I want to do live visualization of a simulation running on a remote
>> cluster. I am able to get this to work for the simulation running on the
>> login node of the cluster:
>>
>> 1. Tunnel an ssh connection of port 1 to the cluster:
>> ssh -L 1:localhost:1 server
>> 2. In the shell that opens, start a paraview server (in the background
>> with '&')
>> 3. Run the simulation with mpirun (simulation runs only on login node)
>> 4. Start my local ParaView client and connect to localhost:1 to
>> connect to the remote pvserver through the ssh tunnel
>> 5. In the client, connect to Catalyst (port 2)
>> 6. A provider for the simulation is created and the live visualization
>> works
>>
>> Now I want to do the same for simulations started on the remote cluster
>> via the batch job system. In this scenario, the parallel processes of
>> the simulation will run on different (randomly chosen) nodes on the
>> cluster. How do I go about getting a connection from my local client to
>> the Catalyst instances running on those nodes?
>>
>> I imagine I will need to set up ssh tunnels from the nodes to the login
>> node where the pvserver is running. I've tried adding a ssh tunnel line
>> to the job script that is executed when the batch job starts. I've tried
>> forwarding and reverse-forwarding port 2 (ssh -L and ssh -R) to no
>> avail. The best I get is "ERROR: In
>> /.../ParaView_git/VTK/Common/System/vtkSocket.cxx, line 206
>> vtkServerSocket (0x18e0930): Socket error in call to bind. Address
>> already in use."
>>
>> My knowledge in networking and ssh is limited, so any pointers to how I
>> would go about this are greatly appreciated.
>>
>> Regards,
>>
>> Timo
>> ___
>> 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] Connecting to Catalyst-Enabled Simulation Running on Remote Cluster

[Timo Oster]

Hi Andy,

I have succeeded in getting it to work by starting a pvserver process on
every node alongside with the simulation instead of just one pvserver on
the login node. I then have a ssh tunnel from the worker nodes to the
login node, and from the login node to my local computer. This appears
to be rather resource-intensive though, and I wonder if there is a more
efficient way to do it. Is such a great number of pvservers really
needed? If somebody has any additional information, that would be very
helpful. Searching the internet for this question hasn't brought up much
helpful information yet.

Regards,

Timo

On 05/19/2015 05:09 PM, Andy Bauer wrote:
> Hi Timo,
> 
> There's a couple of steps that need to be added when connecting to a
> Catalyst-enabled simulation that's been run through a batch job on a
> cluster. This "should" be the same as just running pvserver through a
> batch job and connecting to that. The basics are that there's an
> executable/script that runs on the login node that the batch job
> connects to. Your GUI connects to the login node and has the ports
> forwarded properly through the executable/script to your pvserver. Now
> if your pvserver is running on the login node then it will have to use
> the above connection mechanism to connect to your Catalyst-enabled
> simulation. There may be some emails or something on the wiki that has
> information on the connection executable/script but I haven't tried any
> of that in several years so I'm not sure where it would be. Maybe
> someone else will chime in that's done this more recently than me.
> 
> Good luck and let us know how it goes.
> 
> Andy
> 
> On Mon, May 18, 2015 at 8:48 AM, Timo Oster  > wrote:
> 
> Hi all,
> 
> in an effort to enable live visualization of our simulation code, I have
> written a Catalyst adaptor for it. The live visualization is working
> great when the ParaView client runs on the same machine as the
> simulation, even when the simulation runs in parallel using mpi.
> 
> Now I want to do live visualization of a simulation running on a remote
> cluster. I am able to get this to work for the simulation running on the
> login node of the cluster:
> 
> 1. Tunnel an ssh connection of port 1 to the cluster:
> ssh -L 1:localhost:1 server
> 2. In the shell that opens, start a paraview server (in the background
> with '&')
> 3. Run the simulation with mpirun (simulation runs only on login node)
> 4. Start my local ParaView client and connect to localhost:1 to
> connect to the remote pvserver through the ssh tunnel
> 5. In the client, connect to Catalyst (port 2)
> 6. A provider for the simulation is created and the live
> visualization works
> 
> Now I want to do the same for simulations started on the remote cluster
> via the batch job system. In this scenario, the parallel processes of
> the simulation will run on different (randomly chosen) nodes on the
> cluster. How do I go about getting a connection from my local client to
> the Catalyst instances running on those nodes?
> 
> I imagine I will need to set up ssh tunnels from the nodes to the login
> node where the pvserver is running. I've tried adding a ssh tunnel line
> to the job script that is executed when the batch job starts. I've tried
> forwarding and reverse-forwarding port 2 (ssh -L and ssh -R) to no
> avail. The best I get is "ERROR: In
> /.../ParaView_git/VTK/Common/System/vtkSocket.cxx, line 206
> vtkServerSocket (0x18e0930): Socket error in call to bind. Address
> already in use."
> 
> My knowledge in networking and ssh is limited, so any pointers to how I
> would go about this are greatly appreciated.
> 
> Regards,
> 
> Timo
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