Re: [Paraview] Paraview 5.4.1 FTBS on Debian/Testing with gcc 7.2 when -DPARAVIEW_USE_VISITBRIDGE=ON

[Ben Boeckel]

On Thu, Oct 12, 2017 at 09:39:29 -0400, Ben Boeckel wrote:
> Hmm, my browser history says I searched for this back in July… looking
> around there finds:
> 
> https://gitlab.kitware.com/paraview/paraview/issues/17456
> 
> which seems to have dropped off our radar. Is the Vs reader necessary?
> If not, feel free to disable it, otherwise the reader will need fixed
> (it seems it has never worked though since it did this since its
> addition to visit upstream).

Further investigation shows that the code in the class isn't used at all
anyways. You can just remove the VsStaggeredField.C line from the
Vs/CMakeLists.txt file to fix the build error.

https://gitlab.kitware.com/paraview/visitbridge/merge_requests/45
https://gitlab.kitware.com/paraview/paraview/merge_requests/1965

--Ben
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Re: [Paraview] Overlapping ParaView windows obscuring each other in ParaViewWeb visualizer server

[Sebastien Jourdain]

Hi Louise,

Another option with the current binaries that you have is to ask for
offscreen rendering in the code (Python). The window will still pop-up but
will be black and the correct rendering pixels will be send to the web
client.

Just add those 2 lines

simple.GetRenderView().UseOffscreenRenderingForScreenshots = 1
simple.GetRenderView().UseOffscreenRendering = 1

After the line
https://github.com/Kitware/visualizer/blob/master/server/pvw-visualizer.py#L200
but in the Python script you use to start Visualizer.

Seb

On Thu, Oct 12, 2017 at 6:48 AM, Shawn Waldon 
wrote:

> Hi Louise,
>
> I have seen something like this before when using VTK render windows on
> Linux with NVidia drivers.  There is a bug/feature in the NVidia driver
> where it only renders the part of the window that is shown onscreen.  The
> workaround I used at the time was to enable offscreen rendering (which I
> think ParaView will do by default in the 5.5 when that is released in a few
> months).  In ParaView master/5.5 it will be a command line option too
> --force-offscreen-rendering, but I think for 5.4 and earlier you would need
> to build ParaView with offscreen rendering enabled and then use that
> ParaView for Visualizer.
>
> HTH,
> Shawn
>
> On Thu, Oct 12, 2017 at 5:54 AM,  wrote:
>
>> Hello all,
>>
>>
>>
>> I seem to be observing odd behaviour on my ParaViewWeb server, in that
>> the server works and a client can see their visualisation window fine
>> provided a window does not overlap the ParaView window that is spawned when
>> the user connects to the server. If a new user connects, a new ParaView
>> window is spawned in the exact same place as the previous one, and the
>> first user now sees the image displayed on the second user’s server –
>> seemingly because the first user’s ParaView window is underneath the new
>> user’s window.
>>
>>
>>
>> It’s not just overlapping ParaView windows either. If I connect to my
>> server via VNC and place any window on top, it also obscures the user’s
>> view, although it just blacks out the screen and doesn’t show the actual
>> window itself to the user. Attached are some screenshots of what I’m trying
>> to describe, showing what is happening on the server desktop and what the
>> result is in the Visualizer window.
>>
>>
>>
>> Any ideas on what could possibly be going wrong would be greatly
>> appreciated.
>>
>>
>>
>> Kind regards,
>>
>>
>>
>> Louise Davies
>>
>> ___
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[Paraview] Help files (.pdf) not opening v5.4.1

[Dennis Conklin]

All

Help files (.pdf) clicked on the Help Menu are not launching from PV v5.4.1 on 
Redhat - okular is our system pdf reader - do we need to set something to use 
this?  This all works fine in Windoze.

Thanks for any hint.

Dennis
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Re: [Paraview] reading MATLAB file

[Mauro Fontana]

Hi Randy

I'm not sure if it is what you are asking, but this might be useful:
https://blog.kitware.com/easy-customization-of-the-paraview-python-programmable-filter-property-panel/
.

That way you can have a GUI field for the path of the .mat file to read,
much more convenient that changing the path in the code each time.

Cheers,

On Wed, Oct 11, 2017 at 5:10 PM Heiland, Randy  wrote:

> Not sure, but think it’s irrelevant for my particular use. I'm going to
> try the Programmable Source (Python script) approach (and use scipy.io.loadmat
> to read my .mat file). Maybe I missed it - is there a way to read in this
> script from a file? (copy/pasting into the Pgmable Source widget certainly
> works; just asking)  Thanks!
>
> On Oct 11, 2017, at 1:24 PM, Berk Geveci  wrote:
>
> Is there a Python API to read .mat files? What is the underlying
> structure? I kind of remember them using HDF5 for some stuff...
>
> On Tue, Oct 10, 2017 at 2:18 PM, Heiland, Randy  wrote:
>
>> Hello,
>>
>> I have some matlab files I’d like to get into PV. Initially, the data is
>> quite simple: sphere centers, radii, color attribute (a few 100K spheres).
>> In the past, I’ve manually converted the files into .vtk formats using
>> Python w/ scipy to load/parse the .mat files. But I’d like to avoid
>> creating additional files and just read the .mat files directly.
>>
>> I *think* I’d like to do this w/ Python still (but without creating
>> files), if that’s an option. Basically, I’d welcome suggestions for the
>> simplest approach, at least initially. I’m not terribly concerned about the
>> “slowness” of Python reading/converting the .mat files.
>>
>> Using PV 5.4.1. And the solution needs to be easily adopted by others who
>> will be using PV.
>>
>> I’m sure there are concerns that I’ve side-stepped, e.g. would I ever
>> want to use it in client/server mode, etc.
>>
>> I’ve seen https://www.paraview.org/Wiki/Plugin_HowTo and I was also
>> curious if a “Programmable Source” would be an option.
>>
>> thanks! (and it’s nice to re-join the community after a long absence)
>> -Randy
>>
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>>
>
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Re: [Paraview] Paraview 5.4.1 FTBS on Debian/Testing with gcc 7.2 when -DPARAVIEW_USE_VISITBRIDGE=ON

[Ben Boeckel]

On Thu, Oct 12, 2017 at 11:41:46 +0200, Christophe Trophime wrote:
> /usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem 
> /usr/include/x86_64-linux-gnu/qt5/QtGui -isystem 
> /usr/include/x86_64-linux-gnu/qt5/QtCore -isystem 
> /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 -g -O2 
> -fdebug-prefix-map=/build/paraview-5.4.1=. -fstack-protector-strong -Wformat 
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 
> -D_FORTIFY_SOURCE=2 -fPIC -fPIC -std=c++11 -o 
> CMakeFiles/vtkPVVTKExtensionsRenderingPythonD.dir/vtkZlibImageCompressorPython.cxx.o
>  -c 
> /build/paraview-5.4.1/obj-x86_64-linux-gnu/VTK/Wrapping/Python/vtkZlibImageCompressorPython.cxx
>  
> /build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:
>  In constructor 'VsStaggeredField::VsStaggeredField(size_t)': 
> /build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:30:24:
>  error: 'class std::valarray' has no member named 'clear' 
> this->oriCellDimProd.clear(); 
> ^ 

Hmm, my browser history says I searched for this back in July… looking
around there finds:

https://gitlab.kitware.com/paraview/paraview/issues/17456

which seems to have dropped off our radar. Is the Vs reader necessary?
If not, feel free to disable it, otherwise the reader will need fixed
(it seems it has never worked though since it did this since its
addition to visit upstream).

> extra_flags += -Wno-dev \ 
> -DCMAKE_C_COMPILER=mpicc \ 
> -DCMAKE_CXX_COMPILER=mpic++ \ 

This probably isn't related, but this is not the typical way to use MPI
with CMake projects. They discover and use the information from the
wrappers themselves when they find MPI.

--Ben
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Re: [Paraview] Overlapping ParaView windows obscuring each other in ParaViewWeb visualizer server

[Shawn Waldon]

Hi Louise,

I have seen something like this before when using VTK render windows on
Linux with NVidia drivers.  There is a bug/feature in the NVidia driver
where it only renders the part of the window that is shown onscreen.  The
workaround I used at the time was to enable offscreen rendering (which I
think ParaView will do by default in the 5.5 when that is released in a few
months).  In ParaView master/5.5 it will be a command line option too
--force-offscreen-rendering, but I think for 5.4 and earlier you would need
to build ParaView with offscreen rendering enabled and then use that
ParaView for Visualizer.

HTH,
Shawn

On Thu, Oct 12, 2017 at 5:54 AM,  wrote:

> Hello all,
>
>
>
> I seem to be observing odd behaviour on my ParaViewWeb server, in that the
> server works and a client can see their visualisation window fine provided
> a window does not overlap the ParaView window that is spawned when the user
> connects to the server. If a new user connects, a new ParaView window is
> spawned in the exact same place as the previous one, and the first user now
> sees the image displayed on the second user’s server – seemingly because
> the first user’s ParaView window is underneath the new user’s window.
>
>
>
> It’s not just overlapping ParaView windows either. If I connect to my
> server via VNC and place any window on top, it also obscures the user’s
> view, although it just blacks out the screen and doesn’t show the actual
> window itself to the user. Attached are some screenshots of what I’m trying
> to describe, showing what is happening on the server desktop and what the
> result is in the Visualizer window.
>
>
>
> Any ideas on what could possibly be going wrong would be greatly
> appreciated.
>
>
>
> Kind regards,
>
>
>
> Louise Davies
>
> ___
> 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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[Paraview] Paraview 5.4.1 FTBS on Debian/Testing with gcc 7.2 when -DPARAVIEW_USE_VISITBRIDGE=ON

[Christophe Trophime]

Hi, 
trying to rebuild latest paraview with -DPARAVIEW_USE_VISITBRIDGE=ON 
on Debian/testing with gcc 7.2 I run into this error: 



/usr/include/x86_64-linux-gnu/qt5/QtWidgets -isystem 
/usr/include/x86_64-linux-gnu/qt5/QtGui -isystem 
/usr/include/x86_64-linux-gnu/qt5/QtCore -isystem 
/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++-64 -g -O2 
-fdebug-prefix-map=/build/paraview-5.4.1=. -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 
-D_FORTIFY_SOURCE=2 -fPIC -fPIC -std=c++11 -o 
CMakeFiles/vtkPVVTKExtensionsRenderingPythonD.dir/vtkZlibImageCompressorPython.cxx.o
 -c 
/build/paraview-5.4.1/obj-x86_64-linux-gnu/VTK/Wrapping/Python/vtkZlibImageCompressorPython.cxx
 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:
 In constructor 'VsStaggeredField::VsStaggeredField(size_t)': 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:30:24:
 error: 'class std::valarray' has no member named 'clear' 
this->oriCellDimProd.clear(); 
^ 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:31:21:
 error: 'class std::valarray' has no member named 'clear' 
this->newCellDims.clear(); 
^ 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:32:24:
 error: 'class std::valarray' has no member named 'clear' 
this->newCellDimProd.clear(); 
^ 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:
 In member function 'void VsStaggeredField::getNewNodalData(TYPE*) 
const': 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:139:51:
 error: no match for 'operator*' (operand types are 'std::valarray' and 
'const size_t {aka const long unsigned int}') 
std::valarray newCellInds = oriCellInds*this->numNeighbors + subCellInds; 
~~~^~~ 
In file included from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.h:17:0,
 
from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:8:
 
/usr/include/c++/7/valarray:1174:1: note: candidate: template 
std::_Expr, typename std::__fun::result_type> 
std::operator*(const _Tp&, const std::valarray<_Tp>&) 
_DEFINE_BINARY_OPERATOR(*, __multiplies) 
^ 
/usr/include/c++/7/valarray:1174:1: note: template argument 
deduction/substitution failed: 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:139:58:
 note: mismatched types 'const std::valarray<_Tp>' and 'const size_t {aka const 
long unsigned int}' 
std::valarray newCellInds = oriCellInds*this->numNeighbors + subCellInds; 
^~~~ 
In file included from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.h:17:0,
 
from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:8:
 
/usr/include/c++/7/valarray:1174:1: note: candidate: template 
std::_Expr, typename std::__fun::result_type> 
std::operator*(const std::valarray<_Tp>&, const _Tp&) 
_DEFINE_BINARY_OPERATOR(*, __multiplies) 
^ 
/usr/include/c++/7/valarray:1174:1: note: template argument 
deduction/substitution failed: 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:139:58:
 note: deduced conflicting types for parameter 'const _Tp' ('int' and 'size_t 
{aka long unsigned int}') 
std::valarray newCellInds = oriCellInds*this->numNeighbors + subCellInds; 
^~~~ 
In file included from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.h:17:0,
 
from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:8:
 
/usr/include/c++/7/valarray:1174:1: note: candidate: template 
std::_Expr, typename std::__fun::result_type> 
std::operator*(const std::valarray<_Tp>&, const std::valarray<_Tp>&) 
_DEFINE_BINARY_OPERATOR(*, __multiplies) 
^ 
/usr/include/c++/7/valarray:1174:1: note: template argument 
deduction/substitution failed: 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:139:58:
 note: mismatched types 'const std::valarray<_Tp>' and 'const size_t {aka const 
long unsigned int}' 
std::valarray newCellInds = oriCellInds*this->numNeighbors + subCellInds; 
^~~~ 
In file included from /usr/include/c++/7/valarray:592:0, 
from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.h:17,
 
from 
/build/paraview-5.4.1/Utilities/VisItBridge/databases/readers/Vs/VsStaggeredField.C:8:
 
/usr/include/c++/7/bits/valarray_after.h:404:5: note: candidate: template std::_Expr

Re: [Paraview] simple Programmable Source

[Heiland, Randy]

Yes! (banging forehead)  Thanks very much, Cory.

> On Oct 11, 2017, at 11:10 PM, Cory Quammen  wrote:
> 
> Randy,
> 
> Try setting a name on the array with
> 
> scalars.SetName('array_name')
> 
> This should let you select this array as the color array in ParaView.
> 
> - Cory
> 
> On Wed, Oct 11, 2017 at 9:48 PM, Heiland, Randy  > wrote:
> I create the following in the Pgmable Source in PV, but cannot figure out how 
> to color the resulting points or 3D glyphs using the scalar values. What am I 
> missing?
> -Randy
> 
> # Get a vtk.PolyData object for the output
> pdo = self.GetPolyDataOutput()
> 
> # Create points
> num_pts = 3
> newPts = vtk.vtkPoints()
> scalars = vtk.vtkFloatArray()
> 
> xval = -1.0
> for idx in range(0, num_pts):
>   # rf. PhysiCell User Guide for these array indices to a cell's position.
>   x = xval
>   y = 0.0
>   z = 0.0
>   newPts.InsertPoint(idx, x,y,z)
>   sval = xval*2
>   scalars.InsertNextValue(sval)
>   xval += 1.0
> 
> # Add the points to the vtkPolyData object.
> pdo.SetPoints(newPts)
> pdo.GetPointData().SetScalars(scalars)
> 
> verts = vtk.vtkCellArray()
> for idx in range(0, num_pts):
>   verts.InsertNextCell(1)
>   verts.InsertCellPoint(idx)
> 
> pdo.SetVerts(verts)
> 
> 
> 
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> 
> 
> 
> -- 
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> Staff R Engineer
> Kitware, Inc.



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