Re: [Paraview] [Xdmf] xdmf2 and paraview troubles

2009-03-25 Thread Berk Geveci
Is there a particular reason why you are using hdf5 1.8? Things would
probably go smoother if you used 1.6.X.

-berk

On Wed, Mar 25, 2009 at 5:01 AM, Alin M Elena
alinm.el...@googlemail.com wrote:
 Hi Berk,

 Here is the answer that I got from John on the xdmf list.
 This is after some header problems were solved plus the hdf5 1.8 version
 problem solved too,

 Now the problem seem to be related with some casting of uint64. Anyhow it
 looks like me related with the problem that Mike Jackson fixed last summer in
 June.

 I will not have time to follow John's advice until next week.

 regards,

 Alin

 --
  __
  If the Universities will not study useless subjects, who will?
                             G. F. FitzGerald, Nature, 45/46, 392 (1892)
  __
  Mr  Alin M ELENA
  Irish Centre for High-End Computing -- www.ichec.ie
  The Design Tower, Trinity Technology  Enterprise Campus
  Grand Canal Quay,  Dublin 2, Ireland
  Tel:   +353 (0) 1 5241608 ext 29
  Fax: +353 (0) 1 7645845
  http://alin.elenaworld.net
  alin.el...@ichec.ie
  alinm.el...@gmail.com
  __



 -- Forwarded message --
 From: John Biddiscombe biddi...@cscs.ch
 To: alin.el...@ichec.ie
 Date: Tue, 24 Mar 2009 18:37:45 +0100
 Subject: Re: [Xdmf] xdmf2 and paraview troubles
 Alin


 [ 46%] Building CXX object 
 Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfH5Driver.o
 /home/alin/ParaView3/Utilities/Xdmf2/libsrc/XdmfH5Driver.cxx(165): error: a 
 value of type haddr_t={uint64_t={unsigned long}} (*)(H5FD_t *) cannot be 
 used to initialize an entity of type herr_t={int} (*)(H5FD_t *, 
 H5FD_mem_t={H5FD_mem_t}, hid_t={int}, haddr_t={uint64_t={unsigned long}}, 
 hsize_t={unsigned long long})                                               
        H5FD_dsm_get_eoa,           /*get_eoa       */                        
                                                                              
                                      ^

 Look carefully and you can see a 64bit int is being cast to a standard int 
 (or vice versa). Have a play with Enable SIZE_T and 64 bit compilation 
 options. This error clearly should not occur, but since you're using an intel 
 compiler, some combination might not have been discoverd. (possibly even a 
 CMake issue causing types not to be detected properly, but unlikely)

 See if you can find what settings make the error go away and post the results 
 back. Perhaps it'll help provide a fix for the future.

 NB. I'm guessing, so if I am barking up the wrong tree. Apologies.

 JB




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Re: [Paraview] [Xdmf] xdmf2 and paraview troubles

2009-03-25 Thread Alin M Elena
Hi Berk,

Personally I do not use the xdmf and I am interested only in the molecular 
plots.

The 1.8 version is the one that came default on my opensuse 11.1 box. 
In the face of the issues may be a good idea to bundle, as an option, a 
version that is known to work with paraview.

I try to compile paraview with all plugins as we intend here at ICHEC to offer 
it to the users as a complement/replacement of their visualization tools.

regards,

Alin


-- 
 __
 If the Universities will not study useless subjects, who will?
 G. F. FitzGerald, Nature, 45/46, 392 (1892)
 __
 Mr  Alin M ELENA
 Irish Centre for High-End Computing -- www.ichec.ie
 The Design Tower, Trinity Technology  Enterprise Campus
 Grand Canal Quay,  Dublin 2, Ireland
 Tel:   +353 (0) 1 5241608 ext 29
 Fax: +353 (0) 1 7645845
 http://alin.elenaworld.net
 alin.el...@ichec.ie
 alinm.el...@gmail.com
 __
On Wednesday 25 March 2009 10:40:25 you wrote:
 Is there a particular reason why you are using hdf5 1.8? Things would
 probably go smoother if you used 1.6.X.

 -berk

 On Wed, Mar 25, 2009 at 5:01 AM, Alin M Elena

 alinm.el...@googlemail.com wrote:
  Hi Berk,
 
  Here is the answer that I got from John on the xdmf list.
  This is after some header problems were solved plus the hdf5 1.8 version
  problem solved too,
 
  Now the problem seem to be related with some casting of uint64. Anyhow it
  looks like me related with the problem that Mike Jackson fixed last
  summer in June.
 
  I will not have time to follow John's advice until next week.
 
  regards,
 
  Alin
 
  --
   __
   If the Universities will not study useless subjects, who will?
  G. F. FitzGerald, Nature, 45/46, 392 (1892)
   __
   Mr  Alin M ELENA
   Irish Centre for High-End Computing -- www.ichec.ie
   The Design Tower, Trinity Technology  Enterprise Campus
   Grand Canal Quay,  Dublin 2, Ireland
   Tel:   +353 (0) 1 5241608 ext 29
   Fax: +353 (0) 1 7645845
   http://alin.elenaworld.net
   alin.el...@ichec.ie
   alinm.el...@gmail.com
   __
 
 
 
  -- Forwarded message --
  From: John Biddiscombe biddi...@cscs.ch
  To: alin.el...@ichec.ie
  Date: Tue, 24 Mar 2009 18:37:45 +0100
  Subject: Re: [Xdmf] xdmf2 and paraview troubles
  Alin
 
  [ 46%] Building CXX object
  Utilities/Xdmf2/libsrc/CMakeFiles/Xdmf.dir/XdmfH5Driver.o
  /home/alin/ParaView3/Utilities/Xdmf2/libsrc/XdmfH5Driver.cxx(165):
  error: a value of type haddr_t={uint64_t={unsigned long}} (*)(H5FD_t
  *) cannot be used to initialize an entity of type herr_t={int}
  (*)(H5FD_t *, H5FD_mem_t={H5FD_mem_t}, hid_t={int},
  haddr_t={uint64_t={unsigned long}}, hsize_t={unsigned long long})  
 H5FD_dsm_get_eoa,
/*get_eoa   */
 
   ^
 
  Look carefully and you can see a 64bit int is being cast to a standard
  int (or vice versa). Have a play with Enable SIZE_T and 64 bit
  compilation options. This error clearly should not occur, but since
  you're using an intel compiler, some combination might not have been
  discoverd. (possibly even a CMake issue causing types not to be detected
  properly, but unlikely)
 
  See if you can find what settings make the error go away and post the
  results back. Perhaps it'll help provide a fix for the future.
 
  NB. I'm guessing, so if I am barking up the wrong tree. Apologies.
 
  JB

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Re: [Paraview] Transform surface independently from axes and boxes

2009-03-25 Thread Utkarsh Ayachit
Hopefully, I understand this correctly now. Just go to the Display
tab. If you scroll lower, you'll see a transformation section. Apply
the scale there. The scale will be applied to both the geometry as
well as the annotation, while the annotation will keep on showing
original data values.

Utkarsh

2009/3/25 blende32 blend...@gmx.net:
 Hi,

 the problem still exists. It seems not possible to scale only for display an
 let the
 annotation (Show cube axes) on unscaled values (the original values), which
 are not transformed. If I use the transform filter I manipulate the real
 data an then
 of course the annotation uses also the transformed values. I only will swage
 the
 surface for the display and screenshots, but the axes annotations should
 show the
 real values. Is this not possible? I use no geometry. The data are
 temperatures in Z,
 height in y and time in X.

 Karl

 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 From: jerome.ve...@gmail.com
 To: blend...@gmx.net
 Date: 08:31:33, 03.24.2009
 Subject: Re: [Paraview] Transform surface independently from axes and boxes
 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~



 Hi,

I don't know if this possible. Maybe with the calculator : what about if
 you give as point data the original point coordinate, and then apply the
 transform ? PointData should not be modified. This is a brief idea : I even
 don't know how to set the axes to plot the point data instead of the
 geometry...

Good luck !

Jerome


2009/3/24 blende32 blend...@gmx.net


 Thank you for the explanation, but maybe I described the problem not
 exactly.
 I did not want to plot the surface of  the transformed data apart from
  the outline
 and the axes of the original data. I will to get a nonproportional plot.
  The bounds
 of the data are X(0...3000) Y(0...250) Z(20...31) and this should be
  plotted in a cube
 with the same length of each edge with axes labeled of the original
  data. With the
 Transform filter I did many trials but without success.
 
 Karl
 
 
 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 From: utkarsh.ayac...@kitware.com
 To: blend...@gmx.net
 Date: 14:08:16, 03.23.2009
 Subject: Re: [Paraview] Transform surface independently from axes and
  boxes
 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 
 
 
 
 
 
 Apply the Transform filter to your data to transform it. However,
  also turn on the visibility of your original data source i.e input to
  the transform filter, switch the representation type to outline and
  then show cube axes etc. on that original data.
 
  Utkarsh
 
  On Sat, Mar 21, 2009 at 5:05 PM, Karl Muster blend...@gmx.net
  wrote:
   Hello,
  
   I'm new in using paraview for visualisation and I need some help
   for scaling or transforming surfaceplots independently from axes and 
   boxes.
   The data about X, Y and Z are from different dimensions, thats why I 
   have to
   transform or scale it, but the axes should show the real values and 
   should
   not also be scaled.
  
   Thank you for help.
   --
   Aufgepasst: Sind Ihre Daten beim Online-Banking auch optimal
   geschützt?
   Jetzt absichern: https://homebanking.gmx.net/?mc=m...@footer.hb
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Re: [Paraview] Transform surface independently from axes and boxes

2009-03-25 Thread Karl Muster
This is the problem, when I use the transformation section on the
Display tab the scale will be applied to both, the geometry and 
the annotation (with Show cube axes) but I see on the Information
tab the original values on the Bounds section. And this values should 
be used for the annotation not the transformed values, which are 
used for display. If I want the scale for both I can use the transform filter 
and manipulate the data directly but that is not what I want.

Karl

 Original-Nachricht 
 Datum: Wed, 25 Mar 2009 07:25:31 -0400
 Von: Utkarsh Ayachit utkarsh.ayac...@kitware.com
 An: blende32 blend...@gmx.net
 CC: jerome.ve...@gmail.com, paraview@paraview.org
 Betreff: Re: [Paraview] Transform surface independently from axes and boxes

 Hopefully, I understand this correctly now. Just go to the Display
 tab. If you scroll lower, you'll see a transformation section. Apply
 the scale there. The scale will be applied to both the geometry as
 well as the annotation, while the annotation will keep on showing
 original data values.
 
 Utkarsh
 
 2009/3/25 blende32 blend...@gmx.net:
  Hi,
 
  the problem still exists. It seems not possible to scale only for
 display an
  let the
  annotation (Show cube axes) on unscaled values (the original values),
 which
  are not transformed. If I use the transform filter I manipulate the real
  data an then
  of course the annotation uses also the transformed values. I only will
 swage
  the
  surface for the display and screenshots, but the axes annotations should
  show the
  real values. Is this not possible? I use no geometry. The data are
  temperatures in Z,
  height in y and time in X.
 
  Karl
 
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  From: jerome.ve...@gmail.com
  To: blend...@gmx.net
  Date: 08:31:33, 03.24.2009
  Subject: Re: [Paraview] Transform surface independently from axes and
 boxes
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 
 
 
  Hi,
 
 I don't know if this possible. Maybe with the calculator : what about
 if
  you give as point data the original point coordinate, and then apply
 the
  transform ? PointData should not be modified. This is a brief idea : I
 even
  don't know how to set the axes to plot the point data instead of the
  geometry...
 
 Good luck !
 
 Jerome
 
 
 2009/3/24 blende32 blend...@gmx.net
 
 
  Thank you for the explanation, but maybe I described the problem not
  exactly.
  I did not want to plot the surface of  the transformed data apart
 from
   the outline
  and the axes of the original data. I will to get a nonproportional
 plot.
   The bounds
  of the data are X(0...3000) Y(0...250) Z(20...31) and this should be
   plotted in a cube
  with the same length of each edge with axes labeled of the original
   data. With the
  Transform filter I did many trials but without success.
  
  Karl
  
  
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  From: utkarsh.ayac...@kitware.com
  To: blend...@gmx.net
  Date: 14:08:16, 03.23.2009
  Subject: Re: [Paraview] Transform surface independently from axes and
   boxes
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  
  
  
  
  
  
  Apply the Transform filter to your data to transform it. However,
   also turn on the visibility of your original data source i.e input
 to
   the transform filter, switch the representation type to outline
 and
   then show cube axes etc. on that original data.
  
   Utkarsh
  
   On Sat, Mar 21, 2009 at 5:05 PM, Karl Muster blend...@gmx.net
   wrote:
Hello,
   
I'm new in using paraview for visualisation and I need some help
for scaling or transforming surfaceplots independently from axes
 and boxes.
The data about X, Y and Z are from different dimensions, thats
 why I have to
transform or scale it, but the axes should show the real values
 and should
not also be scaled.
   
Thank you for help.
--
Aufgepasst: Sind Ihre Daten beim Online-Banking auch optimal
geschützt?
Jetzt absichern: https://homebanking.gmx.net/?mc=m...@footer.hb
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Re: [Paraview] [Xdmf] xdmf2 and paraview troubles

2009-03-25 Thread John Biddiscombe

Alin

Paraview is bundled with a version of hdf5 that is known to work. But 
you turned it off, by setting


PARAVIEW_USE_SYSTEM_HDF5:BOOL=ON

turn this back off.

JB


Hi Berk,

Personally I do not use the xdmf and I am interested only in the molecular 
plots.


The 1.8 version is the one that came default on my opensuse 11.1 box. 
In the face of the issues may be a good idea to bundle, as an option, a 
version that is known to work with paraview.


I try to compile paraview with all plugins as we intend here at ICHEC to offer 
it to the users as a complement/replacement of their visualization tools.


regards,

Alin


  



--
John Biddiscombe,email:biddisco @ cscs.ch
http://www.cscs.ch/
CSCS, Swiss National Supercomputing Centre  | Tel:  +41 (91) 610.82.07
Via Cantonale, 6928 Manno, Switzerland  | Fax:  +41 (91) 610.82.82


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[Paraview] Creating Append Attributes filter using python

2009-03-25 Thread tpk
Hi all,



Could anyone advise me how to create an Append Attributes filter using pvpython?



Paraview documentation refers to Group Parts filter which, I believe, is 
obsolete in version 3.4.0.


My purpose is to merge multiple scalar/vector data sets sharing the same 
geometry. The data sets are loaded using PVDReader.

Thanks,
tpk



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Re: [Paraview] Transform surface independently from axes and boxes

2009-03-25 Thread Utkarsh Ayachit
There seems to be a bug, if the transform was applied from the display
tab, the cube-axes should still have been showing the original data
bounds. Please feel free to add a bug report at
www.paraview.org/Bug

Thanks,
Utkarsh

On Wed, Mar 25, 2009 at 7:58 AM, Karl Muster blend...@gmx.net wrote:
 This is the problem, when I use the transformation section on the
 Display tab the scale will be applied to both, the geometry and
 the annotation (with Show cube axes) but I see on the Information
 tab the original values on the Bounds section. And this values should
 be used for the annotation not the transformed values, which are
 used for display. If I want the scale for both I can use the transform filter 
 and manipulate the data directly but that is not what I want.

 Karl

  Original-Nachricht 
 Datum: Wed, 25 Mar 2009 07:25:31 -0400
 Von: Utkarsh Ayachit utkarsh.ayac...@kitware.com
 An: blende32 blend...@gmx.net
 CC: jerome.ve...@gmail.com, paraview@paraview.org
 Betreff: Re: [Paraview] Transform surface independently from axes and boxes

 Hopefully, I understand this correctly now. Just go to the Display
 tab. If you scroll lower, you'll see a transformation section. Apply
 the scale there. The scale will be applied to both the geometry as
 well as the annotation, while the annotation will keep on showing
 original data values.

 Utkarsh

 2009/3/25 blende32 blend...@gmx.net:
  Hi,
 
  the problem still exists. It seems not possible to scale only for
 display an
  let the
  annotation (Show cube axes) on unscaled values (the original values),
 which
  are not transformed. If I use the transform filter I manipulate the real
  data an then
  of course the annotation uses also the transformed values. I only will
 swage
  the
  surface for the display and screenshots, but the axes annotations should
  show the
  real values. Is this not possible? I use no geometry. The data are
  temperatures in Z,
  height in y and time in X.
 
  Karl
 
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  From: jerome.ve...@gmail.com
  To: blend...@gmx.net
  Date: 08:31:33, 03.24.2009
  Subject: Re: [Paraview] Transform surface independently from axes and
 boxes
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
 
 
 
  Hi,
 
 I don't know if this possible. Maybe with the calculator : what about
 if
  you give as point data the original point coordinate, and then apply
 the
  transform ? PointData should not be modified. This is a brief idea : I
 even
  don't know how to set the axes to plot the point data instead of the
  geometry...
 
 Good luck !
 
 Jerome
 
 
 2009/3/24 blende32 blend...@gmx.net
 
 
  Thank you for the explanation, but maybe I described the problem not
  exactly.
  I did not want to plot the surface of  the transformed data apart
 from
   the outline
  and the axes of the original data. I will to get a nonproportional
 plot.
   The bounds
  of the data are X(0...3000) Y(0...250) Z(20...31) and this should be
   plotted in a cube
  with the same length of each edge with axes labeled of the original
   data. With the
  Transform filter I did many trials but without success.
  
  Karl
  
  
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  From: utkarsh.ayac...@kitware.com
  To: blend...@gmx.net
  Date: 14:08:16, 03.23.2009
  Subject: Re: [Paraview] Transform surface independently from axes and
   boxes
  ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
  
  
  
  
  
  
  Apply the Transform filter to your data to transform it. However,
   also turn on the visibility of your original data source i.e input
 to
   the transform filter, switch the representation type to outline
 and
   then show cube axes etc. on that original data.
  
   Utkarsh
  
   On Sat, Mar 21, 2009 at 5:05 PM, Karl Muster blend...@gmx.net
   wrote:
Hello,
   
I'm new in using paraview for visualisation and I need some help
for scaling or transforming surfaceplots independently from axes
 and boxes.
The data about X, Y and Z are from different dimensions, thats
 why I have to
transform or scale it, but the axes should show the real values
 and should
not also be scaled.
   
Thank you for help.
--
Aufgepasst: Sind Ihre Daten beim Online-Banking auch optimal
geschützt?
Jetzt absichern: https://homebanking.gmx.net/?mc=m...@footer.hb
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  Follow 

Re: [Paraview] using netcdf in paraview

2009-03-25 Thread John Biddiscombe

Burlen

You can have an arbitrary number of meshes in the nedCDF file - but only 
one is exported (by default).


Part of the work I was doing recently was to add SIL support to the 
reader so that the GUI panel would display it all, and allow the user to 
select multiple meshes for export. The reader by default generates 
multiblock - but only the first block (biggest rather, decided by size) 
is actually exported. Once I've finished with it, each selected variable 
would be exported as a separate grid. The core code should handle 1-5 
dimensions (considering a vector field stored as a separate dimension, 
which between you and me is annoying).


The reader got messy because I was trying to support different 
conventions, so it's very hard to follow what's doing what. the ability 
to support associated variables for dimensions and stuff really messed 
it up, and different conventions use different systems for the grid 
variables etc.

Some data use time as a separate dimension, other multiple files etc etc

JB




Hi Guys,

By the way I just tried to load her data using the new VisIt database 
bridge and it worked! Does the CSCS plugin you guys have been talking 
about support multiple meshes in the same file? Just curious, cause I 
had to write a custom panel in PV to get that stuff working.


Burlen

John Biddiscombe wrote:

Martha (+put back on paraview list for reference and google)

My Bad. One of the changes I made to the netCDF code was to handle 
series of files (one file per process, or one per timestep) using 
another class in vtkCSCSCommon

Best thing is check out all of it from here...
https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/
and use the cmakelists in the root pv3-plugins folder.
you need CSCSCommomn and netCDF enabled.

Fix the netCDF reader and send me the patches please :)

JB


Katie,

I was able to check out vtkNetCDF from the SVN server; I had tried
before using the web site's instructions,
but it wouldn't work, I suppose because of our firewall; however the
https in the URL that Mr. Biddiscome gave us did make a difference.

However, when I attempted to build ParaView 3.4 with that vtkNetCDF
module, I got an error once again, this
time when for vtkNetCDFReader.cxx; what is missing is
FileSeriesFinder.h.

I cannot find that include file anywhere, in ParaView3.4, ParaView3.3,
etc, so I don't know if it was inadvertently left out of the vtkNetCDF
distribution or what.

Martha



-Original Message-
From: Carbonari, Katie (IS) Sent: Tuesday, March 24, 2009 5:15 PM
To: Tonkin, Martha E (IS)
Subject: FW: [Paraview] using netcdf in paraview




-Original Message-
From: John Biddiscombe [mailto:biddi...@cscs.ch]
Sent: Tue 3/24/2009 5:09 PM
To: Berk Geveci
Cc: Carbonari, Katie (IS); paraview@paraview.org
Subject: Re: [Paraview] using netcdf in paraview
 
Katie

Just looking again at the error messages makes me realize thet you're
using a very old vtkCSCSnetCDF the version in here
https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/vtkNetCDF/ is much more
recent and will at least compile without errors. It ewas intended for
meteo data (ocean/atmosphere) and so you should get something out of it
but the changes I made a few months back will have broken the core load
of data depending on which convention you are using.
My intention was to create subclasses for each supported convention,
rather than try to support all of them with aton of options - which is
what the current reader does. If you're familiar with vtk code, you'll
son work out how to fix it.
I'll take a look at again it in a few weeks.

JB


Hmmm. It sounds like there is version mismatch between ParaView
and
the plugin. We deprecated those classes not long ago. Are you
using
cvs ParaView?
-berk
2009/3/23 Carbonari, Katie (IS) katie.carbon...@ngc.com
mailto:katie.carbon...@ngc.com :
 Hi there. I'm trying to read netcdf data into paraview,
but am having lots
of issues. I was following these directions (from here:

http://www.cscs.ch/index.php?option=com_contenttask=viewid=96Itemid=1 


32):
   Please build ParaView using the CMake advanced option
PARAVIEW_EXTRA_EXTERNAL_MODULES set to CSCSNetCDF rerun
configure and set
PARAVIEW_USE_CSCSNetCDF to ON, then rerun configure and
enter the name of
the directory where the source has been extracted.
Build paraview and the netCDF reader should be embedded.
Building as a vtk module is supported, documentation
will be provided as
soon as possible. (Some changes have recently been made
which may break the
existing build, these will be fixed shortly).
   But when we make Paraview, it's not finding a bunch of
files
(vtkMultiGroupDataInformation.h, vtkMultiGroupDataSet.h,
vtkMultiGroupSetAlgorithm.h).
   Any advice on how to make this work? Or maybe a better
way to read in netcdf
files?
   Thanks,