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List: paraview
Subject: Re: [Paraview] using netcdf in paraview
From: "Moreland, Kenneth" <kmorel () sandia ! gov>
Date: 2009-03-26 16:49:00
Message-ID: C5F10E1D.9C9F%kmorel () sandia ! gov
[Download RAW message or body]
If you are using the CVS root anyway, I just checked in some netCDF readers. So \
hopefully you will now no longer need to do anything special.
-Ken
On 3/26/09 9:33 AM, "Burlen Loring" <burlen.loring@kitware.com> wrote:
I will commit the work next week, along with a Wiki describing how to
build/configure the dependencies. For planning purposes plan on late
next week.
John Biddiscombe wrote:
> Martha
>
> Build paraview as usual, ignore all the guff about
> PARAVIEW_EXTRA_EXTERNAL_MODULES, remove this from your paraview build,
> remove any CSCS addons you might have specified from paraview 'core'
> build.
>
> Then build a new new project which will be plugins, using the
> cmakelists from the root of CSCS stuff. Enter the paraview build dir,
> enable CSCSCommon and netcdf, (netcdf will pick up common when it
> needs it - fingers crossed).
>
> then try making it all. Of course it won't actually work, but that's
> what I've been trying to say all week!
> When it fails, ask Burlen for his netCDF adaptor stuff from visit and
> we can all get on with other stuff...
>
> JB
>
> > John,
> >
> > I must be missing something. I did as you specified below, then went to
> > the ParaView directory,
> > Ran ccmake several times, enabling the correct options per the CSCS web
> > site(PARAVIEW_EXTRA_EXTERNAL_MODULES,
> > PARAVIEW_USE_CSCSNetCDF, and the source directory variable) , and ran
> > make, but again, the same include file was not located, even though I
> > see it is there in the vtkCSCS directory tree.
> >
> > Was I supposed to run ccmake under the vtkCSCS trunk before running
> > ccmake for ParaView? I did try to do this,
> > Only to get an error concering "Policy" and the directions for resolving
> > the error were unclear.
> >
> > I am a novice concerning ccmake, as the first time I have used it was
> > last week.
> >
> > Thanks.
> >
> > Martha Tonkin
> >
> >
> >
> >
> > -----Original Message-----
> > From: John Biddiscombe [mailto:biddisco@cscs.ch]
> > Sent: Wednesday, March 25, 2009 10:21 AM
> > To: Tonkin, Martha E (IS)
> > Cc: Carbonari, Katie (IS); Paraview Mailing List
> > Subject: Re: [Paraview] using netcdf in paraview
> >
> > 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:biddisco@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.Carbonari@ngc.com>
> > > <mailto:Katie.Carbonari@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_content&task=view&id=96&Itemid
> > > =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,
> > > Katie
> > >
> > > _______________________________________________
> > > 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
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > http://www.paraview.org/mailman/listinfo/paraview
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> > >
> > > Follow this link to subscribe/unsubscribe:
> > > http://www.paraview.org/mailman/listinfo/paraview
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
>
>
> --
> 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
> ------------------------------------------------------------------------
>
> _______________________________________________
> 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
> Follow this link to subscribe/unsubscribe:
> http://www.paraview.org/mailman/listinfo/paraview
>
_______________________________________________
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
Follow this link to subscribe/unsubscribe:
http://www.paraview.org/mailman/listinfo/paraview
**** Kenneth Moreland
*** Sandia National Laboratories
***********
*** *** *** email: kmorel@sandia.gov
** *** ** phone: (505) 844-8919
*** web: http://www.cs.unm.edu/~kmorel
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<TITLE>Re: [Paraview] using netcdf in paraview</TITLE>
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<BODY>
<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>If you \
are using the CVS root anyway, I just checked in some netCDF readers. So \
hopefully you will now no longer need to do anything special.<BR> <BR>
-Ken<BR>
<BR>
<BR>
On 3/26/09 9:33 AM, "Burlen Loring" <<a \
href="burlen.loring@kitware.com">burlen.loring@kitware.com</a>> wrote:<BR> <BR>
</SPAN></FONT><BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN \
STYLE='font-size:11pt'>I will commit the work next week, along with a Wiki describing \
how to<BR> build/configure the dependencies. For planning purposes plan on late<BR>
next week.<BR>
<BR>
John Biddiscombe wrote:<BR>
> Martha<BR>
><BR>
> Build paraview as usual, ignore all the guff about<BR>
> PARAVIEW_EXTRA_EXTERNAL_MODULES, remove this from your paraview build,<BR>
> remove any CSCS addons you might have specified from paraview 'core'<BR>
> build.<BR>
><BR>
> Then build a new new project which will be plugins, using the<BR>
> cmakelists from the root of CSCS stuff. Enter the paraview build dir,<BR>
> enable CSCSCommon and netcdf, (netcdf will pick up common when it<BR>
> needs it - fingers crossed).<BR>
><BR>
> then try making it all. Of course it won't actually work, but that's<BR>
> what I've been trying to say all week!<BR>
> When it fails, ask Burlen for his netCDF adaptor stuff from visit and<BR>
> we can all get on with other stuff...<BR>
><BR>
> JB<BR>
><BR>
>> John,<BR>
>><BR>
>> I must be missing something. I did as you specified below, then went \
to<BR> >> the ParaView directory,<BR>
>> Ran ccmake several times, enabling the correct options per the CSCS web<BR>
>> site(PARAVIEW_EXTRA_EXTERNAL_MODULES,<BR>
>> PARAVIEW_USE_CSCSNetCDF, and the source directory variable) , and ran<BR>
>> make, but again, the same include file was not located, even though I<BR>
>> see it is there in the vtkCSCS directory tree.<BR>
>><BR>
>> Was I supposed to run ccmake under the vtkCSCS trunk before running<BR>
>> ccmake for ParaView? I did try to do this,<BR>
>> Only to get an error concering "Policy" and the directions for \
resolving<BR> >> the error were unclear.<BR>
>><BR>
>> I am a novice concerning ccmake, as the first time I have used it was<BR>
>> last week.<BR>
>><BR>
>> Thanks.<BR>
>><BR>
>> Martha Tonkin<BR>
>><BR>
>><BR>
>> <BR>
>><BR>
>> -----Original Message-----<BR>
>> From: John Biddiscombe [<a \
href="mailto:biddisco@cscs.ch">mailto:biddisco@cscs.ch</a>]<BR> >> Sent: \
Wednesday, March 25, 2009 10:21 AM<BR> >> To: Tonkin, Martha E (IS)<BR>
>> Cc: Carbonari, Katie (IS); Paraview Mailing List<BR>
>> Subject: Re: [Paraview] using netcdf in paraview<BR>
>><BR>
>> Martha (+put back on paraview list for reference and google)<BR>
>><BR>
>> My Bad. One of the changes I made to the netCDF code was to handle<BR>
>> series of files (one file per process, or one per timestep) using<BR>
>> another class in vtkCSCSCommon Best thing is check out all of it from<BR>
>> here...<BR>
>> <a href="https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/">https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/</a><BR>
>> and use the cmakelists in the root pv3-plugins folder.<BR>
>> you need CSCSCommomn and netCDF enabled.<BR>
>><BR>
>> Fix the netCDF reader and send me the patches please :)<BR>
>><BR>
>> JB<BR>
>><BR>
>> <BR>
>>> Katie,<BR>
>>><BR>
>>> I was able to check out vtkNetCDF from the SVN server; I had tried<BR>
>>> before using the web site's instructions, but it wouldn't work, I<BR>
>>> suppose because of our firewall; however the "https" in the \
URL that<BR> >>> Mr. Biddiscome gave us did make a difference.<BR>
>>><BR>
>>> However, when I attempted to build ParaView 3.4 with that vtkNetCDF<BR>
>>> module, I got an error once again, this time when for<BR>
>>> vtkNetCDFReader.cxx; what is missing is FileSeriesFinder.h.<BR>
>>><BR>
>>> I cannot find that include file anywhere, in ParaView3.4, \
ParaView3.3,<BR> >>> <BR>
>><BR>
>> <BR>
>>> etc, so I don't know if it was inadvertently left out of the \
vtkNetCDF<BR> >>> <BR>
>><BR>
>> <BR>
>>> distribution or what.<BR>
>>><BR>
>>> Martha<BR>
>>><BR>
>>><BR>
>>><BR>
>>> -----Original Message-----<BR>
>>> From: Carbonari, Katie (IS)<BR>
>>> Sent: Tuesday, March 24, 2009 5:15 PM<BR>
>>> To: Tonkin, Martha E (IS)<BR>
>>> Subject: FW: [Paraview] using netcdf in paraview<BR>
>>><BR>
>>><BR>
>>><BR>
>>><BR>
>>> -----Original Message-----<BR>
>>> From: John Biddiscombe [<a \
href="mailto:biddisco@cscs.ch">mailto:biddisco@cscs.ch</a>]<BR> >>> Sent: \
Tue 3/24/2009 5:09 PM<BR> >>> To: Berk Geveci<BR>
>>> Cc: Carbonari, Katie (IS); <a \
href="paraview@paraview.org">paraview@paraview.org</a><BR> >>> Subject: Re: \
[Paraview] using netcdf in paraview<BR> >>> <BR>
>>> Katie<BR>
>>><BR>
>>> Just looking again at the error messages makes me realize thet \
you're<BR> >>> using a very old vtkCSCSnetCDF the version in here<BR>
>>> <a href="https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/vtkNetCDF/">https://svn.cscs.ch/vtkContrib/trunk/vtkCSCS/vtkNetCDF/</a> \
is much more<BR> >>> recent and will at least compile without errors. It \
ewas intended for<BR> >>> meteo data (ocean/atmosphere) and so you should \
get something out of<BR> >>> it but the changes I made a few months back \
will have broken the core<BR> >>> load of data depending on which convention \
you are using.<BR> >>> My intention was to create subclasses for each \
supported convention,<BR> >>> rather than try to support all of them with \
aton of options - which is<BR> >>> <BR>
>><BR>
>> <BR>
>>> what the current reader does. If you're familiar with vtk code, \
you'll<BR> >>> <BR>
>><BR>
>> <BR>
>>> son work out how to fix it.<BR>
>>> I'll take a look at again it in a few weeks.<BR>
>>><BR>
>>> JB<BR>
>>><BR>
>>><BR>
>>> Hmmm. It sounds like there is version mismatch \
between ParaView<BR> >>> <BR>
>> and<BR>
>> <BR>
>>> the plugin. We deprecated those classes not long \
ago. Are you<BR> >>> <BR>
>> using<BR>
>> <BR>
>>> cvs ParaView?<BR>
>>> <BR>
>>> -berk<BR>
>>> <BR>
>>> 2009/3/23 Carbonari, Katie (IS) <<a \
href="Katie.Carbonari@ngc.com">Katie.Carbonari@ngc.com</a>><BR> >>> \
<<a href="mailto:Katie.Carbonari@ngc.com">mailto:Katie.Carbonari@ngc.com</a>> \
:<BR> >>> <BR>
>>><BR>
>>> Hi \
there. I'm trying to read netcdf data into paraview,<BR> >>> \
<BR> >> but am<BR>
>> <BR>
>>> having lots<BR>
>>> of \
issues. I was following these directions (from here:<BR> >>> \
<BR> >>> <a \
href="http://www.cscs.ch/index.php?option=com_content&task=view&id=96&Item \
id">http://www.cscs.ch/index.php?option=com_content&task=view&id=96&Itemid</a><BR>
>>> =1<BR>
>>> 32):<BR>
>>> <BR>
>>> Please \
build ParaView using the CMake advanced option<BR> >>> \
PARAVIEW_EXTRA_EXTERNAL_MODULES \
set to CSCSNetCDF rerun<BR> >>> <BR>
>> configure<BR>
>> <BR>
>>> and set<BR>
>>> PARAVIEW_USE_CSCSNetCDF \
to ON, then rerun configure and<BR> >>> <BR>
>> enter the<BR>
>> <BR>
>>> name of<BR>
>>> the \
directory where the source has been extracted.<BR> >>> \
Build \
paraview and the netCDF reader should be embedded.<BR> >>> \
Building as a \
vtk module is supported, documentation<BR> >>> <BR>
>> will be<BR>
>> <BR>
>>> provided as<BR>
>>> soon \
as possible. (Some changes have recently been made<BR> >>> \
<BR> >> which may<BR>
>> <BR>
>>> break the<BR>
>>> existing \
build, these will be fixed shortly).<BR> >>> \
<BR> >>> \
But when we \
make Paraview, it's not finding a bunch of<BR> >>> <BR>
>> files<BR>
>> <BR>
>>> (vtkMultiGroupDataInformation.h, \
vtkMultiGroupDataSet.h,<BR> >>> \
vtkMultiGroupSetAlgorithm.h).<BR>
>>> <BR>
>>> Any \
advice on how to make this work? Or maybe a better<BR> >>> \
<BR> >> way to read<BR>
>> <BR>
>>> in netcdf<BR>
>>> files?<BR>
>>> <BR>
>>> Thanks,<BR>
>>> Katie<BR>
>>> <BR>
>>> _______________________________________________<BR>
>>> Powered \
by www.kitware.com<BR> >>> \
<BR> >>> \
Visit other \
Kitware open-source projects at<BR> >>> \
<a \
href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><BR>
>>> <BR>
>>> Please \
keep messages on-topic and check the ParaView<BR> >>> <BR>
>> Wiki at:<BR>
>> <BR>
>>> <a \
href="http://paraview.org/Wiki/ParaView">http://paraview.org/Wiki/ParaView</a><BR> \
>>> <BR> \
>>> Follow \
this link to subscribe/unsubscribe:<BR> >>> \
<a \
href="http://www.paraview.org/mailman/listinfo/paraview">http://www.paraview.org/mailman/listinfo/paraview</a><BR>
>>> <BR>
>>> <BR>
>>> <BR>
>>><BR>
>>> _______________________________________________<BR>
>>> Powered by www.kitware.com<BR>
>>> <BR>
>>> Visit other Kitware open-source projects at<BR>
>>> <a href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><BR>
>>> <BR>
>>> Please keep messages on-topic and check the \
ParaView Wiki at:<BR> >>> <a \
href="http://paraview.org/Wiki/ParaView">http://paraview.org/Wiki/ParaView</a><BR> \
>>> <BR> >>> Follow this \
link to subscribe/unsubscribe:<BR> >>> <a \
href="http://www.paraview.org/mailman/listinfo/paraview">http://www.paraview.org/mailman/listinfo/paraview</a><BR>
>>> <BR>
>>><BR>
>>><BR>
>>><BR>
>>> <BR>
>>> <BR>
>><BR>
>><BR>
>> <BR>
><BR>
><BR>
> --<BR>
> John Biddiscombe, \
&n \
bsp; email:biddisco \
@ cscs.ch<BR> > <a href="http://www.cscs.ch/">http://www.cscs.ch/</a><BR>
> CSCS, Swiss National Supercomputing Centre | Tel: +41 (91) \
610.82.07<BR> > Via Cantonale, 6928 Manno, Switzerland \
| Fax: +41 (91) 610.82.82<BR> > \
------------------------------------------------------------------------<BR> ><BR>
> _______________________________________________<BR>
> Powered by www.kitware.com<BR>
><BR>
> Visit other Kitware open-source projects at <a \
href="http://www.kitware.com/opensource/opensource.html">http://www.kitware.com/opensource/opensource.html</a><BR>
><BR>
> Please keep messages on-topic and check the ParaView Wiki at: <a \
href="http://paraview.org/Wiki/ParaView">http://paraview.org/Wiki/ParaView</a><BR> \
><BR> > Follow this link to subscribe/unsubscribe:<BR>
> <a href="http://www.paraview.org/mailman/listinfo/paraview">http://www.paraview.org/mailman/listinfo/paraview</a><BR>
> <BR>
<BR>
_______________________________________________<BR>
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<BR>
Visit other Kitware open-source projects at <a \
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<BR>
Please keep messages on-topic and check the ParaView Wiki at: <a \
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<BR>
</SPAN></FONT></BLOCKQUOTE><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN \
STYLE='font-size:11pt'><BR> </SPAN></FONT><FONT SIZE="1"><FONT FACE="Monaco, Courier \
New"><SPAN STYLE='font-size:7.5pt'><BR> **** \
Kenneth Moreland<BR> *** \
Sandia National Laboratories<BR>
*********** <BR>
*** *** *** email: <a href="kmorel@sandia.gov">kmorel@sandia.gov</a><BR>
** *** ** phone: (505) 844-8919<BR>
*** web: <a \
href="http://www.cs.unm.edu/~kmorel">http://www.cs.unm.edu/~kmorel</a><BR> \
</SPAN></FONT></FONT><FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN \
STYLE='font-size:11pt'><BR> </SPAN></FONT>
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