Re: [Paraview] [Paraview-developers] [ANNOUNCE] ParaView 5.5.1 now available for download

[Andy Bauer]

Hi Mark,

The VTKm patch issue should be resolved in 5.5.2. I'd love to have the
Catalyst API changes in 5.5.2 but that's a bit much for a patch change. 5.6
will have it though and that's due out in September so people won't have to
wait too long for that.

Best,
Andy

On Thu, Jun 7, 2018 at 11:45 AM Mark Olesen 
wrote:

> If we are looking for 5.5.2 bits:
>
> In 5.5.1 it seems that I still need to patch
> VTK/ThirdParty/vtkm/vtk-m/CMake/VTKmDetermineVersion.cmake
>
> (commit cf91ca520e38faa1afae5d0bcc6788b2b4660c3e)
>
>
> I that Andy's catalyst changes might have made it in, but wasn't really
> surprised not to see them since they do change the API. Nonetheless,
> I'll express them as a wish:
>
> CoProcessing/Catalyst/vtkCPProcessor.cxx
> CoProcessing/Catalyst/vtkCPProcessor.h
> CoProcessing/Catalyst/vtkCPXMLPWriterPipeline.cxx
> Wrapping/Python/paraview/coprocessing.py
>
>
> Cheers,
> /mark
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Re: [Paraview] Adding Filters to Catalyst

[Andy Bauer]

Hi Gregg,

Catalyst will use all of the MPI ranks in the global communicator unless
you pass it another MPI communicator upon initialization. It sounds like
the data isn't getting constructed in the adaptor the way you think it is.
You may want to try the Process Id Scalars filter to see where the data is
really located and add some print statements in the adaptor to verify the
behavior.

Best,
Andy

On Wed, Jun 6, 2018 at 2:08 PM Gregg Streuber <
gregg.streu...@aero.bombardier.com> wrote:

> Hey Andy,
>
>
>
> Apologies, I must have hit “reply” without thinking, rather than reply
> all.  I’ve actually managed to resolve that issue, it turned out to be a
> configuration issue with my build of OpenGL.
>
>
>
> I do have another question though.  I’ve been playing around processing
> some data using Catalyst’s python scripting in parallel and the results
> aren’t quite what I expected.  What I’ve been using is a toy 50,000,000
> node cube mesh with an arbitrary velocity field, and having Catalyst do
> some assorted processing – taking cuts etc.  I’ve divided the mesh into 256
> blocks using the VTKMultiBlockDataSet structure, on 256 cores.  But when I
> load the results into Paraview it only indicates 12 VTKBlocks on the
> VTBBlockColors filter. There are 256 divisions in the mesh, but 244 of them
> are duplicates, coloured with one of the 1st 12 colours.
>
>
>
> Adding new lines to the color map, mapped to values >11, doesn’t appear to
> change anything.
>
>
>
> I’m also not seeing much in the way  of performance variation when I use
> 13-256 cores, it’s only when I drop below 12 that things take appreciably
> longer.
>
>
>
> Is Paraview by default only taking advantage of 12 cores at a time?  Is
> this something I can change?
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Wednesday, June 06, 2018 10:18 AM
> *To:* Gregg Streuber ; Paraview (
> parav...@paraview.org) 
> *Subject:* Re: [Paraview] Adding Filters to Catalyst
>
>
>
> Hi Gregg,
>
>
>
> Please keep the conversations on the mailing list so that everyone can
> participate (also, emails get lost in my inbox so that can also delay a
> quick response).
>
>
>
> I believe that the Catalyst examples should compile properly with all of
> the Catalyst editions (though I haven't tested them). If you were able to
> use an OpenGL with some editions then that should work for any edition that
> depends on OpenGL. Are you working with a Catalyst edition build directory
> or an install directory? If you give me some more information on how to
> reproduce the error I can try and track things down.
>
>
>
> Also, what version of ParaView are you using?
>
>
>
> Cheers,
>
> Andy
>
>
>
> On Fri, Jun 1, 2018 at 3:37 PM Gregg Streuber <
> gregg.streu...@aero.bombardier.com> wrote:
>
> Hi Andy,
>
>
>
> Thanks for the information.  I had a full compile of Paraview running on
> the side just in case, I was just curious if there was an easy and
> efficient way to customize a Catalyst install.
>
>
>
> I’ve since gotten Paraview compiled, but when I try to test the
> functionality using some of the included Catalyst examples
> (Examples/Catalyst) they don’t work.  Specifically several of them throw
> “undefined reference” errors during compilation, referring to a couple of
> OpenGL files in the Paraview install.  These examples worked fine when I
> compiled them with the Catalyst build I was testing before.  Do these
> examples require a specific build of OpenGL (or are they incompatible with
> certain other modules)?
>
>
>
> Thanks,
> Gregg
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Friday, June 01, 2018 11:46 AM
> *To:* Gregg Streuber 
> *Cc:* paraview@public.kitware.com
> *Subject:* Re: [Paraview] Adding Filters to Catalyst
>
>
>
> Hi Gregg,
>
>
>
> You can always use a full build of ParaView for Catalyst to make sure you
> get all of the filters available during Catalyst runs.
>
>
>
> There is information at
> https://blog.kitware.com/paraview-catalyst-editions-what-are-they/ which
> gives details about the editions but there's currently not a lot of details
> on how to make your own edition. Editing the cmake.sh script to add in more
> VTK filters will likely not work as the Catalyst editions don't even have
> all of the source code from the ParaView source.
>
>
>
> As for finding the full list of filters and modules available, the blog
> post has some of that but it's changed some. My recommendation would be to
> build an edition with Python enabled and then use pvpython to see what's
> available. Alternatively y

Re: [Paraview] Adding Filters to Catalyst

[Andy Bauer]

Hi Gregg,

Please keep the conversations on the mailing list so that everyone can
participate (also, emails get lost in my inbox so that can also delay a
quick response).

I believe that the Catalyst examples should compile properly with all of
the Catalyst editions (though I haven't tested them). If you were able to
use an OpenGL with some editions then that should work for any edition that
depends on OpenGL. Are you working with a Catalyst edition build directory
or an install directory? If you give me some more information on how to
reproduce the error I can try and track things down.

Also, what version of ParaView are you using?

Cheers,
Andy

On Fri, Jun 1, 2018 at 3:37 PM Gregg Streuber <
gregg.streu...@aero.bombardier.com> wrote:

> Hi Andy,
>
>
>
> Thanks for the information.  I had a full compile of Paraview running on
> the side just in case, I was just curious if there was an easy and
> efficient way to customize a Catalyst install.
>
>
>
> I’ve since gotten Paraview compiled, but when I try to test the
> functionality using some of the included Catalyst examples
> (Examples/Catalyst) they don’t work.  Specifically several of them throw
> “undefined reference” errors during compilation, referring to a couple of
> OpenGL files in the Paraview install.  These examples worked fine when I
> compiled them with the Catalyst build I was testing before.  Do these
> examples require a specific build of OpenGL (or are they incompatible with
> certain other modules)?
>
>
>
> Thanks,
> Gregg
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Friday, June 01, 2018 11:46 AM
> *To:* Gregg Streuber 
> *Cc:* paraview@public.kitware.com
> *Subject:* Re: [Paraview] Adding Filters to Catalyst
>
>
>
> Hi Gregg,
>
>
>
> You can always use a full build of ParaView for Catalyst to make sure you
> get all of the filters available during Catalyst runs.
>
>
>
> There is information at
> https://blog.kitware.com/paraview-catalyst-editions-what-are-they/ which
> gives details about the editions but there's currently not a lot of details
> on how to make your own edition. Editing the cmake.sh script to add in more
> VTK filters will likely not work as the Catalyst editions don't even have
> all of the source code from the ParaView source.
>
>
>
> As for finding the full list of filters and modules available, the blog
> post has some of that but it's changed some. My recommendation would be to
> build an edition with Python enabled and then use pvpython to see what's
> available. Alternatively you could look at files like filters.xml in the
> Catalyst source code to see what's there. It's not ideal but allows you to
> check on stuff before actually running a simulation.
>
>
>
> Best,
>
> Andy
>
>
>
> On Fri, Jun 1, 2018 at 10:10 AM Gregg Streuber <
> gregg.streu...@aero.bombardier.com> wrote:
>
> Hi All,
>
>
>
> I’ve recently installed the most full-featured version of Catalyst
> available on the website, but I noticed it’s lacking a lot of filters that
> I need very much (streamlines, for example).  I understand the installed
> packages are fully customizable, but can’t find any good documentation on
> how to go about doing this.   Is this as simple as enabling different
> options in the cmake.sh script? And if so, is there a complete list of the
> filters in paraview and the modules that contain them somewhere?
>
>
>
> Cheers,
>
> Gregg
>
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>
> ParaView discussion is moving! Please visit
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>
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Re: [Paraview] Adding Filters to Catalyst

[Andy Bauer]

Hi Gregg,

You can always use a full build of ParaView for Catalyst to make sure you
get all of the filters available during Catalyst runs.

There is information at
https://blog.kitware.com/paraview-catalyst-editions-what-are-they/ which
gives details about the editions but there's currently not a lot of details
on how to make your own edition. Editing the cmake.sh script to add in more
VTK filters will likely not work as the Catalyst editions don't even have
all of the source code from the ParaView source.

As for finding the full list of filters and modules available, the blog
post has some of that but it's changed some. My recommendation would be to
build an edition with Python enabled and then use pvpython to see what's
available. Alternatively you could look at files like filters.xml in the
Catalyst source code to see what's there. It's not ideal but allows you to
check on stuff before actually running a simulation.

Best,
Andy

On Fri, Jun 1, 2018 at 10:10 AM Gregg Streuber <
gregg.streu...@aero.bombardier.com> wrote:

> Hi All,
>
>
>
> I’ve recently installed the most full-featured version of Catalyst
> available on the website, but I noticed it’s lacking a lot of filters that
> I need very much (streamlines, for example).  I understand the installed
> packages are fully customizable, but can’t find any good documentation on
> how to go about doing this.   Is this as simple as enabling different
> options in the cmake.sh script? And if so, is there a complete list of the
> filters in paraview and the modules that contain them somewhere?
>
>
>
> Cheers,
>
> Gregg
> ___
> Powered by www.kitware.com
>
> ParaView discussion is moving! Please visit
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>
> 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:
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Re: [Paraview] catalyst with parallel rendering

[Andy Bauer]

Hi Mark,

If you want to create images from Catalyst runs you'll probably want to
build the ParaView that you're linking to with either OSMesa or EGL (and Qt
disabled). This gets around needing the X context for rendering since I
believe running with offscreen enabled is not sufficient. EGL comes with
most of the NVIDIA drivers -- see
https://blog.kitware.com/off-screen-rendering-through-the-native-platform-interface-egl/
for how to build PV with it. If you want to go the OSMesa route I'd
recommend using the ParaView superbuild (
https://gitlab.kitware.com/paraview/paraview-superbuild) to build it for
you.

Does this answer your question? I just got back from vacation and am trying
to catch up on more things than my brain can currently handle so let me
know if you have more questions.

Best,
Andy



On Mon, May 28, 2018 at 11:25 AM Mark Olesen 
wrote:

> For the mailing list, since this must probably be a FAQ (even if I seem
> to find the answer in the usual places).
>
> I would like to have paraview rendering in parallel for a simulation
> with catalyst. For simplicity, I'm fiddling about on a local
> workstation, but would like to generalize later. it should work without
> live visualization enabled, or requiring a GUI to connect.
>
> I'd presume using something like the following
>
> mpirun -np 12 pvserver --server-port=123456 --force-offscreen-rendering
>
> would be setup a parallel rendering session as usual. However, after
> scouring docs there doesn't seem to be an obvious way to connect this
> within catalyst (without a GUI).
>
> The only access point that I seem to find is to define an MPI
> communicator for initializing catalyst after some how (some hand-waving
> here) querying a pvserver connection for its host topology and defining
> an appropriate communicator.
>
> Cheers,
>
> /mark
> ___
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>
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Re: [Paraview] Resample To Image with Catalyst

[Andy Bauer]

Hi Petr,

Could you try adding in the following to your Python script after the
coprocessor.RegisterWriter() line:
writer.DataMode = 'Ascii'

Please let me know if that fixes the issue for you. This isn't the desired
fix but something to at least verify that I can reproduce your issue.

Thanks,
Andy



On Mon, May 21, 2018 at 12:16 PM Petr Valenta  wrote:

> Hello,
>
> the code which I am using is instrumented with Catalyst.
> I am trying to process simulation data using ResampleToImage filter and
> then to store the result on a disk.
>
> In the Python pipeline I have something like:
>
> adaptor_input = coprocessor.CreateProducer(datadescription, 'input')
> resample = ResampleToImage(Input=adaptor_input)
> resample.UseInputBounds = True
> resample.SamplingDimensions = [256, 256, 256]
> writer = servermanager.writers.XMLPImageDataWriter(Input=resample)
> coprocessor.RegisterWriter(writer, filename='resample_%t.pvti', freq=10)
>
> When I check the results in ParaView, the grid is correct but the data
> array appended on it contains only zeros. When I skip the filter and dump
> directly the adaptor_input, the data array contains correct values. Could
> you, please, help me to resolve this issue?
>
> Thank you.
>
> Kind regards,
> Petr
>
>
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Re: [Paraview] [EXTERNAL] Re: pvtm file format

[Andy Bauer]

No problem. We got where we needed to be eventually -- it would  have gone
faster if I didn't "remember" that the .pvtm isn't a proper VTK file
extension :)

On Tue, May 15, 2018 at 10:58 PM Scott, W Alan <wasc...@sandia.gov> wrote:

> OK, although dense and slow, I finally got it.  Thanks, good explanation
> to both of you.  I will close the bug I wrote.
>
>
>
> Thanks guys,
>
>
>
> Alan
>
>
>
> *From: *Shawn Waldon <shawn.wal...@kitware.com>
> *Date: *Tuesday, May 15, 2018 at 3:09 PM
> *To: *Andy Bauer <andy.ba...@kitware.com>
> *Cc: *W Scott <wasc...@sandia.gov>, "parav...@paraview.org" <
> parav...@paraview.org>
> *Subject: *Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
> An example: If I make a PNG writer in the code and set the filename it is
> supposed to write to "foo.pgn" it will write a file named "foo.pgn" because
> that is what it was programmed to do.  The data in the file will still be
> in the PNG format, the filename will just have the wrong extension.  It is
> still a PNG file and if I rename it to foo.png, most programs will read it
> correctly.  But while the extension is misspelled very few programs (if
> any) will read it.
>
> HTH,
>
> Shawn
>
>
>
> On Tue, May 15, 2018 at 4:53 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
> If the user did that, then he/she explicitly set the file extension to be
> .pvtm instead of the default .vtm when creating the Catalyst multiblock
> dataset writer for the Catalyst script. There is only one XML multiblock
> data reader and writer.
>
> When a user adds a writer when making a Catalyst Python script by default
> it will have the proper file extension but they are allowed to change that
> file extension. The file extension that the user gives the filename doesn't
> affect the file format itself (i.e. what writer is used).
>
> Does that make sense?
>
>
>
> On Tue, May 15, 2018 at 4:12 PM Scott, W Alan <wasc...@sandia.gov> wrote:
>
> Again, does this then mean we should delete pvtm file formats Catalyst
> writers?  I have a user that created a pvtm file recently, I believe using
> Catalyst…
>
>
>
> *From: *Andy Bauer <andy.ba...@kitware.com>
> *Date: *Tuesday, May 15, 2018 at 1:00 PM
> *To: *W Scott <wasc...@sandia.gov>
> *Cc: *Utkarsh Ayachit <utkarsh.ayac...@kitware.com>, "
> parav...@paraview.org" <parav...@paraview.org>
> *Subject: *Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
>
>
> From my investigation and not being able to find any pvtm in either
> today's ParaView or several of the 3.* versions (what Ken's old bug report
> referred to) I'd say that .pvtm was never officially or even unofficially a
> VTK file format extension used by the XML multiblock reader or writer. I'd
> say that .vtm is the one and only XML multiblock data extension and close
> the issue.
>
>
>
> On Tue, May 15, 2018 at 11:48 AM Scott, W Alan <wasc...@sandia.gov> wrote:
>
> Trying to wrap my head around what you said.  Really basic question – is
> .pvtm files a viable file format?  Either it should be supported in
> ParaView readers, or it should be removed from Catalyst and VTK – correct?
>
>
>
> I wrote up a bug here:
> https://gitlab.kitware.com/paraview/paraview/issues/18172
>
>
>
> Alan
>
>
>
> *From: *Andy Bauer <andy.ba...@kitware.com>
> *Date: *Tuesday, May 15, 2018 at 8:33 AM
> *To: *W Scott <wasc...@sandia.gov>
> *Cc: *Utkarsh Ayachit <utkarsh.ayac...@kitware.com>, "
> parav...@paraview.org" <parav...@paraview.org>
> *Subject: *Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
> Hi Alan,
>
>
>
> I wouldn't describe it as a redundant file format, just a redundant file
> extension (like ExodusII with .e, .ex2, etc.). Actually, looking through
> the PV and VTK source code, like Utkarsh did before, there doesn't look to
> be anything that refers to .pvtm so maybe I'm just remembering things wrong
> here. Looking back though (https://www.vtk.org/Bug/view.php?id=10498) it
> does seem like at one time we used the .pvtm file extension but maybe that
> was by accident though.
>
>
>
> As for writing out files from Catalyst, or even from ParaView, a user can
> select the writer and specify whatever they want for the file extension.
> Maybe that's where the issue arose.
>
>
>
> Best,
>
> Andy
>
>
>
> On Mon, May 14, 2018 at 9:37 PM Scott, W Alan <wasc...@sandia.gov> wrote:
>
> Thanks Andy.  I’m hearing of numerous issues like thus, trying to wrap my
> head around same.
>
>
>
> L

Re: [Paraview] [EXTERNAL] Re: pvtm file format

[Andy Bauer]

If the user did that, then he/she explicitly set the file extension to be
.pvtm instead of the default .vtm when creating the Catalyst multiblock
dataset writer for the Catalyst script. There is only one XML multiblock
data reader and writer.

When a user adds a writer when making a Catalyst Python script by default
it will have the proper file extension but they are allowed to change that
file extension. The file extension that the user gives the filename doesn't
affect the file format itself (i.e. what writer is used).

Does that make sense?

On Tue, May 15, 2018 at 4:12 PM Scott, W Alan <wasc...@sandia.gov> wrote:

> Again, does this then mean we should delete pvtm file formats Catalyst
> writers?  I have a user that created a pvtm file recently, I believe using
> Catalyst…
>
>
>
> *From: *Andy Bauer <andy.ba...@kitware.com>
> *Date: *Tuesday, May 15, 2018 at 1:00 PM
> *To: *W Scott <wasc...@sandia.gov>
> *Cc: *Utkarsh Ayachit <utkarsh.ayac...@kitware.com>, "
> parav...@paraview.org" <parav...@paraview.org>
> *Subject: *Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
>
>
> From my investigation and not being able to find any pvtm in either
> today's ParaView or several of the 3.* versions (what Ken's old bug report
> referred to) I'd say that .pvtm was never officially or even unofficially a
> VTK file format extension used by the XML multiblock reader or writer. I'd
> say that .vtm is the one and only XML multiblock data extension and close
> the issue.
>
>
>
> On Tue, May 15, 2018 at 11:48 AM Scott, W Alan <wasc...@sandia.gov> wrote:
>
> Trying to wrap my head around what you said.  Really basic question – is
> .pvtm files a viable file format?  Either it should be supported in
> ParaView readers, or it should be removed from Catalyst and VTK – correct?
>
>
>
> I wrote up a bug here:
> https://gitlab.kitware.com/paraview/paraview/issues/18172
>
>
>
> Alan
>
>
>
> *From: *Andy Bauer <andy.ba...@kitware.com>
> *Date: *Tuesday, May 15, 2018 at 8:33 AM
> *To: *W Scott <wasc...@sandia.gov>
> *Cc: *Utkarsh Ayachit <utkarsh.ayac...@kitware.com>, "
> parav...@paraview.org" <parav...@paraview.org>
> *Subject: *Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
> Hi Alan,
>
>
>
> I wouldn't describe it as a redundant file format, just a redundant file
> extension (like ExodusII with .e, .ex2, etc.). Actually, looking through
> the PV and VTK source code, like Utkarsh did before, there doesn't look to
> be anything that refers to .pvtm so maybe I'm just remembering things wrong
> here. Looking back though (https://www.vtk.org/Bug/view.php?id=10498) it
> does seem like at one time we used the .pvtm file extension but maybe that
> was by accident though.
>
>
>
> As for writing out files from Catalyst, or even from ParaView, a user can
> select the writer and specify whatever they want for the file extension.
> Maybe that's where the issue arose.
>
>
>
> Best,
>
> Andy
>
>
>
> On Mon, May 14, 2018 at 9:37 PM Scott, W Alan <wasc...@sandia.gov> wrote:
>
> Thanks Andy.  I’m hearing of numerous issues like thus, trying to wrap my
> head around same.
>
>
>
> Let’s start with a few questions.  Where is the .pvtm file format
> documented?  Google doesn’t know...  Next, why have two redundant file
> formats?  One should be deprecated.  Why can Catalyst write this file
> format?  And last, of course, why can’t ParaView read it?
>
>
>
> Alan
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Monday, May 14, 2018 7:31 PM
> *To:* Scott, W Alan <wasc...@sandia.gov>
> *Cc:* Ayachit, Utkarsh (External Contacts) <utkarsh.ayac...@kitware.com>;
> Paraview (parav...@paraview.org) <parav...@paraview.org>
> *Subject:* Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
> The .pvtm is the same as the .vtm file, just a redundant file extension.
> Really, the .vtm format is parallel/partition aware where as the other .vt*
> extensions have a partitioned .pvt* format.
>
> I'm a bit surprised that PV doesn't associate the .pvtm file with
> multiblock datasets. If you try to read in a .pvtm file though you just
> need to properly associate it with the XML multiblock data reader.
>
>
>
> On Mon, May 14, 2018 at 9:14 PM Scott, W Alan via ParaView <
> paraview@public.kitware.com> wrote:
>
> I’ve never heard of these files either.  From my user:
>
>
>
>
>
> I am writing planes of data in parallel with XMLMultiBlockWriter and it is
> generating *pvtm files.  However, paraview doesn’t seem to support this
> file format for reading?  I am

Re: [Paraview] [EXTERNAL] Re: pvtm file format

[Andy Bauer]

Hi Alan,

I wouldn't describe it as a redundant file format, just a redundant file
extension (like ExodusII with .e, .ex2, etc.). Actually, looking through
the PV and VTK source code, like Utkarsh did before, there doesn't look to
be anything that refers to .pvtm so maybe I'm just remembering things wrong
here. Looking back though (https://www.vtk.org/Bug/view.php?id=10498) it
does seem like at one time we used the .pvtm file extension but maybe that
was by accident though.

As for writing out files from Catalyst, or even from ParaView, a user can
select the writer and specify whatever they want for the file extension.
Maybe that's where the issue arose.

Best,
Andy

On Mon, May 14, 2018 at 9:37 PM Scott, W Alan <wasc...@sandia.gov> wrote:

> Thanks Andy.  I’m hearing of numerous issues like thus, trying to wrap my
> head around same.
>
>
>
> Let’s start with a few questions.  Where is the .pvtm file format
> documented?  Google doesn’t know...  Next, why have two redundant file
> formats?  One should be deprecated.  Why can Catalyst write this file
> format?  And last, of course, why can’t ParaView read it?
>
>
>
> Alan
>
>
>
> *From:* Andy Bauer [mailto:andy.ba...@kitware.com]
> *Sent:* Monday, May 14, 2018 7:31 PM
> *To:* Scott, W Alan <wasc...@sandia.gov>
> *Cc:* Ayachit, Utkarsh (External Contacts) <utkarsh.ayac...@kitware.com>;
> Paraview (parav...@paraview.org) <parav...@paraview.org>
> *Subject:* Re: [Paraview] [EXTERNAL] Re: pvtm file format
>
>
>
> The .pvtm is the same as the .vtm file, just a redundant file extension.
> Really, the .vtm format is parallel/partition aware where as the other .vt*
> extensions have a partitioned .pvt* format.
>
> I'm a bit surprised that PV doesn't associate the .pvtm file with
> multiblock datasets. If you try to read in a .pvtm file though you just
> need to properly associate it with the XML multiblock data reader.
>
>
>
> On Mon, May 14, 2018 at 9:14 PM Scott, W Alan via ParaView <
> paraview@public.kitware.com> wrote:
>
> I’ve never heard of these files either.  From my user:
>
>
>
>
>
> I am writing planes of data in parallel with XMLMultiBlockWriter and it is
> generating *pvtm files.  However, paraview doesn’t seem to support this
> file format for reading?  I am trying to visualize the results and I can
> read the individual *vtp files, but it doesn’t accept the parallel file.
>
>
>
> Then:
>
>
>
> I will try to put something together for you soon.  I am writing this
> dataset from a slice while running catalyst.  I found a work around by
> using the MergeBlocks filter on the slice and then dumping that as an
> unstructured grid via XMLPUnstructuredGridWriter.
>
>
>
> Back to me.
>
>
>
> “.  I am writing this dataset from a slice while running catalyst.”  So, I
> figured I would start by asking if this is a Catalyst/ ParaView/ VTK file
> format (that I had never heard of)...I have asked user for a dataset.
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
>
>
> *From:* Utkarsh Ayachit [mailto:utkarsh.ayac...@kitware.com]
> *Sent:* Monday, May 14, 2018 7:08 PM
> *To:* Scott, W Alan <wasc...@sandia.gov>
> *Cc:* ParaView <parav...@paraview.org>
> *Subject:* [EXTERNAL] Re: [Paraview] pvtm file format
>
>
>
> I am not sure. A quick grep through the code in ParaView/VTK doesn't yield
> a hit. What's the context in which you encountered this?
>
>
>
> Utkarsh
>
>
>
> On Mon, May 14, 2018 at 9:05 PM Scott, W Alan via ParaView <
> paraview@public.kitware.com> wrote:
>
> What is a .pvtm file?  How can I make one with sources?
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
> 
>
> W. Alan Scott
>
> ParaView Support Manager
>
>
>
> SAIC
>
> Sandia National Laboratories, MS 0807
>
> Org 9326 - Building 880 A1-K
>
> (505) 284-0932   FAX (505) 284-5619
>
>
>
> “When the facts change, I change my mind. What do you do, sir?”
>
> John Maynard Keynes
>
>
>
> -
>
>
>
> ___
> 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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Re: [Paraview] [EXTERNAL] Re: pvtm file format

[Andy Bauer]

The .pvtm is the same as the .vtm file, just a redundant file extension.
Really, the .vtm format is parallel/partition aware where as the other .vt*
extensions have a partitioned .pvt* format.

I'm a bit surprised that PV doesn't associate the .pvtm file with
multiblock datasets. If you try to read in a .pvtm file though you just
need to properly associate it with the XML multiblock data reader.

On Mon, May 14, 2018 at 9:14 PM Scott, W Alan via ParaView <
paraview@public.kitware.com> wrote:

> I’ve never heard of these files either.  From my user:
>
>
>
>
>
> I am writing planes of data in parallel with XMLMultiBlockWriter and it is
> generating *pvtm files.  However, paraview doesn’t seem to support this
> file format for reading?  I am trying to visualize the results and I can
> read the individual *vtp files, but it doesn’t accept the parallel file.
>
>
>
> Then:
>
>
>
> I will try to put something together for you soon.  I am writing this
> dataset from a slice while running catalyst.  I found a work around by
> using the MergeBlocks filter on the slice and then dumping that as an
> unstructured grid via XMLPUnstructuredGridWriter.
>
>
>
> Back to me.
>
>
>
> “.  I am writing this dataset from a slice while running catalyst.”  So, I
> figured I would start by asking if this is a Catalyst/ ParaView/ VTK file
> format (that I had never heard of)...I have asked user for a dataset.
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
>
>
> *From:* Utkarsh Ayachit [mailto:utkarsh.ayac...@kitware.com]
> *Sent:* Monday, May 14, 2018 7:08 PM
> *To:* Scott, W Alan 
> *Cc:* ParaView 
> *Subject:* [EXTERNAL] Re: [Paraview] pvtm file format
>
>
>
> I am not sure. A quick grep through the code in ParaView/VTK doesn't yield
> a hit. What's the context in which you encountered this?
>
>
>
> Utkarsh
>
>
>
> On Mon, May 14, 2018 at 9:05 PM Scott, W Alan via ParaView <
> paraview@public.kitware.com> wrote:
>
> What is a .pvtm file?  How can I make one with sources?
>
>
>
> Thanks,
>
>
>
> Alan
>
>
>
> 
>
> W. Alan Scott
>
> ParaView Support Manager
>
>
>
> SAIC
>
> Sandia National Laboratories, MS 0807
>
> Org 9326 - Building 880 A1-K
>
> (505) 284-0932   FAX (505) 284-5619
>
>
>
> “When the facts change, I change my mind. What do you do, sir?”
>
> John Maynard Keynes
>
>
>
> -
>
>
>
> ___
> 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:
> https://public.kitware.com/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:
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>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
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Re: [Paraview] extract voriticy and follow it in time

[Andy Bauer]

Hi Ufuk,

The threshold filter operates on scalar/single component arrays only. Also,
underneath the covers it operates on cell data exclusively so if you
request thresholding on point data it will do a point data to cell data
operation as well.

I'm not aware of any filters in PV that would allow you to track a
thresholded quantity. Unfortunately I can't think of any moderately easy
way to do this in PV either.

Best,
Andy

On Fri, Apr 20, 2018 at 4:40 PM, Ufuk Turuncoglu <
u.utku.turunco...@be.itu.edu.tr> wrote:

> I could have vorticty as a new variable by using PythonCalculator. now, i
> need to follow points extracted from vorticity field in time and create
> poly line. so, I tried particle tracer and particle path bu no luck yet!
>
> Regards,
>
> --ufuk
>
> - Original Message -
> From: "Ufuk Utku Turuncoglu (BE)" 
> To: "paraview" 
> Sent: Friday, April 20, 2018 3:09:35 PM
> Subject: [Paraview] extract voriticy and follow it in time
>
> Hi,
>
> I would like to use Threshold filter for Vorticity field calculated by
> ComputeDreivatives but in the variables list i could not see Vorticity
> field. So, is it possible to do it with any other way such as
> programmable filter etc. If i extract it from the whole data, then, i
> would like to follow it to create polyline that represent path of the
> selected region. So, is there any simple way to do that?
>
> Best Regards,
>
> --ufuk
>
> ___
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>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
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Re: [Paraview] AppendAttributes issue

[Andy Bauer]

Any chance you could share the datasets and maybe a state file so that I
could try to reproduce your issue?

I can't think of anything off the top of my head that would case this.

On Wed, Apr 4, 2018 at 1:13 PM, Christian Adrián Álvarez Báez <
christian.alvarez...@gmail.com> wrote:

> Hello,
>
> I have an UCD (ASCII) and a DEM, I would like to color the UCD by
> elevation (since the UCD alone just can be color by Material ID, which has
> nothing to do with elevation). For this I got a DEM with the exactly same
> array than the UCD. I apply AppendAtributes to both and I can color now
> with elevation. The problem is that the elevation color is upside down. I
> attached a picture to make sense.
>
> Thank you very much for your attention. I hope you could help me.
> Christian
>
> ___
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Re: [Paraview] Down sample data?

[Andy Bauer]

You could try the Append Attributes filter instead of the programmable
filter if the geometry is the same for both/all inputs into the Append
Attributes filter. To use the Append Attributes filter just select the
filters in the Pipeline Browser that you want to compare.

Note that for 5.4.1 and earlier you'll need to use something like the
Calculator filter to rename the arrays while for the 5.5 release candidate
it will do automatic renaming for you.

On Sat, Mar 31, 2018 at 2:31 PM, John Haase <jhaa...@nd.edu> wrote:

> Andy,
>
> I found that the "plot over line" filter will allow me to do sampling.
> However, that has lead me into a second problem.
>
> So I feed 2 "plot over line" filters into a "programmable" filter (to take
> the difference between the two datasets). I then integrate the difference
> over space using the "integrate variable" filter. Then to extract all the
> time step values, I try to use the "plot selection over time" filter;
> however, Paraview crashes when I try to apply the "plot selection over
> time" filter.
>
> Any advice?
>
> Regards,
>
> John R. Haase
> jhaa...@nd.edu
>
> On Sat, Mar 31, 2018 at 2:24 PM, Andy Bauer <andy.ba...@kitware.com>
> wrote:
>
>> Hi John,
>>
>> It depends on what type of grid you have. For image data, rectilinear
>> grid or structured grid the extract subset filter is probably the best (for
>> other grid types it will be grayed out since it's not applicable to those
>> grid types). Otherwise, you can use resample with dataset.
>>
>> Note that both of these will work nicely with point data but for cell
>> data you may want to use the cell data to point data filter first.
>>
>> On Sat, Mar 31, 2018 at 9:14 AM, John Haase <jhaa...@nd.edu> wrote:
>>
>>> Hello all,
>>>
>>> I'm trying to down select my data so I can do a grid convergence study.
>>> How would I go about doing this?
>>>
>>> I found an old post (https://public.kitware.com/pi
>>> permail/paraview/2010-November/019453.html) that recomended doing an
>>> "extract subset" filter; however that filter is grayed out.
>>>
>>> Any advice would be appreciated
>>>
>>> Regards,
>>>
>>> John
>>>
>>> ___
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
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>>>
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>>>
>>>
>>
>
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Re: [Paraview] Down sample data?

[Andy Bauer]

Hi John,

It depends on what type of grid you have. For image data, rectilinear grid
or structured grid the extract subset filter is probably the best (for
other grid types it will be grayed out since it's not applicable to those
grid types). Otherwise, you can use resample with dataset.

Note that both of these will work nicely with point data but for cell data
you may want to use the cell data to point data filter first.

On Sat, Mar 31, 2018 at 9:14 AM, John Haase  wrote:

> Hello all,
>
> I'm trying to down select my data so I can do a grid convergence study.
> How would I go about doing this?
>
> I found an old post (https://public.kitware.com/pipermail/paraview/2010-
> November/019453.html) that recomended doing an "extract subset" filter;
> however that filter is grayed out.
>
> Any advice would be appreciated
>
> Regards,
>
> John
>
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Re: [Paraview] structured to unstructured when using multiblocks filter

[Andy Bauer]

Hi Ufuk,

If the files are small, could you send them? I'll investigate some. Also,
sending your Catalyst Python script may help clue me into what's going
wrong.

Best,
Andy

On Mon, Mar 19, 2018 at 4:06 PM, Ufuk Turuncoglu <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Thanks for your valuable comments. Yes, for each model component has two
> grid 2d and 3d and they are coming from different channels. It is working
> under 5.4.1 but i'll check the bug and try to fix my version until 5.5
> released. BTW, even if I set whole extend (to test it I hardcoded it) in
> the place that you indicate, the piece and whole extent is same in the
> files.
>
> Regards,
>
> --ufuk
>
>
> ------
> *From: *"Andy Bauer" <andy.ba...@kitware.com>
> *To: *"Ufuk Utku Turuncoglu (BE)" <u.utku.turunco...@be.itu.edu.tr>
> *Cc: *"paraview" <parav...@paraview.org>
> *Sent: *Monday, March 19, 2018 3:51:51 PM
> *Subject: *Re: [Paraview] structured to unstructured when using
> multiblocks filter
>
> Hi Ufuk,
>
> It looks like you're already using multi-channel input as you're adding
> since you have " g_coprocessorData->AddInput(strarr[i]); " unless that's
> always just called once. We're just trying to clarify the "inputs" by
> naming them channels -- I'm not sure it makes it easier to understand but
> it makes it easier to talk about with others that understand that concept
> in Catalyst.
>
> Setting whole extent would look like the following at line 129 in
> adaptor.cpp:
> if (vtkDataSet* grid = vtkDataSet::SafeDownCast(g_coprocessorData->
> GetInputDescriptionByName(name)->GetGrid())) {
> ParaViewCoProcessing::ClearFieldDataFromGrid(grid);
> g_coprocessorData->GetInputDescriptionByName(name)-> SetWholeExtent(ilow,
> ihigh, jlow, jhigh, klow, khigh);
> } else {
>
> Here, *low and *high are global values. For example, for a 1D case if each
> process has 5 points and you have 3 mpi processes
> ilow=jlow=jhigh=klow=khigh=0 and ihigh=12. The
> vtkStructuredGrid::SetExtent() would look like:
> proc 0: 0, 4, 0, 0, 0, 0
> proc 1: 4, 8, 0, 0, 0, 0
> proc 2: 8, 12, 0, 0, 0, 0
>
> This looks like you're doing it properly in grid.cpp though but I didn't
> set the SetWholeExtent() in adaptor.cpp and I'm guessing that's what's
> missing.
>
> The multi-channel input should work in 5.4.1 but I found a bug that's been
> fixed in the upcoming 5.5 that was affecting Live. See
> https://gitlab.kitware.com/paraview/paraview/merge_requests/2212 for
> details on that. It's fairly small so you can probably backport that to
> your 5.4.1 build if you're more comfortable using 5.4.1.
>
> Cheers,
> Andy
>
> On Mon, Mar 19, 2018 at 7:50 AM, Ufuk Utku Turuncoglu (BE) <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Hi Andy,
>>
>> Thanks for your help. Yes, each tile has its own grid information. The
>> problem is that if i set whole extent in the adaptor side and write data to
>> disk using allinputsgridwrite.py, the whole extent is same with piece
>> extent. I am not sure what is going on in the background when live
>> visualization activated. If you want to look at it for possible problem,
>> the code is in following link (adaptor.cpp and grid.cpp),
>>
>> https://github.com/uturuncoglu/RegESM/tree/master/cop
>>
>> The second option is also worth to try but first i need to look at the
>> example. BTW, i am using 5.4.1. Do you think that the multi-channel input
>> also works with 5.4.1? How it is handled by Catalyst in live mode? Do i
>> have multiple visualization pipeline?
>>
>> Regards,
>>
>> --ufuk
>>
>>
>> On 19.03.2018 13:36, Andy Bauer wrote:
>>
>> Hi Ufuk,
>>
>> Currently a multipiece data set always has to be nested under a
>> multiblock dataset. This definitely seems like an unreasonable limitation
>> on a structured grid under a multipiece dataset but I suspect we just
>> haven't had the resources to put into making this work properly. My
>> suggestion would be to try just having your Catalyst adaptor provide a
>> structured grid directly, assuming you only have one grid per mpi process,
>> and then try volume rendering like that. If you do this though, make sure
>> to set the whole extent with vtkCPInputDataDescription::SetWholeExtent().
>>
>>
>> A thought here -- instead of changing your adaptor to generate the
>> structured grid directly instead of a multipiece dataset, maybe create a
>> second "channel" through a second vtkCPInputDataDescription that provides
>> just a structured grid. This way you can provide

Re: [Paraview] structured to unstructured when using multiblocks filter

[Andy Bauer]

Hi Ufuk,

It looks like you're already using multi-channel input as you're adding
since you have " g_coprocessorData->AddInput(strarr[i]); " unless that's
always just called once. We're just trying to clarify the "inputs" by
naming them channels -- I'm not sure it makes it easier to understand but
it makes it easier to talk about with others that understand that concept
in Catalyst.

Setting whole extent would look like the following at line 129 in
adaptor.cpp:
if (vtkDataSet* grid = vtkDataSet::SafeDownCast(g_coprocessorData->
GetInputDescriptionByName(name)->GetGrid())) {
ParaViewCoProcessing::ClearFieldDataFromGrid(grid);
g_coprocessorData->GetInputDescriptionByName(name)-> SetWholeExtent(ilow,
ihigh, jlow, jhigh, klow, khigh);
} else {

Here, *low and *high are global values. For example, for a 1D case if each
process has 5 points and you have 3 mpi processes
ilow=jlow=jhigh=klow=khigh=0 and ihigh=12. The
vtkStructuredGrid::SetExtent() would look like:
proc 0: 0, 4, 0, 0, 0, 0
proc 1: 4, 8, 0, 0, 0, 0
proc 2: 8, 12, 0, 0, 0, 0

This looks like you're doing it properly in grid.cpp though but I didn't
set the SetWholeExtent() in adaptor.cpp and I'm guessing that's what's
missing.

The multi-channel input should work in 5.4.1 but I found a bug that's been
fixed in the upcoming 5.5 that was affecting Live. See
https://gitlab.kitware.com/paraview/paraview/merge_requests/2212 for
details on that. It's fairly small so you can probably backport that to
your 5.4.1 build if you're more comfortable using 5.4.1.

Cheers,
Andy

On Mon, Mar 19, 2018 at 7:50 AM, Ufuk Utku Turuncoglu (BE) <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi Andy,
>
> Thanks for your help. Yes, each tile has its own grid information. The
> problem is that if i set whole extent in the adaptor side and write data to
> disk using allinputsgridwrite.py, the whole extent is same with piece
> extent. I am not sure what is going on in the background when live
> visualization activated. If you want to look at it for possible problem,
> the code is in following link (adaptor.cpp and grid.cpp),
>
> https://github.com/uturuncoglu/RegESM/tree/master/cop
>
> The second option is also worth to try but first i need to look at the
> example. BTW, i am using 5.4.1. Do you think that the multi-channel input
> also works with 5.4.1? How it is handled by Catalyst in live mode? Do i
> have multiple visualization pipeline?
>
> Regards,
>
> --ufuk
>
>
> On 19.03.2018 13:36, Andy Bauer wrote:
>
> Hi Ufuk,
>
> Currently a multipiece data set always has to be nested under a multiblock
> dataset. This definitely seems like an unreasonable limitation on a
> structured grid under a multipiece dataset but I suspect we just haven't
> had the resources to put into making this work properly. My suggestion
> would be to try just having your Catalyst adaptor provide a structured grid
> directly, assuming you only have one grid per mpi process, and then try
> volume rendering like that. If you do this though, make sure to set the
> whole extent with vtkCPInputDataDescription::SetWholeExtent().
>
> A thought here -- instead of changing your adaptor to generate the
> structured grid directly instead of a multipiece dataset, maybe create a
> second "channel" through a second vtkCPInputDataDescription that provides
> just a structured grid. This way you can provide both dataset types as
> needed instead of having to modify code back and forth, recompile, etc. to
> get different functionality. See the 
> Examples/Catalyst/CxxMultiChannelInputExample
> in the 5.5 source code for some more details on this.
>
> I can't remember if you were using the editions or just the full ParaView
> Catalyst build but in 5.5 there will be a volume rendering Catalyst
> addition.
>
> Note that the multiblock/multipiece hierarchy will be undergoing a
> significant change in the near future.
>
> Best,
> Andy
>
>
> On Sun, Mar 18, 2018 at 1:21 PM, Ufuk Turuncoglu <
> u.utku.turunco...@be.itu.edu.tr> wrote:
>
>> Hi,
>>
>> I am using MPI parallel code under Catalyst co-processing. In this case,
>> i am defining data by creating multi-block dataset and putting multi-piece
>> dataset into the first block (0). In this case, each piece is defined as
>> structured grid. The problem is that, to create volume rendering, i need to
>> use MergeBlocks filter under ParaView but it changes data type from
>> structured grid to unstructured one. I just wonder that is there any way to
>> merge blocks without changing type? Programmable filter etc.? Another
>> workaround could be defining dataset without using multi block under
>> co-processing adaptor code. So, is it possible to represent multi-piece
>> data under c

Re: [Paraview] structured to unstructured when using multiblocks filter

[Andy Bauer]

Hi Ufuk,

Currently a multipiece data set always has to be nested under a multiblock
dataset. This definitely seems like an unreasonable limitation on a
structured grid under a multipiece dataset but I suspect we just haven't
had the resources to put into making this work properly. My suggestion
would be to try just having your Catalyst adaptor provide a structured grid
directly, assuming you only have one grid per mpi process, and then try
volume rendering like that. If you do this though, make sure to set the
whole extent with vtkCPInputDataDescription::SetWholeExtent().

A thought here -- instead of changing your adaptor to generate the
structured grid directly instead of a multipiece dataset, maybe create a
second "channel" through a second vtkCPInputDataDescription that provides
just a structured grid. This way you can provide both dataset types as
needed instead of having to modify code back and forth, recompile, etc. to
get different functionality. See the
Examples/Catalyst/CxxMultiChannelInputExample in the 5.5 source code for
some more details on this.

I can't remember if you were using the editions or just the full ParaView
Catalyst build but in 5.5 there will be a volume rendering Catalyst
addition.

Note that the multiblock/multipiece hierarchy will be undergoing a
significant change in the near future.

Best,
Andy


On Sun, Mar 18, 2018 at 1:21 PM, Ufuk Turuncoglu <
u.utku.turunco...@be.itu.edu.tr> wrote:

> Hi,
>
> I am using MPI parallel code under Catalyst co-processing. In this case, i
> am defining data by creating multi-block dataset and putting multi-piece
> dataset into the first block (0). In this case, each piece is defined as
> structured grid. The problem is that, to create volume rendering, i need to
> use MergeBlocks filter under ParaView but it changes data type from
> structured grid to unstructured one. I just wonder that is there any way to
> merge blocks without changing type? Programmable filter etc.? Another
> workaround could be defining dataset without using multi block under
> co-processing adaptor code. So, is it possible to represent multi-piece
> data under co-processing without putting it into multi-bloack dataset.
>
> Regards,
>
> --ufuk
>
> ___
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Re: [Paraview] Detect Catalyst extraction from within a coprocessor

[Andy Bauer]

Hi Simon,

Currently there's nothing that allows the coprocessor to get information
that the user has clicked on the extract icon during a Catalyst Live
connection. You may be able to hack in a solution though by looking at
either vtkLiveInSituLink (
https://www.paraview.org/ParaView/Doc/Nightly/www/cxx-doc/classvtkLiveInsituLink.html)
or coprocessing.py.

By the way, I'm curious about the use case for this -- what functionality
are you hoping to do with this information? FYI: we're hoping to add
significant functionality in the near future for Catalyst Live so something
like that may be supported in the near future.

Best,
Andy

On Tue, Feb 27, 2018 at 9:47 AM, Michalke, Simon 
wrote:

> Hi,
>
> is there any way that the coprocessor can detect if the catalyst user
> clicks on the extract icon? Something like a function that sleeps until a
> new coprocess steps needs to be done.
> Or do I have to continuously poll the catalyst client if it needs a new
> batch of data transmitted?
>
> Simon
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Re: [Paraview] Memory leaks in Catalyst ?

[Andy Bauer]

Hi Yvan,

I have a merge request into VTK at
https://gitlab.kitware.com/vtk/vtk/merge_requests/3971 that hopefully
improves the memory use. I still have 2 tests that are failing and also
want to test with the ParaView tests so there's a bit more work to do. For
the most part it seems ok though so if you want to try taking those change
and test it on your end I wouldn't mind some extra testing on it,
especially since we're getting so close to the ParaView 5.5 release.

Best,
Andy

On Thu, Feb 22, 2018 at 8:26 PM, Yvan Fournier <yvan.fourn...@free.fr>
wrote:

> Hi Andy,
>
> Thanks for checking. Fixing my own bug (by adding vtkSmartPointer where
> needed in ly adaptor) fixed what seemed the larges issue on a small test
> case. A colleague is testing this on a larger case (for a real application)
> and should provide me some feedback on a larger, long-running case.
>
> He also observed some artifacts using transparency on a boundary/surface
> mesh (not fixed by using -DDEFAULT_SOFTWARE_DEPTH_BITS=31 in Mesa's
> CFLAGS and CPPFLAGS, but remind me of issues I had observed on ParaView 5.0
> and which had been fixed in 5.0.1) using llvmpipe. OpenSWR seemed to lead
> to crashes. I'll start by testing this on one of my simpler
> (non-confidential) benchmark cases.
>
> So I'll probably be running a series of additional tests (to update a
> series from 2 years ago) and keep you informed if I encounter any issues
> (and possibly send a few non-confidential screenshots if everything is
> working well).
>
> Cheers,
>
> Yvan
>
> On Thu, 2018-02-22 at 17:33 -0500, Andy Bauer wrote:
>
> Hi Yvan,
>
> The vtkPKdTree ones look like they could be after looking at the code,
> especially vtkPKdTree::InitializeRegionAssignmentLists(). It seems like a
> good idea to replace the int **ProcessAssignmentMap with maybe a
> std::vector. Probably a good idea for the other member variables here as
> well. I'll spend some time refactoring vtkPKdTree to make sure that the
> memory management is leak free.
>
> I don't see anything that suspicious with respect to ParaView in the other
> leak reports, though that doesn't necessarily mean that they aren't leaks.
>
> Cheers,
> Andy
>
> On Thu, Feb 22, 2018 at 4:53 PM, Yvan Fournier <yvan.fourn...@free.fr>
> wrote:
>
> Hello,
>
> Running under Valgrind (memcheck, with --enable-leak-check=full), I have
> some
> warnings about ParaView/Catalyst possibly leaking memory.
>
> Catalyst is called from Code_Saturne, whose adapter code (using ParaView
> Python
> adapters from C++) is here https://www.code-saturne.org/v
> iewvc/saturne/trunk/src
> /fvm/fvm_to_catalyst.cxx?revision=11048=markup
> <https://www.code-saturne.org/viewvc/saturne/trunk/src/fvm/fvm_to_catalyst.cxx?revision=11048=markup>,
> using the attached
> results.py script.
>
> I fixed a leak in my own code following the Valgrind warnings, but some
> remining
> warnings seem related to calls I have no direct control over, so I attach
> a log
> (on one MPI rank) of Valgrind warnings (edited to remove OpenMPI
> initialization
> related warnings). The first part contains memcheck warnings, the part
> after
> "HEAP SUMMARY" the memory leak info.
>
> I'm not sure if the leaks are "one time only" (not too much of an issue),
> or can
> occur at every output timestep (30 in this example, for a small case with
> about
> 8000 mesh elements per MPI rank), so any opinion / checking on that would
> be
> welcome.
>
> Best regards,
>
>   Yvan Fournier
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Re: [Paraview] Memory leaks in Catalyst ?

[Andy Bauer]

Hi Yvan,

The vtkPKdTree ones look like they could be after looking at the code,
especially vtkPKdTree::InitializeRegionAssignmentLists(). It seems like a
good idea to replace the int **ProcessAssignmentMap with maybe a
std::vector. Probably a good idea for the other member variables here as
well. I'll spend some time refactoring vtkPKdTree to make sure that the
memory management is leak free.

I don't see anything that suspicious with respect to ParaView in the other
leak reports, though that doesn't necessarily mean that they aren't leaks.

Cheers,
Andy

On Thu, Feb 22, 2018 at 4:53 PM, Yvan Fournier 
wrote:

> Hello,
>
> Running under Valgrind (memcheck, with --enable-leak-check=full), I have
> some
> warnings about ParaView/Catalyst possibly leaking memory.
>
> Catalyst is called from Code_Saturne, whose adapter code (using ParaView
> Python
> adapters from C++) is here https://www.code-saturne.org/
> viewvc/saturne/trunk/src
> /fvm/fvm_to_catalyst.cxx?revision=11048=markup, using the attached
> results.py script.
>
> I fixed a leak in my own code following the Valgrind warnings, but some
> remining
> warnings seem related to calls I have no direct control over, so I attach
> a log
> (on one MPI rank) of Valgrind warnings (edited to remove OpenMPI
> initialization
> related warnings). The first part contains memcheck warnings, the part
> after
> "HEAP SUMMARY" the memory leak info.
>
> I'm not sure if the leaks are "one time only" (not too much of an issue),
> or can
> occur at every output timestep (30 in this example, for a small case with
> about
> 8000 mesh elements per MPI rank), so any opinion / checking on that would
> be
> welcome.
>
> Best regards,
>
>   Yvan Fournier
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Re: [Paraview] Integrate Variables divide cell data by volume has no effect?

[Andy Bauer]

The DivideCellDataByVolume only operates on cell data and you're
integrating a point data array so it won't work the way you're expecting it
to. You can use the point data to cell data filter and then try using the
integrate variable filter to see if that gives the result that you want.

On Mon, Feb 19, 2018 at 11:59 PM, Shuhao Wu  wrote:

> Hello all,
>
> I've been using the filter IntegrateVariables with the option
> DivideCellDataByVolume = on on a 2D surface. I've noticed that turning this
> option on and off has no effect on the PointData of the output. No
> additional cell data is produced either.
>
> I thought the idea of the the integrate variables filter is (for 2D): it
> sums up the values at each point and multiplied by the area associated with
> that point (*). If the DivideCellDataByVolume option is on, it will divide
> the final result by the total area. If this is the case, why does the
> option do nothing, shouldn't the point data be scaled by a constant factor
> that's the area?
>
> (*) how does it associate the points with their areas?
>
> Thanks,
> Shuhao
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