[Paraview] My own filter as part of pipeline for coprocessing raises "name not defined" error

Thu Oct 3 10:18:34 EDT 2013

Hi Hong,

There won't be a separate library created for Python wrapping your plugin
for doing ParaView. Did you add in the following to your adaptor:

#ifndef BUILD_SHARED_LIBS
#include "pvStaticPluginsInit.h"
#endif

And then in the adaptor initialization step you should have something in it
like:
#ifndef BUILD_SHARED_LIBS
paraview_static_plugins_init();
#endif

If that doesn't work then it will probably take a bit of tinkering to
figure out what's wrong.

Regards,
Andy

On Wed, Oct 2, 2013 at 12:28 PM, Hong Yi <hongyi at renci.org> wrote:

>  Thanks for the helpful info, Andy. I looked at the link and followed the
> code change Burlen posted to add the static linked plugin initialization
> into pvbatch and pvpython and that worked fine. Now pvbatch and pypthon all
> have my filter plugin statically loaded. I still got the “name not defined”
> error when coprocessing parses the pipeline though. I believe the problem
> remains because there is still no python wrapped proxy to my filter since
> there is no change to lib\site-packages after I add the static linked
> plugin initialization into pybatch and pvpython. To make sure I am on the
> right track for my further investigation, I am hoping to get answers to a
> couple of my further questions below:****
>
> ** **
>
> **1.       **What is the right way to go to have the proxy to my filter
> Python wrapped? How can I verity I have the proxy to my filter Python
> wrapped? Is it true that the Python-wrapped proxy to my filter should show
> up in some python file in lib\site-packages if the filter is indeed
> python-wrapped?  ****
>
> **2.       **I made similar changes to CPythonAdaptorAPI.cxx and
> CMakeLists.txt as I did to pvpthon and pvbatch to load and init static
> plugin in function coprocessorinitializewithpython() hoping to have plugin
> loaded when doing coprocessing linked to simulation, however, I still have
> the symbol “pv_plugin_instance_SMVorticity” undefined in built
> PythonCatalyst static lib while the plugin symbol is indeed defined in
> pvpython with the same code changes. Just to confirm, does the plugin need
> to be loaded in Catalyst initialization in order to use it in a
> coprocessing pipeline? In other words, to get my plugin working in catalyst
> linked to simulation, I need to resolve two problems: (1) get the plugin
> statically loaded in Catalyst initialization; (2) get the proxy to the
> plugin Python wrapped and show up in some python file in lib\site-packages.
> Is this true?****
>
> ** **
>
> Yes, I know the gradient of unstructured data set filter can compute
> vorticity, which I referenced to write this custom vorticity filter to make
> it fit our needs better with better performance. I did try to use the
> genetic gradient filter to compute vorticity for coprocessing, but it
> raises a segmentation fault after outputting several images. Will have to
> debug and investigate more to find out more on that.****
>
> ** **
>
> Thanks,****
>
> Hong****
>
> ****
>
> ** **
>
> *From:* Andy Bauer [mailto:andy.bauer at kitware.com]
> *Sent:* Tuesday, October 01, 2013 2:19 PM
>
> *To:* Hong Yi
> *Cc:* David E DeMarle; paraview at paraview.org
> *Subject:* Re: [Paraview] My own filter as part of pipeline for
> coprocessing raises "name not defined" error****
>
> ** **
>
> Hi Hong,****
>
> I don't think you want to do VTK Python wrapping of your class. What you
> want is to have the proxy to the filter Python wrapped such that it's
> available when you import paraview.simple. This is what's needed for
> Catalyst Python pipelines. I don't think you're properly initializing the
> plugins from the previous directions I sent. You may want to look at
> http://public.kitware.com/pipermail/paraview-developers/2013-September/002499.html
> ****
>
> As a side note, the gradient of unstructured data set filter can compute
> vorticity as well. It does require a vtkDataArray with three components to
> use though. ****
>
> Regards,
> Andy****
>
> ** **
>
> On Mon, Sep 30, 2013 at 5:06 PM, Hong Yi <hongyi at renci.org> wrote:****
>
> Thanks, Andy. The CMakeLists.txt for my plugin is copied below with newly
> added lines for python wrapping in orange:
>
> -----------------------------
> if(NOT ParaView_SOURCE_DIR)
>   find_package(ParaView)
>   include("${PARAVIEW_USE_FILE}")
>   include (ParaViewPlugins)
> else()
>   # we're building from within ParaView Source.
> endif()
>
> include_directories(${VTK_INCLUDE_DIRS})
> include(wrap-python.cmake)
>
> # create a paraview plugin containing server manager xml and the server
> # manager classes to build
> # this plugin can be loaded on the server side
>
> ADD_PARAVIEW_PLUGIN(SMVorticity "1.0"
>   SERVER_MANAGER_XML VorticityFilter.xml
>   SERVER_MANAGER_SOURCES VorticityFilter.cxx)
>
> target_link_libraries(SMVorticity ${deps})
>
> if(VTK_WRAP_PYTHON)
>   wrap_python(SMVorticity "${sources}")
> endif()
> -----------------------------
>
> The orange lines are added by following
> http://www.paraview.org/pipermail/paraview/2012-May/024855.html which
> works well and builds my filter and also wraps it in Python (i.e., it
> generates libSMVorticity.a and libSMVorticityPythonD.a). I have also
> verified the plugin is indeed loaded into pvserver and pvpython in paraview
> built bin directory.
>
> However, I still got "name not defined" error in coprocessing script when
> creating this filter by name "VorticityOfUnstructuredDataSet" in python
> script. I have a couple of specific questions I am currently investigating
> and hoping to get some inputs from experts in the list:
>
> 1. I am not sure where this name "VorticityOfUnstructuredDataSet"
> (exported by coprocessing script generator plugin) comes from, the only
> clue I can see is in plugin.cmake, where the plugin is specified with
> DESCRIPTION "Vorticity Of Unstructured DataSet" and in VorticityFilter.xml,
> where the plugin is given a label of "Vorticity Of Unstructured DataSet."
> Should this name be defined somewhere such as in some python file in
> paraview python site-packages?
>
> 2. I did try to add PV_PLUGIN_IMPORT macros to the adaptor since I am
> using Catalyst, however, the plugin symbol "pv_plugin_instance_SMVorticity"
> is undefined in the adaptor static lib (the same plugin symbol is defined
> in pvserver), hence I got an undefined error when linking simulation code
> to the adaptor. I did try to add my plugin static lib (in which the plugin
> symbol is defined) to the adaptor target via target_link_libraries before
> linking to vtkPVPythonCatalyst, but that does not seem to take any effect.
> For some reason I am still investigating, my plugin lib does not get to
> link to the adaptor via target_link_libraries. What I did is to go to src
> directory in the cross target and modified CMakeLists.txt for
> PhastaAdaptor, then went to corresponding paraview-build directory, and did
> "make clean" followed by "make" to rebuild PhastaAdaptor lib. Is there
> something obvious that I did not do correctly?
>
> Thanks for any inputs!
>
> Hong
>
> ****
>  ------------------------------
>
> *From:* Andy Bauer [andy.bauer at kitware.com]
> *Sent:* Friday, September 27, 2013 3:00 PM
> *To:* Hong Yi
> *Cc:* David E DeMarle; paraview at paraview.org****
>
>
> *Subject:* Re: [Paraview] My own filter as part of pipeline for
> coprocessing raises "name not defined" error****
>
> ** **
>
> Can you share your plugin or at least the CMakeLists.txt for your plugin?
> Have you tried with any other plugins that get packaged with ParaView to
> see if they work?****
>
> If you're using Catalyst, I would suggest adding in the
> PV_PLUGIN_IMPORT_INIT macros to the adaptor.****
>
> Andy****
>
> ** **
>
> On Thu, Sep 26, 2013 at 3:40 PM, Hong Yi <hongyi at renci.org> wrote:****
>
> Thanks! I did put my plugin inside ParaView/Plugins in the same way as
> other Plugins, and enabled it when building ParaView superbuild on Titan. I
> can see the static lib for the Plugin is built in paraview-build/lib
> directory. And yes, I did use a plugin and load it via Tools|Manage Plugins
> when creating python coprocessing script. However, it looks like my plugin
> is not loaded automatically even though it is built by ParaView superbuild.
> Perhaps I should still follow the link
> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications but
> I am having some difficulty in following the info in the link to do what is
> suggested. Specifically, to what file should I insert two macros? It does
> not sound right to insert them into my custom plugin cxx file. Where should
> I add two macros to get my custom filter plugin to be loaded and wrapper
> into python module? I see "LoadPlugin" function defined in simple.py to
> call servermanager.LoadPlugin(filename, remote) which I am thinking perhaps
> should be called to load my plugin before my python coprocessing script is
> executed, but not sure whether this is the case or not. ****
>
>  ****
>
> Thanks for any suggestions! ****
>
> ** **
>
> Hong****
>
>  ****
>
>  ****
>
> *From:* David E DeMarle [mailto:dave.demarle at kitware.com]
> *Sent:* Thursday, September 26, 2013 1:28 PM
> *To:* Andy Bauer
> *Cc:* Hong Yi; paraview at paraview.org
> *Subject:* Re: [Paraview] My own filter as part of pipeline for
> coprocessing raises "name not defined" error****
>
>  ****
>
> Utkarsh pointed out that you still need to follow
> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications
> ****
>
> when the plugin is external to ParaView. If you put your plugin inside
> ParaView/Plugins, then it is done automatically.****
>
>
> ****
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909****
>
>  ****
>
> On Thu, Sep 26, 2013 at 12:23 PM, David E DeMarle <
> dave.demarle at kitware.com> wrote:****
>
> I think that information is out of date. I believe that is done
> automatically now.****
>
>  ****
>
> Otherwise Andy is right. Putting the filter inside a plugin a good way to
> go. The plugin infrastructure will make it so that when you provide the XML
> that describes your vtk class, ParaView's build system will automatically
> wrap it into a proxy and python class so that ParaView will be able to use
> it.****
>
>  ****
>
> Also, I recommend trying it on a local static build first. That way the
> build time will be less and development will be quicker. Once you can load
> you plugin locally, then you should only have to compile on titan once.***
> *
>
>  ****
>
>
> ****
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909****
>
>  ****
>
> On Wed, Sep 25, 2013 at 10:34 PM, Andy Bauer <andy.bauer at kitware.com>
> wrote:****
>
> Did you use a plugin to add in your custom filter when creating the Python
> co-processing script? I'm not sure how plugins are "loaded" for static
> builds but you may want to look at
> http://www.paraview.org/Wiki/ParaView/Plugin_HowTo#Plugins_in_Static_Applications.
> If that doesn't work, we'll have to figure out some other way to do it.***
> *
>
> Andy****
>
>  ****
>
>  ****
>
>  ****
>
>  ****
>
> On Wed, Sep 25, 2013 at 9:16 PM, Hong Yi <hongyi at renci.org> wrote:****
>
>   Hello,
>
> I set up a pipeline that used a custom filter I developed and exported it
> as a python script for coprocessing. I have made sure the static library
> for my custom filter is built and available in paraview-build/lib
> directory, and I have also linked this custom filter static library along
> with Catalyst libs to the simulation code for coprocessing. However, when I
> run the simulation linked with ParaView coprocessing for in-situ
> visualization, I got "NameError: name 'MyCustomizedFilterName' is not
> defined" error when the line of my customized filter in my python
> coprocessing script is read in for pipeline coprocessing. What should I do
> to get my custom filter wrapped in python so that it can be recognized and
> used as part of the python pipeline script for coprocessing? Any advice and
> suggestions are very much appreciated.
>
> Thanks,
>
> Hong****
>
>  ****
>
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>  ****
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> ** **
>
> ** **
>
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