[Paraview] VisIt Database Bridge - Custom Plugin of VisIt Reader
Robert Maynard
robert.maynard at kitware.com
Mon Apr 18 09:26:34 EDT 2011
Hi Simon,
I have attached an example CMakeLists.txt that support external library
linking and include directories. Since you are linking to a static build of
HDF5 you will need to manually add each library
to VISIT_PLUGIN_EXTERNAL_LIBS separated by semicolons.
On Mon, Apr 11, 2011 at 5:19 PM, Simon Su <newsgroup4ssu at gmail.com> wrote:
> Hi Robert,
>
> It worked. adding the other file listed under my Files components="M" xml
> block solve the error when the plugin manager tries to loader the plugin.
>
> So I went and try to load my file in ParaView ... but this is what I
> got....
>
>
> sms:/local/home/build/paraview-plugin/gfdl-paraview-loader-build> paraview
> /local/home/tools/ParaView/ParaView-3.10.0/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/lib/paraview-3.10/paraview:
> symbol lookup error:
> /local/home/build/paraview-plugin/gfdl-paraview-loader-build/libVisItReaderGFDL.so:
> undefined symbol: nc_inq_attlen
>
>
> The question now is, where in ccmake can I specify for the plugin when it
> is compiling to also include libnetcdf.a libhdf5_hl.a libhdf5.a libsz.a
> libraries? Which variable do I add the libraries to? my ccmake only show
> three variables when the toggle advanced mode is Off (CMAKE_BUILD_TYPE,
> CMAKE_INSTALL_PREFIX, and ParaView_DIR). When I turn on the advanced mode,
> it gave me many many more... but going through the list, I am also not sure
> which cmake variable to use.
>
> vtkVisItReaderGFDL.cxx is attached and it with generated after I added the
> second file into my CMakeLists.txt. I hope the file is not too big for the
> list. if it is, it is also included at the bottom of this email.
>
> thank you for your help
>
> best,
> -simon
>
>
> /*=========================================================================
>
> Program: ParaView
> Module: vtkVisItReaderGFDL.cxx
>
> Copyright (c) 2005,2006 Sandia Corporation, Kitware Inc.
> All rights reserved.
>
> ParaView is a free software; you can redistribute it and/or modify it
> under the terms of the ParaView license version 1.2.
>
> See License_v1.2.txt for the full ParaView license.
> A copy of this license can be obtained by contacting
> Kitware Inc.
> 28 Corporate Drive
> Clifton Park, NY 12065
> USA
>
> THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
> ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
> LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
> A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS OR
> CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
> EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
> PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
> PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
> LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
> NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
> SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
>
> ========================================================================*/
> #include "vtkVisItReaderGFDL.h"
> #include "vtkInformation.h"
> #include "vtkInformationVector.h"
> #include "vtkObjectFactory.h"
> #include "vtkMultiBlockDataSet.h"
>
> #include "avtCM24FileFormat.h"
> #include "avtDatabaseMetaData.h"
> #include "avtMeshMetaData.h"
> #include "avtVariableCache.h"
>
> /* #undef ARG_VISIT_READER_USES_OPTIONS */
>
> #ifdef ARG_VISIT_READER_USES_OPTIONS
> #include ".h"
> #endif
>
> /* #undef VISIT_READER_USES_INTERFACE */
> #ifdef VISIT_READER_USES_INTERFACE
> #include "vtkVisItReaderGFDL.h"
> #endif
>
> vtkStandardNewMacro(vtkVisItReaderGFDL);
>
>
> //-----------------------------------------------------------------------------
> vtkVisItReaderGFDL::vtkVisItReaderGFDL()
> {
> this->FileName = 0;
> }
>
>
> //-----------------------------------------------------------------------------
> vtkVisItReaderGFDL::~vtkVisItReaderGFDL()
> {
> this->SetFileName(0);
> }
>
> #ifdef VISIT_READER_USES_INTERFACE
>
> //-----------------------------------------------------------------------------
> int vtkVisItReaderGFDL::CanReadFile(const char *fname)
> {
> int valid = 0;
> try
> {
> valid = vtkVisItReaderGFDL::;
> }
> catch(...){}
> return valid;
> }
> #endif
>
>
> //-----------------------------------------------------------------------------
> bool vtkVisItReaderGFDL::InitializeAVTReader( const int& timestep )
> {
> if (!this->MetaData)
> {
> this->MetaData = new avtDatabaseMetaData( );
> }
>
> if (!this->Cache)
> {
> this->Cache = new avtVariableCache( );
> }
>
> if (!this->AvtFile)
> {
> try
> {
> #ifdef ARG_VISIT_READER_USES_OPTIONS
> *options =
> new ();
> this->AvtFile = new avtCM24FileFormat(
> this->FileName, options->GetReadOptions() );
> delete options;
> #else
> this->AvtFile = new avtCM24FileFormat(this->FileName);
> #endif
> }
> catch(...)
> {
> this->AvtFile = NULL;
> return false;
> }
> avtCM24FileFormat *file = dynamic_cast<avtCM24FileFormat*>
> (this->AvtFile);
> if ( file )
> {
> //we have to make sure the visit reader populates its cache
> //before activating a time step
> try
> {
> file->SetCache( this->Cache );
> file->ActivateTimestep(timestep);
>
> //only fill database after choosing timestep to activate
> file->SetDatabaseMetaData( this->MetaData, timestep );
> }
> catch(...)
> {
> return false;
> }
> }
> else
> {
> return false;
> }
> }
>
> return true;
> }
>
>
>
>
> //-----------------------------------------------------------------------------
> void vtkVisItReaderGFDL::PrintSelf(ostream& os, vtkIndent indent)
> {
> this->Superclass::PrintSelf(os, indent);
>
> }
>
>
>
>
>
>
> On Mon, Apr 11, 2011 at 4:41 PM, Robert Maynard <
> robert.maynard at kitware.com> wrote:
>
>> Hi Simon,
>>
>> You do not need to modify the avt file or add the revision macro as that
>> is not the problem you are currently facing. I would try reverting your avt
>> file to its original content, adding all the files listed in the Files
>> components="M" xml block to your SOURCES list, and adding the plugin
>> build folder to your LD_LIBRARY_PATH.
>>
>> Also would you be able to send me the contents of the vtkVisItReaderGFDL.cxx
>> from your build directory and I will confirm the automatic wrapping is
>> working properly.
>>
>>
>> On Mon, Apr 11, 2011 at 3:02 PM, Simon Su <newsgroup4ssu at gmail.com>wrote:
>>
>>> Hi Robert,
>>>
>>> I inferred a CMakeLists.txt from the wiki page
>>>
>>>
>>> ================ CMakeLists.txt for the plugin
>>>
>>> PROJECT(VisItReaderGFDL)
>>>
>>> cmake_minimum_required(VERSION 2.8)
>>>
>>> FIND_PACKAGE(ParaView REQUIRED)
>>> INCLUDE(${PARAVIEW_USE_FILE})
>>>
>>> SET(SOURCES
>>> avtCM24FileFormat.C
>>> )
>>>
>>> ADD_VISIT_PLUGIN_READER(VisItReaderGFDL "1.0"
>>> VISIT_READER_NAME "avtCM24FileFormat"
>>> VISIT_READER_TYPE "MTSD"
>>> VISIT_READER_FILE_PATTERN "nc"
>>> SERVER_SOURCES ${SOURCES}
>>> )
>>>
>>> TARGET_LINK_LIBRARIES(VisItReaderGFDL vtkVisItAVTAlgorithms)
>>> ============================
>>>
>>> I then placed the .C and .h files in the same directory
>>> sms:/local/home/build/paraview-plugin> ls -alF gfdl-paraview-loader
>>> total 112
>>> drwxr-xr-x 2 sms t 4096 Apr 11 14:53 ./
>>> drwxr-xr-x 5 sms t 4096 Apr 11 14:20 ../
>>> -rw-r--r-- 1 sms t 87958 Apr 11 12:51 avtCM24FileFormat.C
>>> -rw-r--r-- 1 sms t 7311 Apr 11 14:25 avtCM24FileFormat.h
>>> -rw-r--r-- 1 sms t 404 Apr 11 13:02 CMakeLists.txt
>>>
>>>
>>> Then in the build directory, I did a ccmake and entered the right text
>>> for ParaView_DIR variable and I got this after configure/generate/make
>>>
>>> sms:/local/home/build/paraview-plugin/gfdl-paraview-loader-build> ls -alF
>>> total 228
>>> drwxr-xr-x 3 sms t 4096 Apr 11 14:25 ./
>>> drwxr-xr-x 5 sms t 4096 Apr 11 14:20 ../
>>> -rw-r--r-- 1 sms t 42197 Apr 11 14:24 CMakeCache.txt
>>> drwxr-xr-x 6 sms t 4096 Apr 11 14:25 CMakeFiles/
>>> -rw-r--r-- 1 sms t 1691 Apr 11 14:24 cmake_install.cmake
>>> -rwxr-xr-x 1 sms t 74174 Apr 11 14:25 libVisItReaderGFDL.so*
>>> -rw-r--r-- 1 sms t 12258 Apr 11 14:24 Makefile
>>> -rw-r--r-- 1 sms t 2685 Apr 11 14:24 moc_VisItReaderGFDL_Plugin.cxx
>>> -rw-r--r-- 1 sms t 3376 Apr 11 14:24 qrc_VisItReaderGFDL.cxx
>>> -rw-r--r-- 1 sms t 578 Apr 11 14:24 VisItReaderGFDLInit.cxx
>>> -rw-r--r-- 1 sms t 4308 Apr 11 14:24 VisItReaderGFDL_Plugin.cxx
>>> -rw-r--r-- 1 sms t 3809 Apr 11 14:24 VisItReaderGFDL_Plugin.h
>>> -rw-r--r-- 1 sms t 163 Apr 11 14:24 VisItReaderGFDL.qrc
>>> -rw-r--r-- 1 sms t 1045 Apr 11 14:24
>>> vtkSMVisItReaderGFDLInstantiator.cxx
>>> -rw-r--r-- 1 sms t 464 Apr 11 14:24 vtkSMVisItReaderGFDLInstantiator.h
>>> -rw-r--r-- 1 sms t 5473 Apr 11 14:24 vtkSMXML_VisItReaderGFDL.h
>>> -rw-r--r-- 1 sms t 4705 Apr 11 14:24 vtkVisItReaderGFDLClientServer.cxx
>>> -rw-r--r-- 1 sms t 4025 Apr 11 14:24 vtkVisItReaderGFDL.cxx
>>> -rw-r--r-- 1 sms t 1740 Apr 11 14:24 vtkVisItReaderGFDLExport.h
>>> -rw-r--r-- 1 sms t 151 Apr 11 14:24 vtkVisItReaderGFDLGUI.xml
>>> -rw-r--r-- 1 sms t 2194 Apr 11 14:24 vtkVisItReaderGFDL.h
>>> -rw-r--r-- 1 sms t 4169 Apr 11 14:24 vtkVisItReaderGFDLSM.xml
>>>
>>>
>>> however, loading the plugin using plugin manager gui resulted in an error
>>>
>>>
>>> Cannot load library
>>> /local/home/build/paraview-plugin/gfdl-paraview-loader-build/libVisItReaderGFDL.so:
>>> (/local/home/build/paraview-plugin/gfdl-paraview-loader-build/libVisItReaderGFDL.so:
>>> undefined symbol: _ZTI17avtCM24FileFormat)
>>>
>>> then from your plugin wiki page, I added the following line into my
>>> avtCM24FileFormat.h file
>>>
>>> vtkCxxRevisionMacro(VisItReaderGFDL, "$Revision$");
>>>
>>> but when I compile, I get
>>>
>>> sms:/local/home/build/paraview-plugin/gfdl-paraview-loader-build> make
>>> [ 9%] Generating moc_VisItReaderGFDL_Plugin.cxx
>>> [ 18%] Generating vtkVisItReaderGFDLClientServer.cxx
>>> [ 27%] Generating qrc_VisItReaderGFDL.cxx
>>> [ 36%] Generating vtkSMXML_VisItReaderGFDL.h
>>> -- Generate module: vtkVisItReaderGFDLSM
>>> [ 45%] Building CXX object
>>> CMakeFiles/VisItReaderGFDL.dir/qrc_VisItReaderGFDL.cxx.o
>>> [ 54%] Building CXX object
>>> CMakeFiles/VisItReaderGFDL.dir/vtkVisItReaderGFDL.cxx.o
>>> /local/home/build/paraview-plugin/gfdl-paraview-loader/avtCM24FileFormat.h:45:
>>> error: 'VisItReaderGFDL' has not been declared
>>> /local/home/build/paraview-plugin/gfdl-paraview-loader/avtCM24FileFormat.h:
>>> In function 'void CollectRevisions(std::ostream&)':
>>> /local/home/build/paraview-plugin/gfdl-paraview-loader/avtCM24FileFormat.h:45:
>>> error: invalid use of 'this' in non-member function
>>> /local/home/build/paraview-plugin/gfdl-paraview-loader/avtCM24FileFormat.h:45:
>>> error: 'Superclass' has not been declared
>>> make[2]: *** [CMakeFiles/VisItReaderGFDL.dir/vtkVisItReaderGFDL.cxx.o]
>>> Error 1
>>> make[1]: *** [CMakeFiles/VisItReaderGFDL.dir/all] Error 2
>>> make: *** [all] Error 2
>>>
>>> and actually, my plugin code also depend on both netcdf and hdf5 library
>>> which is specified in my VisIt xml file
>>>
>>> sms:/local/home/build/paraview-plugin/gfdl-visit-load> cat CM24.xml
>>> <?xml version="1.0"?>
>>> <Plugin name="CM24" type="database" label="NetCDF CM2.4" version="1.0"
>>> enabled="true" mdspecificcode="false" engspecificcode="false"
>>> onlyengine="false" noengine="false" dbtype="MTSD" haswriter="false"
>>> hasoptions="false">
>>> <CXXFLAGS>
>>>
>>> -I/net/sms/tools/VisIt/VisIt-2.2.1/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/current/linux-x86_64/include/netcdf
>>> -Wno-deprecated
>>> </CXXFLAGS>
>>> <LIBS>
>>>
>>> /local/home/tools/VisIt/VisIt-2.2.1/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/current/linux-x86_64/archives/libnetcdf.a
>>>
>>> /local/home/tools/VisIt/VisIt-2.2.1/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/current/linux-x86_64/lib/libhdf5_hl.a
>>>
>>> /local/home/tools/VisIt/VisIt-2.2.1/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/current/linux-x86_64/lib/libhdf5.a
>>>
>>> /local/home/tools/VisIt/VisIt-2.2.1/sms.Linux-2.6.18-194.26.1.el5.x86_64.gcc-4.1.2.release/current/linux-x86_64/lib/libsz.a
>>> </LIBS>
>>> <FilePatterns>
>>> *.nc
>>> </FilePatterns>
>>> <Files components="M">
>>> avtCM24FileFormat.C
>>> NETCDFFileObject.C
>>> </Files>
>>> <Files components="E">
>>> avtCM24FileFormat.C
>>> NETCDFFileObject.C
>>> </Files>
>>> <Attribute name="" purpose="" persistent="true" keyframe="true"
>>> exportAPI="" exportInclude="">
>>> </Attribute>
>>> </Plugin>
>>>
>>> how do I go about adding the appropriate netcdf and hdf5 libraries into
>>> the plugin CMakeLists.txt file?
>>>
>>> any help is much appreciated.
>>>
>>> thank you
>>> -simon
>>>
>>>
>>>
>>>
>>>
>>> On Mon, Apr 11, 2011 at 8:25 AM, Robert Maynard <
>>> robert.maynard at kitware.com> wrote:
>>>
>>>> Hi Simon,
>>>>
>>>> You do not need to place the CMakeLists.txt inside ParaView at all to
>>>> build a plugin. You just need to set that folder as the source folder
>>>> for CMake, and set a different directory as the plugin build
>>>> directory. After that you will need to set ParaView_DIR to your
>>>> ParaView build directory.
>>>>
>>>> I would also look over: http://www.paraview.org/Wiki/Plugin_HowTo for
>>>> my information on building plugins.
>>>>
>>>> On Fri, Apr 8, 2011 at 5:12 PM, Simon Su <newsgroup4ssu at gmail.com>
>>>> wrote:
>>>> > Hi there,
>>>> >
>>>> > I have silo plugin working and now I would like to try out adding my
>>>> own
>>>> > VisIt database plugin to ParaView.
>>>> > http://www.cmake.org/Wiki/VisIt_Database_Bridge mentioned how to
>>>> write the
>>>> > CMakeLists.txt file but where do I need to place the files (
>>>> CMakeLists.txt,
>>>> > and avtMyReaderFileFormat.C) in the source tree of ParaView to be
>>>> pickup by
>>>> > the cmake process?
>>>> >
>>>> > thanks
>>>> > -simon
>>>> >
>>>> > _______________________________________________
>>>> > 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
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Robert Maynard
>>>>
>>>
>>>
>>
>>
>> --
>> Robert Maynard
>>
>
>
--
Robert Maynard
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PROJECT(VisItReaderExample)
cmake_minimum_required(VERSION 2.8)
IF( COMMAND CMAKE_POLICY )
CMAKE_POLICY( SET CMP0003 NEW )
ENDIF( COMMAND CMAKE_POLICY )
FIND_PACKAGE(ParaView REQUIRED)
INCLUDE(${PARAVIEW_USE_FILE})
SET(SOURCES
avtH5NimrodFileFormat.h
avtH5NimrodFileFormat.C
H5utils.C
)
SET(VISIT_PLUGIN_EXTERNAL_LIBS "" CACHE FILEPATH "External link targets")
SET(VISIT_PLUGIN_EXTERNAL_INCLUDE_DIRS "" CACHE PATH "External include directories")
INCLUDE_DIRECTORIES(${EXTERNAL_INCLUDE_DIRS})
ADD_VISIT_PLUGIN_READER(VisItReaderExample "1.0"
VISIT_READER_NAME "avtH5NimrodFileFormat"
VISIT_READER_TYPE "MTSD"
VISIT_READER_FILE_PATTERN "h5"
SERVER_SOURCES ${SOURCES}
)
TARGET_LINK_LIBRARIES(VisItReaderExample vtkVisItAVTAlgorithms ${EXTERNAL_LIBS})
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