[Paraview] VisIt Database Bridge - Custom Plugin of VisIt Reader
Simon Su
newsgroup4ssu at gmail.com
Mon Apr 25 16:52:53 EDT 2011
Hi Robert,
I changed my CMakeLists.txt file to
+++++++++++++++++++++++++++++++++++
PROJECT(VisItReaderGFDL)
cmake_minimum_required(VERSION 2.8)
FIND_PACKAGE(ParaView REQUIRED)
INCLUDE(${PARAVIEW_USE_FILE})
SET(SOURCES
avtCM24FileFormat.h
avtCM24FileFormat.C
NETCDFFileObject.h
NETCDFFileObject.C
)
SET(VISIT_PLUGIN_EXTERNAL_LIBS "" CACHE FILEPATH "External link targets")
SET(VISIT_PLUGIN_EXTERNAL_INCLUDE_DIRS "" CACHE PATH "External include
directories")
INCLUDE_DIRECTORIES(${EXTERNAL_INCLUDE_DIRS})
ADD_VISIT_PLUGIN_READER(VisItReaderGFDL "1.0"
VISIT_READER_NAME "avtCM24FileFormat"
VISIT_READER_TYPE "MTSD"
VISIT_READER_FILE_PATTERN "nc"
SERVER_SOURCES ${SOURCES}
)
TARGET_LINK_LIBRARIES(VisItReaderGFDL vtkVisItAVTAlgorithms
${EXTERNAL_LIBS})
++++++++++++++++++++++++++++++++++++++++
and after I run ccmake to put in the external libraries and include
directories, in my CMakeCache.txt file, I have
+++++++++++++++++
//External include directories
VISIT_PLUGIN_EXTERNAL_INCLUDE_DIRS:PATH=/local/home/build/visit/visit-2.2.2-x86_64-openmpi/visit/netcdf/4.1.1/x86_64_gcc-4.1/include;/local/home/build/visit/visit-2.2.2-x86_64-openmpi/visit/hdf5/1.8.4/x86_64_gcc-4.1/include
//External link targets
VISIT_PLUGIN_EXTERNAL_LIBS:FILEPATH=/local/home/build/visit/visit-2.2.2-x86_64-openmpi/visit/hdf5/1.8.4/x86_64_gcc-4.1/lib/libhdf5.a;/local/home/build/visit/visit-2.2.2-x86_64-openmpi/visit/hdf5/1.8.4/x86_64_gcc-4.1/lib/libhdf5_hl.a;/local/home/build/visit/visit-2.2.2-x86_64-openmpi/visit/netcdf/4.1.1/x86_64_gcc-4.1/lib/libnetcdf.a
+++++++++++++++++
but when I run the plugin, I still get
sms:/local/home/build/paraview-plugin/gfdl-paraview-loader-build> paraview
/local/home/tools/ParaView/ParaView-3.10.1/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
when I do a
make VERBOSE=1 >& make-out
the string netcdf doesn't even show up in the make-out file.
am I missing something? I only have static library for netcdf, is that the
problem?
thank you
-simon
On Mon, Apr 25, 2011 at 11:12 AM, Simon Su <newsgroup4ssu at gmail.com> wrote:
> Hi Robert,
>
> I will give it a try.
>
> thanks
> -simon
>
>
> On Mon, Apr 18, 2011 at 9:26 AM, Robert Maynard <
> robert.maynard at kitware.com> wrote:
>
>> 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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