VisIt avt Integration
TODO
Introduction
This document describes the Visit Database Bridge ParaView plugin. Any references to "plugin" or "bridge" herein refer to this plugin. The motivation for the plugin is simple to allow ParaView to make use of some subset of VisIt's IO components. In ParaView IO components are called "readers" but in VisIt they are called "databases". Besides the nomenclature, there are a number of subtle differences between the two application's implementation of IO components. First VisIt provides a consistent interface both for database implementors and for programmers constructing pipelines using avt. Avt is waht VisIt's visualization pipeline library is called. VisIt database plugin authors implement one of 4 interfaces derived from avtFileFormat. We thus had the option of tying into the VisIt code base here. The file format interface provides a coonstitent albiet low level interface to a given database. We could simply rip out the various database source code and manipulate the code directly. This would require a major restructuring of VisIt's source tree, and result in the direct inclusion of the requisite source in ParaView. It quickly became apparent that if we were to do this we'd have to reinvent a large amount of code that was already available in VisIt higher up in the pipeline. Also doing so would mean essentially a fork of the database and various avt sources that would make upgrading versions of VisIt cumbersome to the point that it would likely never happen. Another more efficient option is to use the database plugins without any alteration. We need not alter the VisIt code base at all. This is a more natural approach, essentially amounting to using VisIt avt classes as a shared library. This approach has the additional benefit of making the process of upgrading VisIt simple.
General Information and Notes
This file is a site-config file that I used to build VisIt as a library for use with ParaView. To do so VisIt's makefiles had to be patched so that its GUI is excluded and ParaView's VTK can be used. The top section of the file is a set of notes as to how I configured VisIt's dependencies and VisIt itself. The bottom of this file is a bash script that VisIt uses to configure itself. You will have to modify the variables to reflect locations of the dependencies on your system. If you are only interested in a specific database plugin then you can skip many of the dependencies. You can't skip szip, silo, or hdf5. Be sure to point ParaView to the version of HDF5 you are using here when you build ParaView.
Notes:
VisIt suggests to use static libraries for its dependencies. This isn't always a good idea. HDF5 for instance should be shared when using with ParaView. Theses notes need to be updated to reflect this. TODO
Windows has a completely different build process because VisIt used visual studio. Mac is as of yet uncharted territory.
In theory one can build all of VisIt's dependencies using the "build_visit" script available from VisIt's web site. If you go that route, then you still should use this file to configure the patched VisIt with the ./configure line below.
You'll need to have Qt 3 development packge around somewhere because VisIt's ./configure script has a Qt 3 dependency.
It's best to try ot use the versions of the libraries I have used here, if not then second best is to use the ones recomended by VisIt. If you do niether you're on your own, but things will probably be OK as long as you stick to the recomended configuration.
Which of VisIt's databases are available?
This depends largely on how VisIt is built because databases only are built if their dependencies are found. Our plugin handles this by scanning the VisIt build at compile time, and only generating server manager XML for those which are present. This list reflects what is available in a full VisIt 1.10.0 build. A number of these however are intentionally skipped since ParaView already has support for them. The databases are skipped based on the contents of a text file included in the plugin sources.
- ANALYZE
- ANSYS
- AUXFile
- AugDecomp
- BOV
- BOW
- Boxlib2D
- Boxlib3D
- CEAucd
- CGNS
- CMAT
- CTRL
- Cale
- Chombo
- Claw
- Cosmos
- CosmosPP
- Curve2D
- DDCMD
- Dune
- Dyna3D
- EnSight
- Enzo
- ExtrudedVol
- FITS
- FLASH
- Fluent
- GDAL
- GGCM
- GTC
- H5Nimrod
- H5Part
- Hex
- Image
- KullLite
- Lines
- M3D
- MFIX
- MM5
- Miranda
- NASTRAN
- NETCDF
- Nek3D
- OVERFLOW
- OpenFOAM
- PATRAN
- PDB
- PFLOTRAN
- PLOT2D
- PLOT3D
- Pixie
- PlainText
- Point3D
- ProteinDataBank
- RAW
- Rect
- S3D
- SAMI
- SAMRAI
- SAR
- SAS
- STL
- Shapefile
- Silo
- SimV1
- SimV1Writer
- Spheral
- StreamGhostTest
- TFT
- TSurf
- Tecplot
- Tetrad
- UNIC
- VASP
- VLI
- Vis5D
- Vista
- WavefrontOBJ
- XDMF
- XYZ
- Xmdv
- ZeusMP
- ZipWrapper
Step 1: Build VisIt's dependencies
szip
LIBS=-lm CFLAGS=-fPIC CXXFLAGS=-fPIC ./configure --prefix=/opt/szip-2.1 --disable-shared make -j 8 sudo make install
HDF4
LIBS=-lm CFLAGS=-fPIC CXXFLAGS=-fPIC ./configure --prefix=/opt/hdf4-4.2r3 --disable-fortran --with-szlib=/opt/szip-2.1/ make -j 8 sudo make install
HDF5
for gcc 4.3 you'll have to edit perform/zip_perf.c change line 549 to "output = open(filename, O_RDWR | O_CREAT, S_IRWXU);"
CFLAGS=-fPIC CXXFLAGS=-fPIC ./configure --prefix=/opt/hdf5-1.6.8_ser --disable-shared --disable-fortran --disable-parallel --with-szlib=/opt/szip-2.1 make -j 8 sudo make install sudo ln -s /opt/szip-2.1/lib/libsz.a /opt/hdf5-1.6.8_ser/lib/libsz.a
BoxLib
For gcc-4.3 add #include <cstdlib> to ParallelDescriptor.cpp Usiing gfortran instead of g77 works well.
cd into boxlib directory in the CCSEApps
edit GNUMakefile, set USE_MPI=false, COMP=g++
mv std std.old
chmod 644 *.H
CXXFLAGS=-fPIC CFLAGS=-fPIC FFLAGS=-fPIC make -j 8
sudo mkdir -p /opt/boxlib/{include/2D,include/3D,lib}
sudo cp libbox3d.Linux.g++.f77.DEBUG.a /opt/boxlib/lib/libbox3D.a
sudo cp *.H /opt/boxlib/include/3D/
edit GNUMakefile,set DIM=2
CXXFLAGS=-fPIC CFLAGS=-fPIC FFLAGS=-fPIC make -j 8
sudo cp libbox2d.Linux.g++.f77.DEBUG.a /opt/boxlib/lib/libbox2D.a
sudo cp *.H /opt/boxlib/include/2D/
NetCDF
For gcc-4.3 add #include <cstring> to ./cxx/ncvalues.cpp
CXXFLAGS=-fPIC CFLAGS=-fPIC ./configure --prefix=/opt/netcdf-3.6.0-p1 make -j 8 sudo mkdir /opt/netcdf-3.6.0-p1 sudo make install
Silo
4.6.2 doesn't work with VisIt and gcc 4.3 as of this writing(2009-02-25). Some sort of link issue, may be libtool.?
./configure --prefix=/opt/silo-4.6.1 --without-readline --with-hdf5=/opt/hdf5-1.6.8_ser/include/,/opt/hdf5-1.6.8_ser/lib/ --without-exodus --with-szlib=/opt/szip-2.1 --disable-fortran --disable-browser --disable-shared --disable-silex make -j 8 sudo make install sudo ln -s /opt/silo-4.6.2/lib/libsiloh5.a /opt/silo-4.6.2/lib/libsilo.a
CGNS
Only use hdf5 if you need it.
CXXFLAGS=-fPIC CFLAGS=-fPIC ./configure --prefix=/opt/cgns-2.4 --with-szip=/opt/szip-2.1/lib/libsz.a --with-hdf5=/opt/hdf5-1.6.8_ser/
make -j 8
sudo mkdir -p /opt/cgns-2.4/{include,lib}
sudo make install
CFITSIO
./configure --prefix=/opt/cfitsio make -j 8 sudo make install
H5Part
CFLAGS=-fPIC ./configure --prefix=/opt/h5part-1.3.3 --with-hdf5path=/opt/hdf5-1.6.8_ser/ make -j 8 sudo make install
CCMIO
Didn't work & looks like it uses qmake ?!?. If some one complains we'll get it working.
GDAL
For gcc-4.3 download gdal-1.6.0, the following config works with both version
CFLAGS=-fPIC CXXFLAGS=-fPIC ./configure --prefix=/opt/gdal-1.6.0 --enable-static --disable-shared --with-libtiff=internal --with-gif=internal --with-png=internal --with-jpeg=internal --with-libz=internal --with-netcdf=no --without-jasper --without-python make -j 8 sudo make install
Qt 3
We don't have to link against Qt but VisIt plugin system requires Qt to build.
export QTDIR=`pwd` export LD_LIBRARY_PATH=$QTDIR/lib ./configure --prefix=/opt/qt-3.3.8 make -j 8 sudo make install
Step 2: Build and install VisIt
Once some subset of VisIt's dependencies ahave been built on the target system it's time to build VisIt itself.
NOTE for now set VTK_USE_64BIT_IDS to OFF
NOTE should we force the use of static libs when both shared and static are available? -Bstatic ??
patch -p6 < /home/burlen/ext/kitware_cvs/VisitPluginTool/VisItPV3Build.in.patch
./configure --prefix=/opt/VisIt-1.10.0 --with-config=/home/burlen/ext/kitware_cvs/VisitPluginTool/building_visit/vtkVisitDatabaseBridge.conf --with-hdf5=/opt/hdf5-1.6.8_ser/include,/opt/hdf5-1.6.8_ser/lib --enable-parallel --disable-scripting --disable-visitmodule --disable-viewer-mesa-stub --disable-icet --disable-bilib --disable-glew --disable-bzip2 --with-dbs=all
Step 3: Build the ParaView plugin
Building the database plugin for ParaView is a two step process, namely:
cd bin; ccmake ../ ===> Set BOOTSTRAP to ON make ccmake ../ ===> Set BOOSTRAP to OFF make
Step 1:
BootstrapConfigure.
During this pass a local copy of the VisIt libraries and database
plugins are made. On Windows a copy of the "third party dependencies"
is also made. This is done to facilitate the crossplatform build
and configuration which is necessary due the large differences between
the VisIt build system accross platforms, and to mitigate differneces
in how various platforms handle shared libraries at run time. The final
step of this pass is to generate the CMake files, ServerManager and
Pq xml for the vtkVisItDatabaseBridge plugin upon the VisIt configuration
found.
Step 2:
vtkVisItDatabaseBridge ParaView Plugin.
During this pass the paraview plugin is built from the configuration
generated during the first pass.
Windows
Configure PV for shared libs, using system HDF5. Point both ZLIB and HDF5 include and lib to HDF5 of VisIt/windowsbuild.
C:\VisitPluginTool\plugin\bin\Debug\MSVC8.Net\Debug
set PATH=%PATH%;C:\VisitPluginTool\plugin\bin\Debug;C:\VisitPluginTool\plugin\bin\Debug\MSVC8.Net\Debug;C:\VisitPluginTool\plugin\bin\Debug\MSVC8.Net\Debug\databases;C:\VisitPluginTool\plugin\bin\Debug\MSVC8.Net\ThirdParty
What's Not Done
- We need to map VisIt ghost cells to VTK ghost cells.
- Finish MIR. Part of the MIR code has been written (it's commented out). Basically we need to inquire with the VisIt devs about what is the right way to do this.
- Finish Experssions.Part of the expression code has been written (it's commented out). Expressions will be expected by VisIt users.They can be trivially added. See the avtExpresssionEvaluationFilter.
- Leaks! Run the plugin through valgrind and you'll find all kinds of leaks. These are certainly coming from within VisIt, however we have to
be certain it's not ourfault before asking them for help. I've been careful but now need to go over thoroughly.
