VisIt avt Integration
TODO
Introduction
This document describes the Visit Database Bridge ParaView plugin. The motivation for our plugin is to allow ParaView to make use VisIt's IO components, and to explore the re-usable capabilities of VisIt and its underlying pipeline library avt. Like ParaView VisIt is a scientific data visualization application based on VTK and Qt. There are a number of subtle differences between the two application's implementation. Despite these differences there are more similarities than differences and hence porting subsets of finctionality form one ot the other is very doable and potentially very beneficial as both applications have large stable thoroughly tested code base.
In ParaView IO components are called "readers" while in VisIt they are called "databases". VisIt developers have provided a consistent interface both for database authors, who are typically scientists, via the file format interface and for avt developers writing pipelines via the database plugin interface. VisIt database plugin authors implement one of the concrete interfaces derived from avtFileFormat. We thus had the option of accessing VisIt databases via this interface. The file format interface provides a consistent, albeit low level interface, to any given database. We could simply manipulate file format directly using this interface and linking to various database implementations. This is a minimalistic approach isolating the essential code to read data from disk. However, it very quickly became apparent that if we were to take the file format approach we'd have to forgo quite a lot of VisIt's implemented functionality and have to re-invent a large amount of tested code. Fortunately there was a second option, namely to manipulate the database plugins using the avtGenericDatabase interface. This turns out to be quite a bit more efficient from a coding point of view than the file format interface.
In our implementation we have a single VTK class called the vtkVisItDatabase that exposes all of VisIt's 84 database plugins in a general way. At run time a database name is passed into the vtkVisItDatabase via a vtkSetStringMacro. Internally the vtkVisItDtabase owns an avt DatabasePluginManager object which is used to load one of VisIt's available database plugins, returning an avtGenericDatabase object from which meta data can be extracted and an avtSource object can be created. The source object can then be used to construct a simple avt pipeline from which we can extract VTK objects. The vtkVisItDatabase class is layered inside of a VTK algorithm implementation class named vtkVisItDatabaseBridge. To expose the bridge as a reader in ParaView we generate a server manager XML source proxy tag for each of VisIt's database plugin's. The tags name the specific database plugin to use with the given list of file extensions. Due to VisIt's long list of external library dependencies, there can be quite a bit of variability between builds in the available database plugins. We handle this by probing the VisIt installation and generating XML for only those database plugins that are found as the bridge is compiled.
The database concept is very general, and as such very powerful. VisIt's database abstraction means that storage formats and file contents all appear the same to the application. For instance a database represents some collection of data, providing a means to query and access what is available. There are few restrictions on what data can be provided. For example a database is not restricted to providing a single dataset, it can provide many. Further the database concept implies nothing about how the provided data is organized. For that purpose VisIt uses the avtSILSet object. Literally a SIL is a subset inclusion lattice. The avtSILSet can be thought of as a directed graph that describes a collection of VTK datasets. The data available is is given a SIL set ID and is hierarchically organized. This scheme allows for collections or groupings of data to be simply constructed. For example an mechanical assemblies can be handled by creating a SIL set with edges to a number of domains.
SIL sets are used throughout VisIt's avt pipeline inside of avtDataRequest objects which are passed through the pipeline and modified until they reach the database object. The database object processes the request loading the selected sets and providing the resulting dataset to the pipeline in an avtDataSet object. The avtDataSet is something like a vtkCompositeDataSet. In the bridge we have exposed the avtDataRequest to the user directly inside the ParaView U.I. via a custom Qt panel. Each of the generated ParaView readers (source proxies) are associated with this panel, thus all of the 84 database plugins have the same user interface. When the VTK pipeline executes during the request information phase the database plugin is querried and the discovered SIL set is displayed in the ParaView client. The user then interacts with the SIL set before initiating the request data pipeline phase during which the user's selections are translated into an avtDataRequest and fed into an avt pipeline. At this point the avt pipeline is executed and the resulting avt data set is translated into a VTK data object where it is passed off to ParaView's underlying VTK pipeline. Because we are building an avt pipeline we have the option of doing things in the native avt way which lets us provide expected VisIt functionality such as expression evaluation, material interface reconstruction (MIR), and sub-setting operations. The great thing about this design is that for the price of three classes we can access the entirety of VisIt's database plugin collection, and provide a general flexible interface to disparate collections of data.
In this approach the database plugins are used with out alteration, in essence using VisIt avt classes as a shared library to programatically manipulate the plugins in a general way. This approach should have additional benefit of making the process of upgrading VisIt as simple as installing the new version and reconfiguring the bridge. Unfortunately a number aspects of VisIt's design complicate things. The first and largest complication is that VisIt has forked VTK at release 5.0 2006. Inorder to use VisIt from within ParaView we have to use the same version of VTK thus we need to have the capability of compiling VisIt against our version of VTK. Unfortunately, VTK has changed a lot in between 5.0 and present, and not all of VisIt's new or modified VTK code is compatible with the current revision of VTK. Some of the major incompatibilities are in VisIt's rendering additions and are a result of VTK's interface changing from int to vtkIdType. Further, VisIt was not designed as a library but rather as a stand alone application so are large unnamed interdependencies between compiled objects leading to a situation where dynamic loaders don't know how to resolve undefined symbols. To work around both of these issues we ended up patching VisIt's build system. Fortunately only the build system configuration files needed to be modified, no modifications to VisIt sources were required.
The structure of our bridge is as follows:
- vtkVisItDatabase -- VTK object that encapsulates all avt code, providing clients with an API for manipulating database plugins, the meta-data produced from files they can load, configuration of data requests and conversion the data returned from actual read operations into VTK data objects. Contains a DatabasePluginManager.
- vtkVisItDatabaseBridge -- A VTK algorithm that implements the VTK pipline required of a ParaView reader. Contains a vtkVisItDatabase.
- pqVisItDatabaseBridgePanel -- A custom QT panel for ParaView that can read the directed graph describing the data available in any given file.
On Linux and Mac VisIt makes use of autotools, while on Windows VisIt makes use of Visual Studio solutions.
An additional complication when developing our bridge plugin was that VisIt builds only those plugins whose dependencies can be resolved at compile time so that a static build configuration was impractical. We have handled this by writing a bootsrap configuration utility that probes the named VisIt install loading database plugins one by one, extracting name, and file extensions as we go and generating the servermanager XML. The one complication of the bootstrap is that ParaView plugins which require a custom panel have to name that panel in the CMake file. We don't know which plugin's are going to be required until we are not able to modify the CMake files while CMake is running. To work around this we build the plugin in two steps, a bootstrap step and a build step.
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.
