NEMoSys

The Nuclear Energy Modeling System is a modular, extensible resource designed to be used in typical application development systems as well as in distributed web-services environments. The focus of the project is on providing a framework for robust, automated mesh generation, mesh quality analysis, adaptive mesh refinement and data transfer between arbitrary meshes. Python bindings to the Nemosys library can also be enabled.

Getting Started

To acquire NEMosys, you can download it from Illinois Rocstar's GitHub or clone it with the following command:

$ git@github.com:snatesh/NEMoSys_fork.git

Build Instructions

Build Dependencies

You will need to apt install at least the following dependencies:

• build-essential
• cmake
• libproj-dev
• libmetis-dev
• libfltk1.3-dev
• liblapack-dev
• libgmp-dev
• libjpeg-dev
• libsm-dev
• libice-dev
• gfortran
• libxt-dev
• zlib1g-dev
• tcl-dev
• tk-dev
• libxmu-dev
• python-dev
• swig (if you want python bindings)
• an MPI compiler

Once these dependencies are installed, the easiest way to build the required third party libraries is with the script build.sh. Assume $NEMOSYS_PROJECT_PATH is the path to Nemosys, and $NEMOSYS_INSTALL_PATH is the desired installation location. Make sure to use absolute paths and execute the following:

$ NEMOSYS_PROJECT_PATH=/full/path/to/Nemosys
$ NEMOSYS_INSTALL_PATH=/full/path/to/install
$ $NEMOSYS_PROJECT_PATH/scripts/build.sh $NEMOSYS_PROJECT_PATH $NEMOSYS_PROJECT_PATH/contrib/nemosys_tpls.tar.gz $NEMOSYS_INSTALL_PATH

Build Nemosys

Now, we can compile the Nemosys library, create its python bindings and other utilities:

$ cd $NEMOSYS_PROJECT_PATH
$ mkdir build && cd build
$ export CC=mpicc
$ export CXX=mpicxx
$ CMAKE_PREFIX_PATH=$NEMOSYS_INSTALL_PATH/vtk:$NEMOSYS_INSTALL_PATH/madlib:$NEMOSYS_INSTALL_PATH/gmsh:$NEMOSYS_INSTALL_PATH/hdf5:$NEMOSYS_INSTALL_PATH/cgns:$NEMOSYS_INSTALL_PATH/netgen cmake -DCMAKE_INSTALL_PREFIX=$NEMOSYS_INSTALL_PATH -DENABLE_PYTHON_BINDINGS=ON -DENABLE_BUILD_UTILS=ON -DENABLE_TESTING=ON -DENABLE_MPI=ON -DBUILD_SHARED_LIBS=ON .. 
$ make -j6 (or however many threads you'd like to use)
$ make install (sudo if install location requires it)
$ export LD_LIBRARY_PATH=$NEMOSYS_INSTALL_PATH/Nemosys/lib:$NEMOSYS_INSTALL_PATH/vtk/lib:$LD_LIBRARY_PATH
$ export PYTHONPATH=$NEMOSYS_INSTALL_PATH/Nemosys/python/lib/python2.7/site-packages:$PYTHONPATH

Executing the commands above will build all libraries, executables and bindings. The libraries are installed in $NEMOSYS_INSTALL_PATH/Nemosys/lib. Executables are installed in $NEMOSYS_INSTALL_PATH/Nemosys/bin. If python bindings are enabled, the pyNemosys module files are installed in $NEMOSYS_INSTALL_PATH/Nemosys/python/lib/python2.7/site-packages. The pyNemosys module can be imported in python as import pyNemosys. The build configuration can modified through the CMake curses interface (ccmake) or by passing the command line options to cmake.

Testing Nemosys

From the build directory, execute the following command to test the installation:

$ make test

This will execute several tests found in $NEMOSYS_PROJECT_PATH/testing.

Manually Build Third Party Libraries

If execution of build.sh fails, or you have already installed some of the dependecies, you can try building the remaining tpls independently Extract the whole archive as such:

$ cd $NEMOSYS_PROJECT_PATH/
$ tar zxf contrib/nemosys_tpls.tar.gz 
$ cd nemosys_tpls

Building Gmsh

Unpack Gmsh from the neomsys_tpls directory:

$ tar zxf gmsh-2.15.0-source.tgz
$ cd gmsh-2.15.0-source

Build Gmsh by running the following commands:

$ mkdir lib
$ cd lib
$ cmake -DCMAKE_INSTALL_PREFIX=$NEMOSYS_INSTALL_PATH/gmsh -DDEFAULT=0
        -DENABLE_BUILD_LIB=1 -DENABLE_BUILD_SHARED=1 ..
$ make lib shared install/fast -j8
$ cp ./Mesh/meshPartitionObjects.h $NEMOSYS_INSTALL_PATH/gmsh/include/gmsh/

Building madlib

Unpack madlib from the neomsys_tpls directory:

$ tar zxf madlib-1.3.0.tar.gz
$ cd madlib-1.3.0/

Build madlib:

$ ./configure --prefix=$NEMOSYS_INSTALL_PATH/madlib --enable-moveIt
              --enable-benchmarks --enable-ann
              --enable-gmsh --with-gmsh-prefix=$NEMOSYS_INSTAL_PATH/gmsh
$ make -j8
$ make install

Afterwards, a number of header files from the madlib source directory will need to be manually copied into $NEMOSYS_INSTALL_PATH/madlib/include/MAdLib:

• Mesh/MeshDataBase.h
• Mesh/MeshDataBaseInterface.h
• Mesh/MeshDataBaseIterators.h
• Mesh/MeshDataBaseAttachable.h
• Mesh/MeshDataBaseMiniMesh.h
• Mesh/MshTags.h
• Mesh/MeshDataBaseIO.h
• Mesh/CheckOrientation.h
• Common/MAdMessage.h
• Common/MAdSingleton.h
• Geo/GmshEntities.h
• Geo/Physical.h
• Adapt/utils/NodalDataManager.h

Building HDF5

Unpack HDF5 from the nemosys_tpls directory:

$ tar zxf hdf5-1.8.21.tar.gz
$ cd hdf5-1.8.21

Build hdf5:

$ ./configure --prefix=$NEMOSYS_INSTALL_PATH/hdf5
$ make -j8
$ make install

Building CGNS

Unpack CGNS from the neomsys_tpls directory:

$ tar zxf cgnslib_3.2.1.tar.gz
$ cd cgnslib_3.2.1

Build cgns:

$ mkdir build
$ cd build
$ cmake -DCMAKE_INSTALL_PREFIX=$NEMOSYS_INSTALL_PATH/cgns -DCGNS_BUILD_SHARED=ON -DCGNS_BUILD_CGNSTOOLS=ON -DCGNS_ENABLE_HDF5=ON -DHDF5_INCLUDE_PATH=$NEMOSYS_INSTALL_PATH/hdf5/include -DHDF5_LIBRARY=$NEMOSYS_INSTALL_PATH/hdf5/lib/libhdf5.so ..
$ make -j8
$ make install

Building Netgen

Unpack Netgen from the nemosys_tpls directory:

$ tar xzf netgen-meshter-git.tar.gz
$ cd netgen-mesher-git

Build Netgen:

$ mkdir build && cd build
$ cmake -DCMAKE_INSTALL_PREFIX=$NEMOSYS_PROJECT_PATH/install/netgen -DUSE_GUI=OFF ..
$ make -j8
$ make install

Build VTK

Unpack VTK from the nemosys_tpls directory:

$ tar xzf VTK-8.1.1.tar.gz
cd VTK-8.1.1

Build vtk:

$ mkdir build
$ cd build
$ export CC=mpicc
$ export CXX=mpicxx
$ cmake -DVTK_Group_MPI=ON -DCMAKE_INSTALL_PREFIX=$NEMOSYS_INSTALL_PATH/vtk ..
$ make -j8
$ make install

See the building Nemosys section to proceed from this point and complete the build.

License

This project is licensed under the University of Illinois/NCSA Open Source License- see LICENSE for more details.