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Building the DAGMC Cubit plugin from source

This guide is intended for developers and maintainers of the Cubit plugin. For installation instructions see the installation guide.

Prerequisites

In order to build the plugin, you must have access to Cubit and the Cubit SDK. Additionally, the following system packages must be present on your computer:

  • EIGEN3
  • HDF5

On Ubuntu, these packages can be obtained by running

sudo apt install libeigen3-dev libhdf5-dev

The following packages are not available from the package manager and must be built yourself:

Notes on Build Instructions

A non-source directory build is recommended. These build instructions assume that the plugin build will take place in the ${HOME}/plugin-build directory, and they assume that the Cubit-plugin repo has been cloned into ${HOME}/plugin-build/Cubit-plugin.

Before building anything, ensure that the LD_LIBRARY_PATH environment variable is empty. Ensure that it remains empty when running Cubit as well.

unset LD_LIBRARY_PATH

Build MOAB

MOAB must be built with HDF5 enabled. On Ubuntu 18.04, HDF5 is located in the /usr/lib/x86_64-linux-gnu/hdf5/serial directory, but it may be located somewhere else on other flavors or versions of Linux. MOAB should be built with the Eigen matrix algebra library instead of LAPACK. The _GLIBCXX_USE_CXX11_ABI=0 flag is required for compatibility with Cubit.

The following commands show how to correctly build the MOAB dependency. If HDF5 is located somewhere other than /usr/lib/x86_64-linux-gnu/hdf5/serial, then replace the directory with the correct one.

cd ${HOME}/plugin-build
mkdir -pv moab/bld
cd moab
git clone https://bitbucket.org/fathomteam/moab -b 5.3.0
cd moab
# patching MOAB CMakeLists.txt to use default find(HDF5)
$SED -i "s/HDF5_MOAB/HDF5/" CMakeLists.txt
cd ..
#end of patch
cd bld
cmake ../moab -DENABLE_HDF5=ON \
        -DHDF5_ROOT=$HDF5_PATH \
        -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS} \
        -DENABLE_BLASLAPACK=OFF \
        -DENABLE_FORTRAN=OFF \
        $CMAKE_ADDITIONAL_FLAGS \
        -DCMAKE_INSTALL_PREFIX=${PLUGIN_ABS_PATH}/moab
make
make install
cd ../..
rm -rf moab/moab moab/bld

Build DAGMC

The following commands show how to build the DAGMC dependency. The uwuw and make_watertight features should be turned on, while other features should be turned off. The MOAB_DIR variable should point to the location of the previously-built MOAB library. The _GLIBCXX_USE_CXX11_ABI=0 flag is once again required.

The following commands show how to correctly build the DAGMC dependency.

cd ${HOME}/plugin-build
mkdir -pv DAGMC/bld
cd DAGMC
git clone https://github.com/svalinn/DAGMC -b develop
cd bld
cmake ../DAGMC -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
               -DMOAB_DIR=${HOME}/plugin-build/moab \
               -DBUILD_UWUW=ON \
               -DBUILD_TALLY=OFF \
               -DBUILD_BUILD_OBB=OFF \
               -DBUILD_MAKE_WATERTIGHT=ON \
               -DBUILD_SHARED_LIBS=ON \
               -DBUILD_STATIC_LIBS=OFF \
               -DCMAKE_BUILD_TYPE=Release \
               -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build/DAGMC
make -j`grep -c processor /proc/cpuinfo`
make install

Build the Plugin

The following commands show how to build the plugin itself. The CUBIT_ROOT variable should point to the location of Cubit. The DAGMC_DIR variable should point to the location of the previously-built DAGMC library.

cd ${HOME}/plugin-build
mkdir -pv bld
cd bld
cmake ../Cubit-plugin -DCUBIT_ROOT=PATH_TO_CUBIT \
                       -DDAGMC_DIR=${HOME}/plugin-build/DAGMC \
                       -DCMAKE_BUILD_TYPE=Release \
                       -DCMAKE_CXX_FLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
                       -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build
make -j`grep -c processor /proc/cpuinfo`
make install

Submodules

The plugin depends on another external repository called mcnp2cad. mcnp2cad is available in this repo as a git submodule. It is pulled by default during the cmake configuration step above.

If a custom version of mcnp2cad is needed, this behavior pulling can be disabled by adding -DUPDATE_SUBMODULES=OFF to the cmake configuration. mcnp2cad can then be manually updated with the following commands:

cd ${HOME}/plugin-build/Cubit-plugin
git submodule update --init

Create the Tarball

The following commands show how to create the tarall for the plugin. Once again, the location of HDF5 might be different than what is presented here depending on what flavor or version of Linux is being used.

Set up the directory which will contain the libraries

cd ${HOME}/plugin-build
mkdir -p pack/bin/plugins/svalinn
cd pack/bin/plugins/svalinn

Copy all needed libraries into current directory

cp -pPv /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.100* .
cp -pPv ${HOME}/plugin-build/moab/lib/libMOAB.so* .
cp -pPv ${HOME}/plugin-build/DAGMC/lib/libdagmc.so* .
cp -pPv ${HOME}/plugin-build/DAGMC/lib/libmakeWatertight.so* .
cp -pPv ${HOME}/plugin-build/DAGMC/lib/libpyne_dagmc.so* .
cp -pPv ${HOME}/plugin-build/DAGMC/lib/libuwuw.so* .
cp -pPv ${HOME}/plugin-build/lib/* .
chmod 644 *

The resulting shared library objects require an update to their RPATH (runtime path) attribute to ensure that the correct set of libraries is discovered when starting Cubit and loading the plugin library.

patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libMOAB.so
patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libdagmc.so
patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libmakeWatertight.so
patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libpyne_dagmc.so
patchelf --set-rpath PATH_TO_CUBIT/bin/plugins/svalinn libuwuw.so

Create the Svalinn plugin tarball

cd ..
ln -sv svalinn/libsvalinn_plugin.so .
cd ../..
tar --sort=name -czvf svalinn-plugin-17.1.tgz bin
mv -v svalinn-plugin-17.1.tgz ..
cd ..
rm -rf pack

The Svalinn plugin tarball should now be located at ${HOME}/plugin-build/svalinn-plugin-17.1.tgz.

Install the Plugin

To install the plugin, simply run

cd PATH_TO_CUBIT
sudo tar -xzvf ${HOME}/plugin-build/svalinn-plugin.tgz