Beta: This software is currently under early development. It has been demonstrated to work on a wide range of problems, but the build system is not finalized.

The plugin has been tested and is confirmed to work with Trelis versions 16.5 and 17.1. These build instructions assume that Trelis 17.1 is being used, but other versions can be used by replacing instances of "17.1" with the version being used.

In order to build the plugin, you must have access to Trelis and the Trelis 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:

• MOAB 5.1.0
• DAGMC

Trelis can be installed by obtaining the Trelis .deb package and installing it with the package manager; i.e.

sudo dpkg -i Trelis-17.1.0-Lin64.deb

This installs Trelis to /opt/Trelis-17.1.

The Trelis 17 SDK can be installed with these commands:

cd /opt
sudo tar -xzvf /path/to/Trelis-SDK-17.1.0-Lin64.tar.gz

The SDK for Trelis 16 should be unpacked from /opt/Trelis-16.5 instead of just /opt; i.e.

cd /opt/Trelis-16.5
sudo tar -xzvf /path/to/Trelis-SDK-16.5.4-Lin64.tar.gz

There is also a bug (or some other unknown issue) in Trelis 16 which requires a file in the Trelis SDK to be modified. The following commands show how to make this change. This issue is not present in Trelis 17, so these commands do not need to be run for Trelis 17.

cd /opt/Trelis-16.5/bin
sudo cp -pv CubitExport.cmake CubitExport.cmake.orig
sudo sed -i "s/\"cubit_util\" \"showviz_base\"/\"cubit_util\"/" CubitExport.cmake

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 Trelis-plugin repo has been cloned into ${HOME}/plugin-build/Trelis-plugin.

Before building anything, ensure that the LD_LIBRARY_PATH environment variable is empty. This variable is not needed to build MOAB, DAGMC, or the plugin, and if it is not empty it can only cause problems. Ensure that it remains empty when running Trelis as well.

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 Trelis.

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 ${HOME}/plugin-build
mkdir -pv moab/bld
cd moab
git clone https://bitbucket.org/fathomteam/moab -b Version5.1.0
cd moab
autoreconf -fi
cd ../bld
../moab/configure CXXFLAGS=-D_GLIBCXX_USE_CXX11_ABI=0 \
                  --enable-shared \
                  --enable-optimize \
                  --disable-debug \
                  --disable-blaslapack \
                  --with-eigen3=/usr/include/eigen3 \
                  --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
                  --prefix=${HOME}/plugin-build/moab
make -j`grep -c processor /proc/cpuinfo`
make install

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

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

cd ${HOME}/plugin-build
mkdir -pv bld
cd bld
cmake ../Trelis-plugin -CUBIT_ROOT=/opt/Trelis-17.1 \
                       -DDAGMC_DIR=${HOME}/plugin-build/DAGMC \
                       -DCMAKE_BUILD_TYPE=Release \
                       -DCMAKE_INSTALL_PREFIX=${HOME}/plugin-build
make -j`grep -c processor /proc/cpuinfo`
make install

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/Trelis-plugin
git submodule update --init

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 *

# Set the RPATH to be the current directory for the DAGMC libraries
patchelf --set-rpath /opt/Trelis-17.1/bin/plugins/svalinn libMOAB.so
patchelf --set-rpath /opt/Trelis-17.1/bin/plugins/svalinn libdagmc.so
patchelf --set-rpath /opt/Trelis-17.1/bin/plugins/svalinn libmakeWatertight.so
patchelf --set-rpath /opt/Trelis-17.1/bin/plugins/svalinn libpyne_dagmc.so
patchelf --set-rpath /opt/Trelis-17.1/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.

To install the plugin, simply run

cd /opt/Trelis-17.1
sudo tar -xzvf ${HOME}/plugin-build/svalinn-plugin-17.1.tgz

Run trelis. If the plugin was installed correctly, after the Trelis GUI finishes loading, the following output should appear in the Trelis command line:

Loaded Svalinn plugin.
-- DAGMC export command available.
-- iGeom_test command available.
-- MCNP import command available.
Journaled Command: undo on

Trelis>

If this output does not appear, then the plugin was not installed correctly.

To view the available command line options for the MCNP importer, type help mcnp in the Trelis command line. Similarly for the DAGMC exporter, type help dagmc in the Trelis command line.

Some sample files have been included in the test_plugin directory of this repository. Navigate to that directory, then run trelis. In the Trelis command line, type import mcnp test.i. This should result in the MCNP geometry and material mapping contained within the MCNP input file test.i being imported into Trelis.

Next, run export acis test.sat overwrite attributes_on. This will save the geometry in ACIS format to test.sat.

Lastly, run export dagmc "test.h5m" faceting_tolerance 1e-3 make_watertight verbose. This will facet the geometry and save it in a format that can be used by DAGMC.

The plugin can also be run in command line mode, without needing to load the Trelis GUI. The file test.jou in the test_plugin directory contains the five commands mentioned in the previous section of this readme. To execute these commands in command line mode, run trelis -batch -nographics -nojournal test.jou from the regular command line.

It is through this command line interface that one would replicate the workflows of years past which involved the now-defunct mcnp2cad and dagmc_preproc executables.