coupling_xolotl

This is a MOOSE application wrapping Xolotl a cluster dynamics code.

Here is how to install this application:

git clone https://github.com/SciDAC-MOOSE-Xolotl-coupling-group/coupling_xolotl.git
cd coupling_xolotl
git submodule init
git submodule update
cd moose
./scripts/update_and_rebuild_petsc.sh --download-hdf5 --download-boost
./scripts/update_and_rebuild_libmesh.sh
cd ..
make

Tests can be run through:

./run_tests

If your machine has N cores available the installation can go faster by using:

MOOSE_JOBS=N ./scripts/update_and_rebuild_libmesh.sh

for libMesh; and:

make -j N

for the coupling code.

If you have your own Boost installation you can define BOOST_ROOT before starting the installation.

If you have your own MOOSE installation you can define MOOSE_DIR and skip libmesh and potentially PETSc.

Troubleshouting

PETSc and MUMPS

If you get an error at the build PETSc step related to the MUMPS package, you can try to download this package manually and point to it through:

./scripts/update_and_rebuild_petsc.sh --download-hdf5 --download-mumps=/yourselectedlocation/packagename.tar.gz

Clang and OpenMP

If you use Clang with OpenMP support but still get an error in the build libmesh step stating that your compiler does not support OpenMP, try setting:

export OPENMP_CXXFLAGS='-Xpreprocessor -fopenmp -lomp'
export FFLAGS='-L/usr/local/lib'