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RayfireMesh::init() fixes for restart

README.md

GRINS

General Reacting Incompressible Navier-Stokes (GRINS) was initiated
to house common modeling work centered around using the incompressible and variable-density (low-Mach) Navier-Stokes equations utilizing the libMesh finite element library, including both MPI and MPI+threads parallelism, as provided by libMesh. GRINS has now become a tool for rapidly developing formulations and algorithms for the solution of complex multiphysics applications. GRINS originally lived within the PECOS center at the Institute for Computational Engineering and Sciences (ICES) at The University of Texas at Austin.

We encourage pull requests for new features, bug fixes, etc. For questions regarding development, we have a grins-devel Google group setup. For user related questions, please use the grins-users group.

Dependencies

Requirements

In addition to a modern C++ compiler, GRINS requires an up-to-date installation of the libMesh finite element library. If your C++ compiler does not support smart pointers, than the Boost C++ library is also required (header only).

libMesh

GRINS development both drives and is driven by libMesh development. Thus, the required minimum master hash of libMesh may change in GRINS master. The current required libMesh master hash is 8be0a4e, as of GRINS PR #499. GRINS release 0.5.0 can use libMesh versions as old as 0.9.4. Subsequent to the 0.5.0 release requires at least libMesh 1.0.0.

Optional Packages

To enable the reacting low Mach Navier-Stokes physics class, GRINS must be compiled with an external chemistry library. While Cantera is partially supported, Antioch is fully supported.

The current required minimum hash for using Antioch is libantioch/antioch@ad78595 (libantioch/antioch#240).

Building GRINS

GRINS uses an Autotools build system, so typical GNU build commands are used.

  1. ./bootstrap (generate configure script)
  2. ./configure --prefix=/path/to/install --with-libmesh=/path/to/libMesh --with-boost=/path/to/boost (for more options, do ./configure --help)
  3. make (note parallel builds are supported)
  4. make check (note parallel-tests are supported)
  5. make install

LD_LIBRARY_PATH

If you've compiled libMesh with PETSc or other external libraries and have compiled GRINS with Antioch, Cantera, or other external libraries, you will need to add them to your LD_LIBRARY_PATH as we do not use -rpath when linking to the libraries.

METHOD

By default, GRINS leverages the METHOD environment variable (described here) in order to retrieve the CXXFLAGS variable from the libMesh installation (if METHOD is not present, the default is "opt"). Note that unlike libMesh, GRINS currently only supports building one METHOD at a time. Hence, we use METHOD and not METHODS. For example


./configure METHOD=devel

is valid.

The user can define their own CXXFLAGS variable by passing


--disable-libmesh-flags CXXFLAGS="your flags here"

to configure.

Examples

Upon running make install, there are several examples in the /path/to/install/examples directory. Each example can be run with the local run.sh script. You may set the environment variable GRINS_RUN to run with more than one processor, e.g. export GRINS_RUN="mpiexec -np 4". Additionally, you can set the environment variable GRINS_SOLVER_OPTIONS to pass solver options, e.g. to use MUMPS through PETSc (if you built libMesh with PETSc and built PETSc with MUMPS), export GRINS_SOLVER_OPTIONS="-ksp_type preonly -pc_type lu -pc_factor_mat_solver_package mumps".