2. Installation and Configuration¶
2.1. Installing on Linux/Mac with conda-forge¶
Conda is an open source package management system and environment management system for installing multiple versions of software packages and their dependencies and switching easily between them. conda-forge is a community-led conda channel of installable packages. For instructions on installing conda, please consult their documentation.
Once you have conda installed on your system, add the conda-forge channel to your configuration with:
conda config --add channels conda-forge
Once the conda-forge channel has been enabled, OpenMC can then be installed with:
conda install openmc
It is possible to list all of the versions of OpenMC available on your platform with:
conda search openmc --channel conda-forge
2.2. Installing on Ubuntu with PPA¶
For users with Ubuntu 15.04 or later, a binary package for OpenMC is available through a Personal Package Archive (PPA) and can be installed through the APT package manager. First, add the following PPA to the repository sources:
sudo apt-add-repository ppa:paulromano/staging
Next, resynchronize the package index files:
sudo apt update
Now OpenMC should be recognized within the repository and can be installed:
sudo apt install openmc
Binary packages from this PPA may exist for earlier versions of Ubuntu, but they are no longer supported.
2.3. Building from Source¶
A Fortran compiler such as gfortran
In order to compile OpenMC, you will need to have a Fortran compiler installed on your machine. Since a number of Fortran 2003/2008 features are used in the code, it is recommended that you use the latest version of whatever compiler you choose. For gfortran, it is necessary to use version 4.8.0 or above.
If you are using Debian or a Debian derivative such as Ubuntu, you can install the gfortran compiler using the following command:sudo apt install gfortran
A C/C++ compiler such as gcc
OpenMC includes various source files written in C and C++, respectively. These source files have been tested to work with a wide variety of compilers. If you are using a Debian-based distribution, you can install the g++ compiler using the following command:sudo apt install g++
CMake cross-platform build system
The compiling and linking of source files is handled by CMake in a platform-independent manner. If you are using Debian or a Debian derivative such as Ubuntu, you can install CMake using the following command:sudo apt install cmake
HDF5 Library for portable binary output format
OpenMC uses HDF5 for many input/output files. As such, you will need to have HDF5 installed on your computer. The installed version will need to have been compiled with the same compiler you intend to compile OpenMC with. If compiling with gcc from the APT repositories, users of Debian derivatives can install HDF5 and/or parallel HDF5 through the package manager:sudo apt install libhdf5-dev
Parallel versions of the HDF5 library called libhdf5-mpich-dev and libhdf5-openmpi-dev exist which are built against MPICH and OpenMPI, respectively. To link against a parallel HDF5 library, make sure to set the HDF5_PREFER_PARALLEL CMake option, e.g.:FC=mpifort.mpich cmake -DHDF5_PREFER_PARALLEL=on ..
Note that the exact package names may vary depending on your particular distribution and version.
If you are using building HDF5 from source in conjunction with MPI, we recommend that your HDF5 installation be built with parallel I/O features. An example of configuring HDF5 is listed below:FC=mpifort ./configure --enable-fortran --enable-parallel
You may omit
--enable-parallelif you want to compile HDF5 in serial.
If you are building HDF5 version 1.8.x or earlier, you must include
--enable-fortran2003when configuring HDF5 or else OpenMC will not be able to compile.
An MPI implementation for distributed-memory parallel runs
To compile with support for parallel runs on a distributed-memory architecture, you will need to have a valid implementation of MPI installed on your machine. The code has been tested and is known to work with the latest versions of both OpenMPI and MPICH. OpenMPI and/or MPICH can be installed on Debian derivatives with:sudo apt install mpich libmpich-dev sudo apt install openmpi-bin libopenmpi-dev
git version control software for obtaining source code
2.3.2. Obtaining the Source¶
All OpenMC source code is hosted on GitHub. You can download the source code directly from GitHub or, if you have the git version control software installed on your computer, you can use git to obtain the source code. The latter method has the benefit that it is easy to receive updates directly from the GitHub repository. GitHub has a good set of instructions for how to set up git to work with GitHub since this involves setting up ssh keys. With git installed and setup, the following command will download the full source code from the GitHub repository:
git clone https://github.com/mit-crpg/openmc.git
By default, the cloned repository will be set to the development branch. To switch to the source of the latest stable release, run the following commands:
cd openmc git checkout master
2.3.3. Build Configuration¶
Compiling OpenMC with CMake is carried out in two steps. First,
cmake is run
to determine the compiler, whether optional packages (MPI, HDF5) are available,
to generate a list of dependencies between source files so that they may be
compiled in the correct order, and to generate a normal Makefile. The Makefile
is then used by
make to actually carry out the compile and linking
commands. A typical out-of-source build would thus look something like the
mkdir build && cd build cmake .. make
Note that first a build directory is created as a subdirectory of the source directory. The Makefile in the top-level directory will automatically perform an out-of-source build with default options.
220.127.116.11. CMakeLists.txt Options¶
The following options are available in the CMakeLists.txt file:
- Enables debugging when compiling. The flags added are dependent on which compiler is used.
- Enables profiling using the GNU profiler, gprof.
- Enables high-optimization using compiler-dependent flags. For gfortran and Intel Fortran, this compiles with -O3.
- Enables shared-memory parallelism using the OpenMP API. The Fortran compiler being used must support OpenMP. (Default: on)
- Compile and link code instrumented for coverage analysis. This is typically used in conjunction with gcov.
- Maximum number of nested coordinate levels in geometry. Defaults to 10.
To set any of these options (e.g. turning on debug mode), the following form should be used:
cmake -Ddebug=on /path/to/openmc
18.104.22.168. Compiling with MPI¶
To compile with MPI, set the
CC environment variables
to the path to the MPI Fortran and C wrappers, respectively. For example, in a
export FC=mpif90 export CC=mpicc cmake /path/to/openmc
Note that in many shells, environment variables can be set for a single command, i.e.
FC=mpif90 CC=mpicc cmake /path/to/openmc
22.214.171.124. Selecting HDF5 Installation¶
CMakeLists.txt searches for the
h5pfc HDF5 Fortran wrapper on
your PATH environment variable and subsequently uses it to determine library
locations and compile flags. If you have multiple installations of HDF5 or one
that does not appear on your PATH, you can set the HDF5_ROOT environment
variable to the root directory of the HDF5 installation, e.g.
export HDF5_ROOT=/opt/hdf5/1.8.15 cmake /path/to/openmc
This will cause CMake to search first in /opt/hdf5/1.8.15/bin for
h5pfc before it searches elsewhere. As noted above, an environment variable
can typically be set for a single command, i.e.
HDF5_ROOT=/opt/hdf5/1.8.15 cmake /path/to/openmc
2.3.4. Compiling on Linux and Mac OS X¶
To compile OpenMC on Linux or Max OS X, run the following commands from within the root directory of the source code:
mkdir build && cd build cmake .. make make install
This will build an executable named
openmc and install it (by default in
/usr/local/bin). If you do not have administrative privileges, you can install
OpenMC locally by specifying an install prefix when running cmake:
cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local ..
CMAKE_INSTALL_PREFIX variable can be changed to any path for which you
2.3.5. Compiling on Windows 10¶
Recent versions of Windows 10 include a subsystem for Linux that allows one to
run Bash within Ubuntu running in Windows. First, follow the installation guide
here to get
Bash on Ubuntu on Windows setup. Once you are within bash, obtain the necessary
apt. Finally, follow the
instructions for compiling on linux.
2.3.6. Compiling for the Intel Xeon Phi¶
For the second generation Knights Landing architecture, nothing special is required to compile OpenMC. You may wish to experiment with compiler flags that control generation of vector instructions to see what configuration gives optimal performance for your target problem.
For the first generation Knights Corner architecture, it is necessary to
cross-compile OpenMC. If you are using the Intel Fortran compiler, it is
necessary to specify that all objects be compiled with the
-mmic flag as
mkdir build && cd build FC=ifort CC=icc FFLAGS=-mmic cmake -Dopenmp=on .. make
Note that unless an HDF5 build for the Intel Xeon Phi (Knights Corner) is already on your target machine, you will need to cross-compile HDF5 for the Xeon Phi. An example script to build zlib and HDF5 provides several necessary workarounds.
2.4. Python Prerequisites¶
OpenMC’s Python API works with either Python 2.7 or Python 3.2+. In addition to Python itself, the API relies on a number of third-party packages. All prerequisites can be installed using conda (recommended), pip, or through the package manager in most Linux distributions.
- The Python API works with both Python 2.7+ and 3.2+. To do so, the six compatibility library is used.
- NumPy is used extensively within the Python API for its powerful N-dimensional array.
- SciPy’s special functions, sparse matrices, and spatial data structures are used for several optional features in the API.
- Pandas is used to generate tally DataFrames as demonstrated in Pandas Dataframes example notebook.
- h5py provides Python bindings to the HDF5 library. Since OpenMC outputs various HDF5 files, h5py is needed to provide access to data within these files from Python.
- Matplotlib is used to providing plotting functionality in the API like the
Universe.plot()method and the
- Uncertainties are used for decay data in the
- lxml is used for the openmc-validate-xml script and various other parts of the Python API.
- Cython is used for resonance reconstruction for ENDF data converted to
- The Python VTK bindings are needed to convert voxel and track files to VTK format.
- The silomesh package is needed to convert voxel and track files to SILO format.
- The pytest framework is used for unit testing the Python API.
2.5. Configuring Input Validation with GNU Emacs nXML mode¶
The GNU Emacs text editor has a built-in mode that extends functionality for
editing XML files. One of the features in nXML mode is the ability to perform
real-time validation of XML files against a RELAX NG schema. The OpenMC
source contains RELAX NG schemas for each type of user input file. In order for
nXML mode to know about these schemas, you need to tell emacs where to find a
“locating files” description. Adding the following lines to your
file will enable real-time validation of XML input files:
(require 'rng-loc) (add-to-list 'rng-schema-locating-files "~/openmc/schemas.xml")
Make sure to replace the last string on the second line with the path to the schemas.xml file in your own OpenMC source directory.