To get OpenMD up and running, there are some required (and optional) software packages you should have to create a functioning build environment:

On a Mac (OS X 10.5 or greater)

  1. Install Xcode
  2. Install MacPorts
  3. Open a Terminal window, and update your MacPorts installation to the latest portfiles:
    sudo port -v selfupdate
    sudo port -d sync
    (Note that the port command is usually located in /opt/local/bin)
  4. Install the relevant prerequisite packages:
    sudo port install cmake openbabel qhull zlib fftw-3 openmpi py37-numpy py37-scipy

    You can go have lunch or coffee while these are being built and installed.

  5. Select python3 as the default python variant, and openmpi as a default:
    sudo port select --set python python37
    sudo port select --set python3 python37
    sudo port select --set mpi openmpi-mp
  6. Install some optional software if you want to use and interact with the data produced by OpenMD:
    sudo port install jmol xmgr grace 
  7. Install some optional software if you want to develop or add to OpenMD:
    sudo port install antlr gengetopt doxygen

On Linux

  1. Use yum, apt-get, or the package manager in your favorite distribution to install the following packages and all of their prerequisites. Package names depend on the Linux variant, so in Fedora (and Red Hat) the package names are:
    fftw
    fftw-devel
    cmake
    openbabel
    openbabel-devel
    openmpi3
    openmpi3-devel
    perl
    python3-numpy
    python3-scipy qhull qhull-devel zlib zlib-devel

    In Ubuntu (and probably other Debian-based versions), the packages are:

    libfftw3-3
    libfftw3-dev
    cmake
    openbabel
    libopenbabel-dev
    openmpi-bin
    libopenmpi-dev
    perl
    python3-numpy
    python3-scipy qhull-bin libqhull-dev minizip zlib1g-dev
  2. Install some optional packages if you want to use and interact with the data produced by OpenMD:
    jmol
    grace
    
  3. Install some optional software if you want to develop or add to OpenMD:
    antlr
    gengetopt
    doxygen

On Windows

You’re largely on your own here. CMake will generate a working build of OpenMD 2.4 in Windows with the Visual Studio 2015 C++ compiler, but we don’t routinely test the code on this operating system.  One alternative is to use cygwin:

  1. You can use cygwin to get a lot of the relevant packages installed on a windows machine. One suggestion is to follow the Cygwin Installation How-To guide
  2. Refer to the list of packages for linux above to get the correct packages installed

Building from source

If you are building all of the prerequisites from source, you’ll need (in addition to a C++ compiler):

  1. CMake – This cross-platform build system is required for building OpenMD.  You need to install CMake 2.8.11 or newer. This is available as a binary package from the KitWare website; alternatively, it may be available through your package manager (on Linux). If necessary, you can also compile it yourself from the source code.
  2. perl and python – interpreted scripting languages that some of the OpenMD utilities use to parse and process data files.
    You probably already have these.
  3. Open MPI – A very good implementation of the MPI-2 specification for parallel computing.
  4. qhull – A computational geometry toolbox for computing convex hulls and Delaunay triangulations. qhull is required for the LangevinHull integrator and for any of the tools that compute the Hull atoms or hull volumes of nanoparticles and clusters.
  5. openbabel – a chemical toolbox for converting between different data formats.  This is required for building the atom2omd program which helps prepare initial “metadata” or omd files for simulations.
  6. fftw – a library for computing discrete Fourier transforms. This is required for surface undulation spectra (Hxy in staticProps). Get version 3.
  7. zlib – required to support reading compressed trajectory files.

You’ll also likely want to download and compile the following useful tools for interacting with the data:

  1. Jmol
  2. xmgr
  3. grace
  4. NumPy
  5. SciPy
  6. vmd

If you are going to be extending or developing OpenMD, you’ll need the following tool:

  1. antlr – our tool for parsing meta-data files.  You’ll want version 2.7, not 3.
  2. gengetopt – a tool to generate C code to parse the command line arguments argc and argv that are part of every C or C++ program

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