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install.python.md

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The following instruction explain how to compile, use and test the Python interface to Atomistica.

  1. Setup your compiler. Edit setup.cfg

    For GNU Fortran/C use:

    [config_fc] fcompiler=gnu95 f90flags=-cpp -ffree-line-length-none [-fopenmp]

    For Intel Fortran/C (intel64) use:

    [config_fc] fcompiler=intelem f90flags=-fpp [-openmp]

    [config_cc] compiler=intel

    There may be error messages complaining about undefined symbols when loading Atomistica in step 3 below. It is then necessary to force linking to the respective libraries. Additional libraries can be specified in the build_ext section:

    [build_ext] libraries=ifcore,ifport,iomp5,pthread

    This example is the link line typically required to compile with the Intel compiler suite and OpenMP enabled. ifcore contains is the Intel Fortran runtime and ifport additional portability functions. iomp5 is the Intel OpenMP runtime which requires to additionally link to the posix pthread library. The respective libraries for the GNU compiler are gfortran and gomp.

    You can get a list of available Fortran and C compilers by executing:

    python setup.py build --help-fcompiler python setup.py build --help-compiler

    More information can be found here:

    http://docs.python.org/2/install/index.html http://thread.gmane.org/gmane.comp.python.numeric.general/15793

  2. Compile the Python extension. Execute

    python setup.py build

    This will build and link all Fortran and C sources required for the Python interface. You may need to edit setup.py if the LAPACK libraries are not automatically detected.

    Note: You will need to

    python setup.py clean

    • or - python setup.py build --force

    if the source has changed. Unfortunately, the current numpy distutils won't relink the module even if the library has been recompiled without --force present.

  3. Test if the Python interface imports with errors. Type

    source path-to-atomistica/env.sh

    which sets up the environment. To test if Atomistica can be imported into Python execute"

    python -c "import atomistica"

    To resolve undefined symbol errors link to the relevant library. (See step 1 above.)

  4. Test if the Python interface gives correct results. Type

    cd path-to-atomistica/tests python run_tests.py

    Each test can also be run directly. This will produce more diagnostic output:

    python bulk_properties.py python forces_and_virial.py python rebo2_molecules.py