Installation

FluidSim is part of the FluidDyn project. Some issues regarding the installation of Python packages are discussed in the main documentation of the project.

Dependencies

Starting from fluidsim>=0.3.0 the Python dependencies are installed automatically. So for most cases, manual intervention is not required.

  • Python >= 3.6

  • Numpy, transonic

  • fluiddyn

    The base package of the FluidDyn project.

  • fluidfft

    Pseudospectral solvers of fluidsim needs fluidfft. If you have not configured it before installing, it will be installed automatically and you won’t be able to use fancy FFT libraries (using for example MPI with 2D decomposition or GPU with CUDA). If you do not need a pseudospectral solver, or if you are not too concerned about performance, no problem. Otherwise, install fluidfft as explained here.

  • h5py (optionally, with MPI support, but only if you know what you do)

    Warning

    Prebuilt installations (for eg. via h5py wheels) may lack MPI support. Most of the time, this is what you want. However, you can install h5py from source and link it to a hdf5 built with MPI support, as follows:

    $ CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/path/to/parallel-hdf5 pip install --no-deps --no-binary=h5py h5py
    $ python -c 'import h5py; h5py.run_tests()'
    

    In some cases you need to set C_INCLUDE_PATH variable before h5py installation. For example on Debian stretch:

    $ export C_INCLUDE_PATH=/usr/include/openmpi/
    $ CC="mpicc" HDF5_MPI="ON" HDF5_DIR=/path/to/parallel-hdf5 pip install --no-deps --no-binary=h5py h5py
    

    See the h5py documentation for more details.

  • A C++11 compiler (for example GCC 4.9 or clang)

  • Pythran

    We choose to use the new static Python compiler Pythran for some functions. Our microbenchmarks show that the performances are as good as what we are able to get with Fortran or C++!

    Warning

    To reach good performance, we advice to try to put in the file ~/.pythranrc the lines (it seems to work well on Linux, see the Pythran documentation):

    [pythran]
    complex_hook = True
    

    Warning

    The compilation of C++ files produced by Pythran can be long and can consume a lot of memory. If you encounter any problems, you can try to use clang (for example with conda install clangdev) and to enable its use in the file ~/.pythranrc with:

    [compiler]
    CXX=clang++
    CC=clang
    blas=openblas
    
  • Optionally (for MPI runs), mpi4py (which depends on a MPI implementation).

    Warning

    If the system has multiple MPI libraries, it is adviced to explicitly mention the MPI command. For instance to use Intel MPI:

    CC=mpiicc pip install mpi4py
    
  • Optionally (for some command-line tools), Pandas.

Basic installation with pip

If you are in a hurry and that you are not really concerned about performance, you can use pip:

pip install fluidsim --no-cache-dir

or (without virtualenv):

pip install fluidsim --no-cache-dir --user

Note

The build is different depending on whether some packages (namely mpi4py and pythran) are importable or not. Suppose you perform a barebones installation and later on you decide to install any of those packages. If you have fluidsim in the pip cache, the extensions in fluidsim will not installed properly. The option --no-cache-dir would avoid such trouble arising from pip reinstalling a cached copy of fluidsim.

You can also configure the installation of fluidsim by creating the file ~/.fluidsim-site.cfg and modify it to fit your requirements before the installation with pip:

wget https://foss.heptapod.net/fluiddyn/fluidsim/raw/default/site.cfg.default -O ~/.fluidsim-site.cfg

Install from the repository

Get the source code

For fluidsim, we use the revision control software Mercurial and the main repository is hosted here in Heptapod. Download the source with something like:

hg clone https://foss.heptapod.net/fluiddyn/fluidsim

If you are new with Mercurial and Heptapod, you can also read this short tutorial.

If you don’t want to use Mercurial, you can also just manually download the package from the PyPI page.

Configuration file

For particular installation setup, copy the default configuration file to site.cfg:

cp site.cfg.default site.cfg

and modify it to fit your requirements.

Build/install

Build/install in development mode (with a virtualenv or with conda), by running from the top-level directory:

pip install -e .

or (without virtualenv):

pip install -e . --user

To install Fluidsim with all optional dependencies and all capacities:

pip install mpi4py pythran
pip install -e .[full]

Run the tests!

You can run some unit tests by running make tests (shortcut for fluidsim-test -v) or make tests_mpi (shortcut for mpirun -np 2 fluidsim-test -v). Alternatively, you can also run python -m unittest discover from the root directory or from any of the “test” directories.

Environment variables

Fluidsim builds its binaries in parallel. It speedups the build process a lot on most computers. However, it can be a very bad idea on computers with not enough memory. If you encounter problems, you can force the number of processes used during the build using the environment variable FLUIDDYN_NUM_PROCS_BUILD:

export FLUIDDYN_NUM_PROCS_BUILD=2

Fluidsim is also sensitive to the environment variables:

  • FLUIDSIM_PATH: path where the simulation results are saved.

    In Unix systems, you can for example put this line in your ~/.bashrc:

    export FLUIDSIM_PATH=$HOME/Data
    
  • FLUIDDYN_PATH_SCRATCH: working directory (can be useful on some clusters).

  • TRANSONIC_COMPILE_JIT: set this variable to force JIT compilation using transonic while running tests. This is not necessary, but could be useful for troubleshooting if simulations freeze. For example:

    TRANSONIC_COMPILE_JIT=1 fluidsim-test -m fluidsim.solvers.sw1l
    
  • Customize compilers to build Cython extensions, if the defaults do not work for you, either using the environment variables:

    • MPICXX: for Cython extensions in fluidfft (default: mpicxx)

    • CC: command to generate object files in fluidsim

    • LDSHARED: command to link and generate shared libraries in fluidsim

    • CARCH: to cross compile (default: native)

    or by using a site.cfg or ~/.fluidsim-site.cfg file as described above.