mpi4py-fft /

Filename Size Date modified Message
.circleci
conf
docs
examples
mpi4py_fft
tests
195 B
Shaping up new code
470 B
Moving import h5py and netCDF inside __init__ functions to avoid problems with missing dependency
1.4 KB
Renaming mispelled lisense
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Working on release
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Bump version number
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Documenting that we are using serial FFTW libraries
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Small changes to documentation
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Back to setup.py
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Getting rid of six and modifying setup
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Fixing issue 5

mpi4py-fft

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mpi4py-fft is a Python package for computing Fast Fourier Transforms (FFTs). Large arrays are distributed and communications are handled under the hood by MPI for Python (mpi4py). To distribute large arrays we are using a new and completely generic algorithm that allows for any index set of a multidimensional array to be distributed. We can distribute just one index (a slab decomposition), two index sets (pencil decomposition) or even more for higher-dimensional arrays.

mpi4py-fft comes with its own Python interface to the serial FFTW library. This interface can be used much like pyfftw, and even for real-to-real transforms, like discrete cosine or sine transforms.

Further documentation is found at readthedocs.

Installation

The mpi4py-fft package can be installed using:

pip install mpi4py-fft

or, to get the latest version from bitbucket:

pip install git+https://bitbucket.org/mpi4py/mpi4py-fft@master

Install with conda from the coda-forge channel:

conda install -c conda-forge mpi4py-fft

or build it with conda build from the main source directory:

conda build -c conda-forge conf/
conda create --name mpi4py_fft mpi4py_fft --use-local

which will pull in the required dependencies from the conda-forge channel.

Note that mpi4py-fft depends on Python packages

  • mpi4py
  • numpy
  • cython

and the serial C-library

Note in particular that mpi4py requires that you have a working MPI installation, with the compiler wrapper mpicc, on your search path. The FFTW header and libraries must also be available on the search path, and we will build wrappers for any precision found of the FFTW libraries.

All of the above dependencies are available and will be downloaded through the conda-forge channel if conda is used for installation. However, pip will not help you with MPI or FFTW.

For IO you need to install either h5py or netCDF4 with support for MPI. The first one is available from the coda-forge channel through:

conda install -c conda-forge h5py=*=mpi_mpich_*

NetCDF4, on the other hand, is not available with MPI on the conda-forge channel. The library is available, though, for both OSX and linux from the spectralDNS channel on anaconda cloud:

conda install -c spectralDNS netcdf4-parallel