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Fixing NetCDF4 documentation now that it is available on conda-forge
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README.rst

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@@ -81,13 +81,7 @@ will not help you with MPI or FFTW.
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For IO you need to install either `h5py <https://www.h5py.org>`_ or
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`netCDF4 <http://unidata.github.io/netcdf4-python/>`_ with support for
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MPI. The first one is available from the coda-forge channel through::
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MPI. Both are available from the coda-forge channel through::
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conda install -c conda-forge h5py=*=mpi_mpich_*
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conda install -c conda-forge h5py=*=mpi* netcdf4=*=mpi*
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NetCDF4, on the other hand, is not available with MPI on the conda-forge
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channel. The library is available, though, for both OSX and
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linux from the `spectralDNS <https://anaconda.org/spectralDNS>`_ channel
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on anaconda cloud::
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conda install -c spectralDNS netcdf4-parallel

docs/source/installation.rst

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@@ -8,6 +8,7 @@ Mpi4py-fft has a few dependencies
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* `numpy`_
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* `cython`_ (build dependency)
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* `h5py`_ (runtime dependency, optional)
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* `netCDF4`_ (runtime dependency, optional)
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that are mostly straight-forward to install, or already installed in
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most Python environments. The first two are usually most troublesome.
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::
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conda create --name mpi4py-fft -c conda-forge mpi4py-fft h5py=*=mpi*
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conda create --name mpi4py-fft -c conda-forge mpi4py-fft
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conda activate mpi4py-fft
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Note that this gives you mpi4py-fft with default settings. This means that
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you will probably get the openmpi backend, and it is also likely that
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conda-forge chooses numpy with the mkl backend. Unfortunately, the mkl
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python package makes adjustments to the FFTW library and hard to resolve
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bugs may arise. For this reason it is advisable to make sure that mkl
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is not installed. This can be achieved with, e.g.,
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you will probably get the openmpi backend. To make a specific choice of
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backend just specify which, like this
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::
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conda create --name mpi4py-fft -c conda-forge mpi4py-fft mpich nomkl h5py=*=mpi*
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Note that the nomkl package makes sure that numpy is installed without
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mkl, whereas mpich here chooses this backend over openmpi.
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conda create --name mpi4py-fft -c conda-forge mpi4py-fft mpich
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If you do not use `conda`_, then you need to make sure that MPI
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and FFTW are installed by some other means. You can then install
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-----------------------
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For storing and retrieving data you need either `HDF5`_ or `netCDF4`_, compiled
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with support for MPI. `HDF5`_ is already available
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with parallel support on `conda-forge`_ and, if it was not installed at the same
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time as mpi4py-fft, it can be installed (with the mpich backend for MPI) as
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::
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conda install -c conda-forge h5py=*=mpi_mpich_*
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A parallel version of `netCDF4`_ cannot be found on the conda-forge channel,
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but a precompiled version has been made available for python 2.7, 3.6 and 3.7
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on the `spectralDNS channel`_, for both osx and linux
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with support for MPI. Both are available
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with parallel support on `conda-forge`_ and can be installed into the
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current conda environment as
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::
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conda install -c spectralDNS netcdf4-parallel
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conda install -c conda-forge h5py=*=mpi* netcdf4=*=mpi*
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Note that parallel HDF5 and NetCDF4 often are available as modules on
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Note that parallel HDF5 and NetCDF4 often are available as optimized modules on
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supercomputers. Otherwise, see the respective packages for how to install
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with support for MPI.
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