@@ -8,6 +8,7 @@ Mpi4py-fft has a few dependencies
88 * `numpy `_
99 * `cython `_ (build dependency)
1010 * `h5py `_ (runtime dependency, optional)
11+ * `netCDF4 `_ (runtime dependency, optional)
1112
1213that are mostly straight-forward to install, or already installed in
1314most Python environments. The first two are usually most troublesome.
@@ -25,22 +26,16 @@ can be achieved with
2526
2627::
2728
28- conda create --name mpi4py-fft -c conda-forge mpi4py-fft h5py=*=mpi*
29+ conda create --name mpi4py-fft -c conda-forge mpi4py-fft
2930 conda activate mpi4py-fft
3031
3132Note that this gives you mpi4py-fft with default settings. This means that
32- you will probably get the openmpi backend, and it is also likely that
33- conda-forge chooses numpy with the mkl backend. Unfortunately, the mkl
34- python package makes adjustments to the FFTW library and hard to resolve
35- bugs may arise. For this reason it is advisable to make sure that mkl
36- is not installed. This can be achieved with, e.g.,
33+ you will probably get the openmpi backend. To make a specific choice of
34+ backend just specify which, like this
3735
3836::
3937
40- conda create --name mpi4py-fft -c conda-forge mpi4py-fft mpich nomkl h5py=*=mpi*
41-
42- Note that the nomkl package makes sure that numpy is installed without
43- mkl, whereas mpich here chooses this backend over openmpi.
38+ conda create --name mpi4py-fft -c conda-forge mpi4py-fft mpich
4439
4540If you do not use `conda `_, then you need to make sure that MPI
4641and FFTW are installed by some other means. You can then install
@@ -78,23 +73,15 @@ Additional dependencies
7873-----------------------
7974
8075For storing and retrieving data you need either `HDF5 `_ or `netCDF4 `_, compiled
81- with support for MPI. `HDF5 `_ is already available
82- with parallel support on `conda-forge `_ and, if it was not installed at the same
83- time as mpi4py-fft, it can be installed (with the mpich backend for MPI) as
84-
85- ::
86-
87- conda install -c conda-forge h5py=*=mpi_mpich_*
88-
89- A parallel version of `netCDF4 `_ cannot be found on the conda-forge channel,
90- but a precompiled version has been made available for python 2.7, 3.6 and 3.7
91- on the `spectralDNS channel `_, for both osx and linux
76+ with support for MPI. Both are available
77+ with parallel support on `conda-forge `_ and can be installed into the
78+ current conda environment as
9279
9380::
9481
95- conda install -c spectralDNS netcdf4-parallel
82+ conda install -c conda-forge h5py=*=mpi* netcdf4=*=mpi*
9683
97- Note that parallel HDF5 and NetCDF4 often are available as modules on
84+ Note that parallel HDF5 and NetCDF4 often are available as optimized modules on
9885supercomputers. Otherwise, see the respective packages for how to install
9986with support for MPI.
10087
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