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Unidata / netcdf4-python

netcdf4-python: python/numpy interface to the netCDF C library
http://unidata.github.io/netcdf4-python
MIT License
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installing netcdf4 with conda in parallel mode #845

Closed carlestena closed 5 years ago

carlestena commented 5 years ago

I'm having that error while trying to run my job when installing netcdf4 using conda: ValueError: parallel mode requires MPI enabled netcdf-c

my yml file is using that (and more much libraries) channels:

dependencies:

So, Have I to add --enable-parallel in somewhere? Will I have the same problem with HDF5?

jswhit commented 5 years ago

You have to build the netcdf-c and hdf5 libraries with MPI enabled (see https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html#build_parallel).

carlestena commented 5 years ago

Thanks @jswhit. I know how to install HDF5 and NEtCDF4-C in bash, but not using conda. Is to make easier the installation of my future package

jswhit commented 5 years ago

I don't either. There may already be conda packages though (https://anaconda.org/spectraldns/libnetcdf-parallel and https://anaconda.org/spectralDNS/hdf5-parallel)

carlestena commented 5 years ago

I've already tried to use hdf5-parallel and libnetcdf-parallel.

But I cannot tested it because I have another dependency: esmpy[version='>=7.1.0r'] -> esmf==7.1.0r -> hdf5[version='>=1.10.2,<1.10.3.0a0']

and the hdf5-parallel is <= 1.8.17

lanougue commented 5 years ago

As a temporary work around, using conda, I downgraded netcdf4 to version 1.2.4. which seems to be linked to parallel libraries. As a side-effect, this also downgrade numpy. You can still check if it still match your dependencies.

carlestena commented 5 years ago

But i thought that parallel netcdf starts at 1.3.1 version

jswhit commented 5 years ago

hope you got this straightened out, closing now...