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Update HDF5 and add option to compile Fortran2003 interface #31781

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merged 4 commits into from Nov 25, 2017
Merged

Update HDF5 and add option to compile Fortran2003 interface #31781

merged 4 commits into from Nov 25, 2017

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robertodr
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@robertodr robertodr commented Nov 17, 2017 •
edited

Motivation for this change

The HDF5 package is updated from 1.8.18 to 1.10.1, as recommended on the HDF5 group website.
In addition, the possibility to compile the Fortran2003 interface is exposed via the fortran2003 option for the 1.8.19 version of the package.

Things done
  • Add a hdf5_1_8, updated from 1.8.18 to 1.8.19, to still provide the older version of HDF5.
  • Add a fortran2003 option to hdf5_1_8. This allows compiling the Fortran2003 bindings, by passing --enable-fortran2003 to the configure script. This option was removed from 1.10.1, for which --enable-fortran suffices to get the newer bindings compiled.
  • Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Fits CONTRIBUTING.md.

orivej
orivej reviewed Nov 17, 2017
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pkgs/tools/misc/hdf5/default.nix Outdated
@@ -14,17 +15,20 @@
# (--enable-unsupported could be used to force the build)
assert !cpp || mpi == null;

# Need a Fortran compiler for Fortran2003 bindings
assert fortran2003 -> gfortran == null;
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Shouldn't this be != null?

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Whoops! Yes, it should.

veprbl
veprbl reviewed Nov 18, 2017
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pkgs/tools/misc/hdf5/default.nix Outdated
@@ -45,6 +49,7 @@ stdenv.mkDerivation rec {
configureFlags = []
++ optional cpp "--enable-cxx"
++ optional (gfortran != null) "--enable-fortran"
++ optional fortran2003 "--enable-fortran2003"
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Why not just throw --enable-fortran2003 in with --enable-fortran?

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Users might want to use the Fortran90 bindings instead of the Fortran2003 ones.

@lsix
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lsix commented Nov 18, 2017

The doc states that:

Due to the requirements of some of the new features, the format of a 1.10.x HDF5 file is likely to be different from that of a 1.8.x HDF5 file. This means that tools and applications built to read 1.10.x files will be able to read a 1.8.x file, but tools built to read 1.8.x files may not be able to read a 1.10.x file.

I am fine with updating to 1.10 branch as default, but I think it would be preferable to keep the 1.8 branch around since it is still widely used (and default in many distributions).

@robertodr
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@lsix that's a good point, but I am not sure how to accomplish it...

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lsix commented Nov 18, 2017

@robertodr just copy the old version of the pkgs/tools/misc/hdf5/default.nix file as pkgs/tools/misc/hdf5/1_8.nix and add something like:

  hdf5_1_8 = callPackage ../tools/misc/hdf5/1.8.nix {
    gfortran = null;
    szip = null;
    mpi = null;
  };

in pkgs/top-level/all-packages.nix file next the the hdf5 definition.

This is how I would do it. Users should then use the override mechanism to use the 1.8 branch on their systems.

@robertodr
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Thanks for the explanation @lsix!

@robertodr robertodr mentioned this pull request Nov 19, 2017
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@FRidh
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FRidh commented Nov 21, 2017

Last time I checked, this bump broke several packages.

The following packages seem to build:

hdf5-cpp
hdf5-fortran
hdf5-mpi
netcdf
netcdf-mpi
netcdfcxx4
netcdffortran
octaveFull
python36Packages.h5py
python36Packages.h5py-mpi
python36Packages.netcdf4
python36Packages.odo
python36Packages.pandas
python36Packages.tables

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FRidh commented Nov 21, 2017

Can you squash commits per expression.

@FRidh FRidh merged commit 88eea69 into NixOS:master Nov 25, 2017
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