mirror of
https://github.com/NixOS/nixpkgs.git
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6dba41fbcb
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
{
mpi = super.mpich;
}
All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
89 lines
3.1 KiB
Nix
89 lines
3.1 KiB
Nix
{ lib, stdenv
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, fetchurl
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, pkg-config
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, automake
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, autoconf
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, libtool
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, ncurses
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, readline
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, which
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, python ? null
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, useMpi ? false
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, mpi
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, iv
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}:
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stdenv.mkDerivation rec {
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pname = "neuron";
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version = "7.5";
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nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
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buildInputs = [ ncurses readline python iv ]
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++ lib.optional useMpi mpi;
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src = fetchurl {
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url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
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sha256 = "0f26v3qvzblcdjg7isq0m9j2q8q7x3vhmkfllv8lsr3gyj44lljf";
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};
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patches = (lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
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# With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
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postPatch = lib.optionalString stdenv.cc.isClang ''
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substituteInPlace src/gnu/neuron_gnu_builtin.h \
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--replace 'double abs(double arg);' "" \
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--replace 'float abs(float arg);' "" \
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--replace 'short abs(short arg);' "" \
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--replace 'long abs(long arg);' ""
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'' + lib.optionalString stdenv.isDarwin ''
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# we are darwin, but we don't have all the quirks the source wants to compensate for
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substituteInPlace src/nrnpython/setup.py.in --replace 'readline="edit"' 'readline="readline"'
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for f in src/nrnpython/*.[ch] ; do
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substituteInPlace $f --replace "<Python/Python.h>" "<Python.h>"
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done
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'';
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enableParallelBuilding = true;
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## neuron install by default everything under prefix/${host_arch}/*
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## override this to support nix standard file hierarchy
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## without issues: install everything under prefix/
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preConfigure = ''
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./build.sh
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export prefix="''${prefix} --exec-prefix=''${out}"
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'';
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configureFlags = with lib;
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[ "--with-readline=${readline}" "--with-iv=${iv}" ]
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++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
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++ (if useMpi then ["--with-mpi" "--with-paranrn"]
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else ["--without-mpi"]);
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postInstall = lib.optionals (python != null) [ ''
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## standardise python neuron install dir if any
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if [[ -d $out/lib/python ]]; then
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mkdir -p ''${out}/${python.sitePackages}
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mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/
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fi
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''];
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propagatedBuildInputs = [ readline ncurses which libtool ];
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meta = with lib; {
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description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
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longDescription = "NEURON is a simulation environment for developing and exercising models of
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neurons and networks of neurons. It is particularly well-suited to problems where
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cable properties of cells play an important role, possibly including extracellular
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potential close to the membrane), and where cell membrane properties are complex,
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involving many ion-specific channels, ion accumulation, and second messengers";
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license = licenses.bsd3;
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homepage = "http://www.neuron.yale.edu/neuron";
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maintainers = [ maintainers.adev ];
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# source claims it's only tested for x86 and powerpc
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platforms = platforms.x86_64 ++ platforms.i686;
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};
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}
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