Merge pull request #3316 from aherrmann/pr_mpi
MPI support for HDF5 and SGE support for OpenMPI
This commit is contained in:
commit
0078bc5d8f
@ -1,4 +1,13 @@
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{stdenv, fetchurl, gfortran}:
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{stdenv, fetchurl, gfortran
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# Enable the Sun Grid Engine bindings
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, enableSGE ? false
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# Pass PATH/LD_LIBRARY_PATH to point to current mpirun by default
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, enablePrefix ? false
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}:
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with stdenv.lib;
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stdenv.mkDerivation {
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stdenv.mkDerivation {
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name = "openmpi-1.6.5";
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name = "openmpi-1.6.5";
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@ -7,6 +16,10 @@ stdenv.mkDerivation {
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sha256 = "11gws4d3z7934zna2r7m1f80iay2ha17kp42mkh39wjykfwbldzy";
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sha256 = "11gws4d3z7934zna2r7m1f80iay2ha17kp42mkh39wjykfwbldzy";
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};
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};
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buildInputs = [ gfortran ];
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buildInputs = [ gfortran ];
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configureFlags = []
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++ optional enableSGE "--with-sge"
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++ optional enablePrefix "--enable-mpirun-prefix-by-default"
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;
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meta = {
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meta = {
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homePage = http://www.open-mpi.org/;
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homePage = http://www.open-mpi.org/;
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description = "Open source MPI-2 implementation";
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description = "Open source MPI-2 implementation";
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43
pkgs/development/python-modules/h5py/default.nix
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43
pkgs/development/python-modules/h5py/default.nix
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@ -0,0 +1,43 @@
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{ stdenv, fetchurl, python, buildPythonPackage
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, numpy, hdf5, cython
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, mpiSupport ? false, mpi4py ? null, mpi ? null }:
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assert mpiSupport == hdf5.mpiSupport;
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assert mpiSupport -> mpi != null
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&& mpi4py != null
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&& mpi == mpi4py.mpi
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&& mpi == hdf5.mpi
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;
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with stdenv.lib;
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buildPythonPackage rec {
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name = "h5py-2.3.1";
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src = fetchurl {
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url = "https://pypi.python.org/packages/source/h/h5py/${name}.tar.gz";
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md5 = "8f32f96d653e904d20f9f910c6d9dd91";
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};
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setupPyBuildFlags = [ "--hdf5=${hdf5}" ]
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++ optional mpiSupport "--mpi"
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;
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setupPyInstallFlags = setupPyBuildFlags;
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preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";
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buildInputs = [ hdf5 cython ]
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++ optional mpiSupport mpi
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;
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propagatedBuildInputs = [ numpy ]
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++ optional mpiSupport mpi4py
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;
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meta = {
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description = "
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The h5py package is a Pythonic interface to the HDF5 binary data format.
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";
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homepage = "http://www.h5py.org/";
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license = stdenv.lib.licenses.bsd2;
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};
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}
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45
pkgs/development/python-modules/mpi4py/default.nix
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45
pkgs/development/python-modules/mpi4py/default.nix
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@ -0,0 +1,45 @@
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{ stdenv, fetchurl, python, buildPythonPackage, mpi, openssh }:
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buildPythonPackage rec {
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name = "mpi4py-1.3.1";
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src = fetchurl {
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url = "https://bitbucket.org/mpi4py/mpi4py/downloads/${name}.tar.gz";
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sha256 = "e7bd2044aaac5a6ea87a87b2ecc73b310bb6efe5026031e33067ea3c2efc3507";
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};
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passthru = {
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inherit mpi;
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};
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configurePhase = "";
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installPhase = ''
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mkdir -p "$out/lib/${python.libPrefix}/site-packages"
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export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
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${python}/bin/${python.executable} setup.py install \
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--install-lib=$out/lib/${python.libPrefix}/site-packages \
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--prefix="$out"
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# --install-lib:
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# sometimes packages specify where files should be installed outside the usual
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# python lib prefix, we override that back so all infrastructure (setup hooks)
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# work as expected
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'';
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setupPyBuildFlags = ["--mpicc=${mpi}/bin/mpicc"];
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buildInputs = [ mpi ];
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# Requires openssh for tests. Tests of dependent packages will also fail,
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# if openssh is not present. E.g. h5py with mpi support.
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propagatedBuildInputs = [ openssh ];
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meta = {
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description = "
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Provides Python bindings for the Message Passing Interface standard.
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";
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homepage = "http://code.google.com/p/mpi4py/";
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license = stdenv.lib.licenses.bsd3;
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};
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}
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@ -3,6 +3,8 @@
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, fetchurl
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, fetchurl
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, zlib ? null
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, zlib ? null
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, szip ? null
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, szip ? null
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, mpi ? null
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, enableShared ? true
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}:
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}:
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stdenv.mkDerivation rec {
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stdenv.mkDerivation rec {
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version = "1.8.13";
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version = "1.8.13";
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@ -12,11 +14,23 @@ stdenv.mkDerivation rec {
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sha256 = "1h9qdl321gzm3ihdhlijbl9sh9qcdrw94j7izg64yfqhxj7b7xl2";
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sha256 = "1h9qdl321gzm3ihdhlijbl9sh9qcdrw94j7izg64yfqhxj7b7xl2";
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};
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};
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passthru = {
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mpiSupport = (mpi != null);
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inherit mpi;
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};
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buildInputs = []
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buildInputs = []
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++ stdenv.lib.optional (zlib != null) zlib
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++ stdenv.lib.optional (zlib != null) zlib
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++ stdenv.lib.optional (szip != null) szip;
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++ stdenv.lib.optional (szip != null) szip;
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configureFlags = if szip != null then "--with-szlib=${szip}" else "";
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propagatedBuildInputs = []
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++ stdenv.lib.optional (mpi != null) mpi;
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configureFlags = "
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${if szip != null then "--with-szlib=${szip}" else ""}
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${if mpi != null then "--enable-parallel" else ""}
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${if enableShared then "--enable-shared" else ""}
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";
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patches = [./bin-mv.patch];
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patches = [./bin-mv.patch];
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@ -1286,6 +1286,12 @@ let
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hdf5 = callPackage ../tools/misc/hdf5 {
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hdf5 = callPackage ../tools/misc/hdf5 {
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szip = null;
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szip = null;
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mpi = null;
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};
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hdf5-mpi = hdf5.override {
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szip = null;
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mpi = pkgs.openmpi;
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};
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};
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heimdall = callPackage ../tools/misc/heimdall { };
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heimdall = callPackage ../tools/misc/heimdall { };
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@ -90,6 +90,19 @@ rec {
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'';
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'';
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};
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};
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h5py = callPackage ../development/python-modules/h5py {
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inherit (pkgs) stdenv fetchurl;
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inherit python buildPythonPackage cython numpy;
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hdf5 = pkgs.hdf5.override { mpi = null; };
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};
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h5py-mpi = h5py.override {
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mpiSupport = true;
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mpi = pkgs.openmpi;
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hdf5 = pkgs.hdf5.override { mpi = pkgs.openmpi; enableShared = true; };
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inherit mpi4py;
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};
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ipython = import ../shells/ipython {
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ipython = import ../shells/ipython {
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inherit (pkgs) stdenv fetchurl sip pyqt4;
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inherit (pkgs) stdenv fetchurl sip pyqt4;
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inherit buildPythonPackage pythonPackages;
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inherit buildPythonPackage pythonPackages;
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@ -106,6 +119,12 @@ rec {
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pylabQtSupport = false;
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pylabQtSupport = false;
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});
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});
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mpi4py = callPackage ../development/python-modules/mpi4py {
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inherit (pkgs) stdenv fetchurl openssh;
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inherit python buildPythonPackage;
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mpi = pkgs.openmpi;
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};
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nixpart = callPackage ../tools/filesystems/nixpart { };
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nixpart = callPackage ../tools/filesystems/nixpart { };
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# This is used for NixOps to make sure we won't break it with the next major
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# This is used for NixOps to make sure we won't break it with the next major
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