Merge pull request #3316 from aherrmann/pr_mpi

MPI support for HDF5 and SGE support for OpenMPI
This commit is contained in:
Michael Raskin 2014-08-29 01:22:02 +04:00
commit 0078bc5d8f
6 changed files with 142 additions and 2 deletions

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@ -1,4 +1,13 @@
{stdenv, fetchurl, gfortran}:
{stdenv, fetchurl, gfortran
# Enable the Sun Grid Engine bindings
, enableSGE ? false
# Pass PATH/LD_LIBRARY_PATH to point to current mpirun by default
, enablePrefix ? false
}:
with stdenv.lib;
stdenv.mkDerivation {
name = "openmpi-1.6.5";
@ -7,6 +16,10 @@ stdenv.mkDerivation {
sha256 = "11gws4d3z7934zna2r7m1f80iay2ha17kp42mkh39wjykfwbldzy";
};
buildInputs = [ gfortran ];
configureFlags = []
++ optional enableSGE "--with-sge"
++ optional enablePrefix "--enable-mpirun-prefix-by-default"
;
meta = {
homePage = http://www.open-mpi.org/;
description = "Open source MPI-2 implementation";

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@ -0,0 +1,43 @@
{ stdenv, fetchurl, python, buildPythonPackage
, numpy, hdf5, cython
, mpiSupport ? false, mpi4py ? null, mpi ? null }:
assert mpiSupport == hdf5.mpiSupport;
assert mpiSupport -> mpi != null
&& mpi4py != null
&& mpi == mpi4py.mpi
&& mpi == hdf5.mpi
;
with stdenv.lib;
buildPythonPackage rec {
name = "h5py-2.3.1";
src = fetchurl {
url = "https://pypi.python.org/packages/source/h/h5py/${name}.tar.gz";
md5 = "8f32f96d653e904d20f9f910c6d9dd91";
};
setupPyBuildFlags = [ "--hdf5=${hdf5}" ]
++ optional mpiSupport "--mpi"
;
setupPyInstallFlags = setupPyBuildFlags;
preBuild = if mpiSupport then "export CC=${mpi}/bin/mpicc" else "";
buildInputs = [ hdf5 cython ]
++ optional mpiSupport mpi
;
propagatedBuildInputs = [ numpy ]
++ optional mpiSupport mpi4py
;
meta = {
description = "
The h5py package is a Pythonic interface to the HDF5 binary data format.
";
homepage = "http://www.h5py.org/";
license = stdenv.lib.licenses.bsd2;
};
}

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@ -0,0 +1,45 @@
{ stdenv, fetchurl, python, buildPythonPackage, mpi, openssh }:
buildPythonPackage rec {
name = "mpi4py-1.3.1";
src = fetchurl {
url = "https://bitbucket.org/mpi4py/mpi4py/downloads/${name}.tar.gz";
sha256 = "e7bd2044aaac5a6ea87a87b2ecc73b310bb6efe5026031e33067ea3c2efc3507";
};
passthru = {
inherit mpi;
};
configurePhase = "";
installPhase = ''
mkdir -p "$out/lib/${python.libPrefix}/site-packages"
export PYTHONPATH="$out/lib/${python.libPrefix}/site-packages:$PYTHONPATH"
${python}/bin/${python.executable} setup.py install \
--install-lib=$out/lib/${python.libPrefix}/site-packages \
--prefix="$out"
# --install-lib:
# sometimes packages specify where files should be installed outside the usual
# python lib prefix, we override that back so all infrastructure (setup hooks)
# work as expected
'';
setupPyBuildFlags = ["--mpicc=${mpi}/bin/mpicc"];
buildInputs = [ mpi ];
# Requires openssh for tests. Tests of dependent packages will also fail,
# if openssh is not present. E.g. h5py with mpi support.
propagatedBuildInputs = [ openssh ];
meta = {
description = "
Provides Python bindings for the Message Passing Interface standard.
";
homepage = "http://code.google.com/p/mpi4py/";
license = stdenv.lib.licenses.bsd3;
};
}

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@ -3,6 +3,8 @@
, fetchurl
, zlib ? null
, szip ? null
, mpi ? null
, enableShared ? true
}:
stdenv.mkDerivation rec {
version = "1.8.13";
@ -12,11 +14,23 @@ stdenv.mkDerivation rec {
sha256 = "1h9qdl321gzm3ihdhlijbl9sh9qcdrw94j7izg64yfqhxj7b7xl2";
};
passthru = {
mpiSupport = (mpi != null);
inherit mpi;
};
buildInputs = []
++ stdenv.lib.optional (zlib != null) zlib
++ stdenv.lib.optional (szip != null) szip;
configureFlags = if szip != null then "--with-szlib=${szip}" else "";
propagatedBuildInputs = []
++ stdenv.lib.optional (mpi != null) mpi;
configureFlags = "
${if szip != null then "--with-szlib=${szip}" else ""}
${if mpi != null then "--enable-parallel" else ""}
${if enableShared then "--enable-shared" else ""}
";
patches = [./bin-mv.patch];

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@ -1286,6 +1286,12 @@ let
hdf5 = callPackage ../tools/misc/hdf5 {
szip = null;
mpi = null;
};
hdf5-mpi = hdf5.override {
szip = null;
mpi = pkgs.openmpi;
};
heimdall = callPackage ../tools/misc/heimdall { };

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@ -90,6 +90,19 @@ rec {
'';
};
h5py = callPackage ../development/python-modules/h5py {
inherit (pkgs) stdenv fetchurl;
inherit python buildPythonPackage cython numpy;
hdf5 = pkgs.hdf5.override { mpi = null; };
};
h5py-mpi = h5py.override {
mpiSupport = true;
mpi = pkgs.openmpi;
hdf5 = pkgs.hdf5.override { mpi = pkgs.openmpi; enableShared = true; };
inherit mpi4py;
};
ipython = import ../shells/ipython {
inherit (pkgs) stdenv fetchurl sip pyqt4;
inherit buildPythonPackage pythonPackages;
@ -106,6 +119,12 @@ rec {
pylabQtSupport = false;
});
mpi4py = callPackage ../development/python-modules/mpi4py {
inherit (pkgs) stdenv fetchurl openssh;
inherit python buildPythonPackage;
mpi = pkgs.openmpi;
};
nixpart = callPackage ../tools/filesystems/nixpart { };
# This is used for NixOps to make sure we won't break it with the next major