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mpi: use mpi attribute consistently as the default MPI implementations

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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
}
This commit is contained in:
Markus Kowalewski 2021-01-10 13:40:19 +01:00
parent f6a583eeec
commit 6dba41fbcb
No known key found for this signature in database
GPG Key ID: D865C8A91D7025EB
27 changed files with 90 additions and 102 deletions
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4
pkgs/applications/graphics/paraview/default.nix
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@ -1,6 +1,6 @@
{ boost, cmake, fetchFromGitHub, ffmpeg, qtbase, qtx11extras, { boost, cmake, fetchFromGitHub, ffmpeg, qtbase, qtx11extras,
qttools, qtxmlpatterns, qtsvg, gdal, gfortran, libXt, makeWrapper, qttools, qtxmlpatterns, qtsvg, gdal, gfortran, libXt, makeWrapper,
mkDerivation, ninja, openmpi, python3, lib, stdenv, tbb, libGLU, libGL }: mkDerivation, ninja, mpi, python3, lib, stdenv, tbb, libGLU, libGL }:
mkDerivation rec { mkDerivation rec {
pname = "paraview"; pname = "paraview";
@ -65,7 +65,7 @@ mkDerivation rec {
buildInputs = [ buildInputs = [
libGLU libGL libGLU libGL
libXt libXt
openmpi mpi
tbb tbb
boost boost
ffmpeg ffmpeg

4
pkgs/applications/science/biology/migrate/default.nix
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@ -1,4 +1,4 @@
{ gccStdenv, fetchurl, zlib, openmpi }: { gccStdenv, fetchurl, zlib, mpi }:
gccStdenv.mkDerivation rec { gccStdenv.mkDerivation rec {
version = "3.7.2"; version = "3.7.2";
@ -9,7 +9,7 @@ gccStdenv.mkDerivation rec {
sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v"; sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v";
}; };
buildInputs = [ zlib openmpi ]; buildInputs = [ zlib mpi ];
setSourceRoot = ''sourceRoot=$(echo */src)''; setSourceRoot = ''sourceRoot=$(echo */src)'';
buildFlags = [ "thread" "mpis" ]; buildFlags = [ "thread" "mpis" ];
preInstall = "mkdir -p $out/man/man1"; preInstall = "mkdir -p $out/man/man1";

9
pkgs/applications/science/biology/neuron/default.nix
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@ -8,7 +8,8 @@
, readline , readline
, which , which
, python ? null , python ? null
, mpi ? null , useMpi ? false
, mpi
, iv , iv
}: }:
@ -17,7 +18,8 @@ stdenv.mkDerivation rec {
version = "7.5"; version = "7.5";
nativeBuildInputs = [ which pkg-config automake autoconf libtool ]; nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
buildInputs = [ ncurses readline python mpi iv ]; buildInputs = [ ncurses readline python iv ]
++ lib.optional useMpi mpi;
src = fetchurl { src = fetchurl {
url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz"; url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
@ -54,7 +56,7 @@ stdenv.mkDerivation rec {
configureFlags = with lib; configureFlags = with lib;
[ "--with-readline=${readline}" "--with-iv=${iv}" ] [ "--with-readline=${readline}" "--with-iv=${iv}" ]
++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ] ++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
++ (if mpi != null then ["--with-mpi" "--with-paranrn"] ++ (if useMpi then ["--with-mpi" "--with-paranrn"]
else ["--without-mpi"]); else ["--without-mpi"]);
@ -84,4 +86,3 @@ stdenv.mkDerivation rec {
platforms = platforms.x86_64 ++ platforms.i686; platforms = platforms.x86_64 ++ platforms.i686;
}; };
} }

10
pkgs/applications/science/biology/raxml/default.nix
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@ -1,7 +1,7 @@
{ lib, stdenv { lib, stdenv
, fetchFromGitHub , fetchFromGitHub
, pkgs , useMpi ? false
, mpi ? false , mpi
}: }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
@ -15,16 +15,16 @@ stdenv.mkDerivation rec {
sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"; sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh";
}; };
buildInputs = lib.optionals mpi [ pkgs.openmpi ]; buildInputs = lib.optionals useMpi [ mpi ];
# TODO darwin, AVX and AVX2 makefile targets # TODO darwin, AVX and AVX2 makefile targets
buildPhase = if mpi then '' buildPhase = if useMpi then ''
make -f Makefile.MPI.gcc make -f Makefile.MPI.gcc
'' else '' '' else ''
make -f Makefile.SSE3.PTHREADS.gcc make -f Makefile.SSE3.PTHREADS.gcc
''; '';
installPhase = if mpi then '' installPhase = if useMpi then ''
mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin
'' else '' '' else ''
mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin

4
pkgs/applications/science/chemistry/openmolcas/default.nix
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@ -1,6 +1,6 @@
{ lib, stdenv, fetchFromGitLab, cmake, gfortran, perl { lib, stdenv, fetchFromGitLab, cmake, gfortran, perl
, openblas, hdf5-cpp, python3, texlive , openblas, hdf5-cpp, python3, texlive
, armadillo, openmpi, globalarrays, openssh , armadillo, mpi, globalarrays, openssh
, makeWrapper, fetchpatch , makeWrapper, fetchpatch
} : } :
@ -33,7 +33,7 @@ in stdenv.mkDerivation {
hdf5-cpp hdf5-cpp
python python
armadillo armadillo
openmpi mpi
globalarrays globalarrays
openssh openssh
]; ];

7
pkgs/applications/science/chemistry/quantum-espresso/default.nix
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@ -1,6 +1,7 @@
{ lib, stdenv, fetchurl { lib, stdenv, fetchurl
, gfortran, fftw, blas, lapack , gfortran, fftw, blas, lapack
, mpi ? null , useMpi ? false
, mpi
}: }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
@ -21,9 +22,9 @@ stdenv.mkDerivation rec {
''; '';
buildInputs = [ fftw blas lapack gfortran ] buildInputs = [ fftw blas lapack gfortran ]
++ (lib.optionals (mpi != null) [ mpi ]); ++ (lib.optionals useMpi [ mpi ]);
configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; configureFlags = if useMpi then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ];
makeFlags = [ "all" ]; makeFlags = [ "all" ];

9
pkgs/applications/science/chemistry/siesta/default.nix
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@ -1,6 +1,7 @@
{ lib, stdenv, fetchurl { lib, stdenv, fetchurl
, gfortran, blas, lapack , gfortran, blas, lapack, scalapack
, mpi ? null, scalapack , useMpi ? false
, mpi
}: }:
stdenv.mkDerivation { stdenv.mkDerivation {
@ -17,7 +18,7 @@ stdenv.mkDerivation {
}; };
buildInputs = [ blas lapack gfortran ] buildInputs = [ blas lapack gfortran ]
++ (lib.optionals (mpi != null) [ mpi scalapack ]); ++ lib.optionals useMpi [ mpi scalapack ];
enableParallelBuilding = true; enableParallelBuilding = true;
@ -29,7 +30,7 @@ stdenv.mkDerivation {
cp gfortran.make arch.make cp gfortran.make arch.make
''; '';
preBuild = if (mpi != null) then '' preBuild = if useMpi then ''
makeFlagsArray=( makeFlagsArray=(
CC="mpicc" FC="mpifort" CC="mpicc" FC="mpifort"
FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="." FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="."

5
pkgs/applications/science/electronics/openems/default.nix
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@ -11,16 +11,15 @@
, cmake , cmake
, octave , octave
, gl2ps , gl2ps
, mpi
, withQcsxcad ? true , withQcsxcad ? true
, withMPI ? false , withMPI ? false
, withHyp2mat ? true , withHyp2mat ? true
, qcsxcad ? null , qcsxcad ? null
, openmpi ? null
, hyp2mat ? null , hyp2mat ? null
}: }:
assert withQcsxcad -> qcsxcad != null; assert withQcsxcad -> qcsxcad != null;
assert withMPI -> openmpi != null;
assert withHyp2mat -> hyp2mat != null; assert withHyp2mat -> hyp2mat != null;
stdenv.mkDerivation { stdenv.mkDerivation {
@ -50,7 +49,7 @@ stdenv.mkDerivation {
csxcad csxcad
(octave.override { inherit hdf5; }) ] (octave.override { inherit hdf5; }) ]
++ lib.optionals withQcsxcad [ qcsxcad ] ++ lib.optionals withQcsxcad [ qcsxcad ]
++ lib.optionals withMPI [ openmpi ] ++ lib.optionals withMPI [ mpi ]
++ lib.optionals withHyp2mat [ hyp2mat ]; ++ lib.optionals withHyp2mat [ hyp2mat ];
postFixup = '' postFixup = ''

6
pkgs/applications/science/math/cntk/default.nix
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@ -1,5 +1,5 @@
{ lib, stdenv, fetchgit, fetchFromGitHub, cmake { lib, stdenv, fetchgit, fetchFromGitHub, cmake
, openblas, blas, lapack, opencv3, libzip, boost, protobuf, openmpi , openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
, onebitSGDSupport ? false , onebitSGDSupport ? false
, cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11 , cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11
, cudnnSupport ? cudaSupport, cudnn , cudnnSupport ? cudaSupport, cudnn
@ -33,7 +33,7 @@ in stdenv.mkDerivation rec {
# Force OpenMPI to use g++ in PATH. # Force OpenMPI to use g++ in PATH.
OMPI_CXX = "g++"; OMPI_CXX = "g++";
buildInputs = [ openblas opencv3 libzip boost protobuf openmpi ] buildInputs = [ openblas opencv3 libzip boost protobuf mpi ]
++ lib.optional cudaSupport cudatoolkit ++ lib.optional cudaSupport cudatoolkit
++ lib.optional cudnnSupport cudnn; ++ lib.optional cudnnSupport cudnn;
@ -43,7 +43,7 @@ in stdenv.mkDerivation rec {
"--with-openblas=${openblas}" "--with-openblas=${openblas}"
"--with-boost=${boost.dev}" "--with-boost=${boost.dev}"
"--with-protobuf=${protobuf}" "--with-protobuf=${protobuf}"
"--with-mpi=${openmpi}" "--with-mpi=${mpi}"
"--cuda=${if cudaSupport then "yes" else "no"}" "--cuda=${if cudaSupport then "yes" else "no"}"
# FIXME # FIXME
"--asgd=no" "--asgd=no"

4
pkgs/applications/science/math/getdp/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, openmpi, petsc, python3 }: { lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, mpi, petsc, python3 }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
name = "getdp-${version}"; name = "getdp-${version}";
@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
}; };
nativeBuildInputs = [ cmake gfortran ]; nativeBuildInputs = [ cmake gfortran ];
buildInputs = [ blas lapack openmpi petsc python3 ]; buildInputs = [ blas lapack mpi petsc python3 ];
meta = with lib; { meta = with lib; {
description = "A General Environment for the Treatment of Discrete Problems"; description = "A General Environment for the Treatment of Discrete Problems";

4
pkgs/applications/science/math/scotch/default.nix
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@ -1,11 +1,11 @@
{ lib, stdenv, fetchurl, bison, openmpi, flex, zlib}: { lib, stdenv, fetchurl, bison, mpi, flex, zlib}:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
version = "6.0.4"; version = "6.0.4";
pname = "scotch"; pname = "scotch";
src_name = "scotch_${version}"; src_name = "scotch_${version}";
buildInputs = [ bison openmpi flex zlib ]; buildInputs = [ bison mpi flex zlib ];
src = fetchurl { src = fetchurl {
url = "https://gforge.inria.fr/frs/download.php/file/34618/${src_name}.tar.gz"; url = "https://gforge.inria.fr/frs/download.php/file/34618/${src_name}.tar.gz";

4
pkgs/applications/science/molecular-dynamics/gromacs/default.nix
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@ -3,10 +3,10 @@
, cmake , cmake
, hwloc , hwloc
, fftw , fftw
, openmpi
, perl , perl
, singlePrec ? true , singlePrec ? true
, mpiEnabled ? false , mpiEnabled ? false
, mpi
, cpuAcceleration ? null , cpuAcceleration ? null
}: }:
@ -33,7 +33,7 @@ in stdenv.mkDerivation rec {
nativeBuildInputs = [ cmake ]; nativeBuildInputs = [ cmake ];
buildInputs = [ fftw perl hwloc ] buildInputs = [ fftw perl hwloc ]
++ (lib.optionals mpiEnabled [ openmpi ]); ++ (lib.optionals mpiEnabled [ mpi ]);
cmakeFlags = [ cmakeFlags = [
"-DGMX_SIMD:STRING=${SIMD cpuAcceleration}" "-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"

4
pkgs/applications/science/molecular-dynamics/lammps/default.nix
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@ -1,6 +1,7 @@
{ lib, stdenv, fetchFromGitHub { lib, stdenv, fetchFromGitHub
, libpng, gzip, fftw, blas, lapack , libpng, gzip, fftw, blas, lapack
, mpi ? null , withMPI ? false
, mpi
}: }:
let packages = [ let packages = [
"asphere" "body" "class2" "colloid" "compress" "coreshell" "asphere" "body" "class2" "colloid" "compress" "coreshell"
@ -8,7 +9,6 @@ let packages = [
"opt" "peri" "qeq" "replica" "rigid" "shock" "snap" "srd" "user-reaxc" "opt" "peri" "qeq" "replica" "rigid" "shock" "snap" "srd" "user-reaxc"
]; ];
lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64"; lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
withMPI = (mpi != null);
in in
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
# LAMMPS has weird versioning converted to ISO 8601 format # LAMMPS has weird versioning converted to ISO 8601 format

4
pkgs/applications/science/physics/elmerfem/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, openmpi, blas, liblapack, qt4, qwt6_qt4, pkg-config }: { lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, qt4, qwt6_qt4, pkg-config }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "elmerfem"; pname = "elmerfem";
@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
hardeningDisable = [ "format" ]; hardeningDisable = [ "format" ];
nativeBuildInputs = [ cmake pkg-config git ]; nativeBuildInputs = [ cmake pkg-config git ];
buildInputs = [ gfortran openmpi blas liblapack qt4 qwt6_qt4 ]; buildInputs = [ gfortran mpi blas liblapack qt4 qwt6_qt4 ];
preConfigure = '' preConfigure = ''
patchShebangs ./ patchShebangs ./

7
pkgs/development/libraries/boost/generic.nix
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@ -14,7 +14,8 @@
, enableNumpy ? false , enableNumpy ? false
, taggedLayout ? ((enableRelease && enableDebug) || (enableSingleThreaded && enableMultiThreaded) || (enableShared && enableStatic)) , taggedLayout ? ((enableRelease && enableDebug) || (enableSingleThreaded && enableMultiThreaded) || (enableShared && enableStatic))
, patches ? [] , patches ? []
, mpi ? null , useMpi ? false
, mpi
, extraB2Args ? [] , extraB2Args ? []
# Attributes inherit from specific versions # Attributes inherit from specific versions
@ -94,7 +95,7 @@ let
++ optional (variant == "release") "debug-symbols=off" ++ optional (variant == "release") "debug-symbols=off"
++ optional (toolset != null) "toolset=${toolset}" ++ optional (toolset != null) "toolset=${toolset}"
++ optional (!enablePython) "--without-python" ++ optional (!enablePython) "--without-python"
++ optional (mpi != null || stdenv.hostPlatform != stdenv.buildPlatform) "--user-config=user-config.jam" ++ optional (useMpi || stdenv.hostPlatform != stdenv.buildPlatform) "--user-config=user-config.jam"
++ optionals (stdenv.hostPlatform.libc == "msvcrt") [ ++ optionals (stdenv.hostPlatform.libc == "msvcrt") [
"threadapi=win32" "threadapi=win32"
] ++ extraB2Args ] ++ extraB2Args
@ -140,7 +141,7 @@ stdenv.mkDerivation {
substituteInPlace tools/build/src/tools/clang-darwin.jam \ substituteInPlace tools/build/src/tools/clang-darwin.jam \
--replace '@rpath/$(<[1]:D=)' "$out/lib/\$(<[1]:D=)"; --replace '@rpath/$(<[1]:D=)' "$out/lib/\$(<[1]:D=)";
fi; fi;
'' + optionalString (mpi != null) '' '' + optionalString useMpi ''
cat << EOF >> user-config.jam cat << EOF >> user-config.jam
using mpi : ${mpi}/bin/mpiCC ; using mpi : ${mpi}/bin/mpiCC ;
EOF EOF

4
pkgs/development/libraries/globalarrays/default.nix
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@ -1,5 +1,5 @@
{ lib, stdenv, fetchpatch, fetchFromGitHub, autoreconfHook { lib, stdenv, fetchpatch, fetchFromGitHub, autoreconfHook
, blas, gfortran, openssh, openmpi , blas, gfortran, openssh, mpi
} : } :
let let
@ -17,7 +17,7 @@ in stdenv.mkDerivation {
}; };
nativeBuildInputs = [ autoreconfHook ]; nativeBuildInputs = [ autoreconfHook ];
buildInputs = [ openmpi blas gfortran openssh ]; buildInputs = [ mpi blas gfortran openssh ];
preConfigure = '' preConfigure = ''
configureFlagsArray+=( "--enable-i8" \ configureFlagsArray+=( "--enable-i8" \

4
pkgs/development/libraries/precice/default.nix
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@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub, cmake, gcc, boost, eigen, libxml2, openmpi, python3, petsc }: { lib, stdenv, fetchFromGitHub, cmake, gcc, boost, eigen, libxml2, mpi, python3, petsc }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "precice"; pname = "precice";
@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
NIX_CFLAGS_COMPILE = lib.optional stdenv.isDarwin [ "-D_GNU_SOURCE" ]; NIX_CFLAGS_COMPILE = lib.optional stdenv.isDarwin [ "-D_GNU_SOURCE" ];
nativeBuildInputs = [ cmake gcc ]; nativeBuildInputs = [ cmake gcc ];
buildInputs = [ boost eigen libxml2 openmpi python3 python3.pkgs.numpy ]; buildInputs = [ boost eigen libxml2 mpi python3 python3.pkgs.numpy ];
meta = { meta = {
description = "preCICE stands for Precise Code Interaction Coupling Environment"; description = "preCICE stands for Precise Code Interaction Coupling Environment";

8
pkgs/development/python-modules/cntk/default.nix
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@ -3,7 +3,7 @@
, pkgs , pkgs
, numpy , numpy
, scipy , scipy
, openmpi , mpi
, enum34 , enum34
, protobuf , protobuf
, pip , pip
@ -17,8 +17,8 @@ in
buildPythonPackage { buildPythonPackage {
inherit (cntk) name version src; inherit (cntk) name version src;
nativeBuildInputs = [ swig openmpi ]; nativeBuildInputs = [ swig mpi ];
buildInputs = [ cntk openmpi ]; buildInputs = [ cntk mpi ];
propagatedBuildInputs = [ numpy scipy enum34 protobuf pip ]; propagatedBuildInputs = [ numpy scipy enum34 protobuf pip ];
CNTK_LIB_PATH = "${cntk}/lib"; CNTK_LIB_PATH = "${cntk}/lib";
@ -28,7 +28,7 @@ buildPythonPackage {
postPatch = '' postPatch = ''
cd bindings/python cd bindings/python
sed -i 's,"libmpi.so.12","${openmpi}/lib/libmpi.so",g' cntk/train/distributed.py sed -i 's,"libmpi.so.12","${mpi}/lib/libmpi.so",g' cntk/train/distributed.py
# Remove distro and libs checks; they aren't compatible with NixOS and besides we guarantee # Remove distro and libs checks; they aren't compatible with NixOS and besides we guarantee
# compatibility by providing a package. # compatibility by providing a package.

8
pkgs/development/python-modules/pytorch/default.nix
View File

@ -1,7 +1,7 @@
{ stdenv, lib, fetchFromGitHub, fetchpatch, buildPythonPackage, python, { stdenv, lib, fetchFromGitHub, fetchpatch, buildPythonPackage, python,
cudaSupport ? false, cudatoolkit ? null, cudnn ? null, nccl ? null, magma ? null, cudaSupport ? false, cudatoolkit ? null, cudnn ? null, nccl ? null, magma ? null,
mklDnnSupport ? true, useSystemNccl ? true, mklDnnSupport ? true, useSystemNccl ? true,
openMPISupport ? false, openmpi ? null, MPISupport ? false, mpi,
buildDocs ? false, buildDocs ? false,
cudaArchList ? null, cudaArchList ? null,
@ -29,8 +29,6 @@
isPy3k, pythonOlder }: isPy3k, pythonOlder }:
assert !openMPISupport || openmpi != null;
# assert that everything needed for cuda is present and that the correct cuda versions are used # assert that everything needed for cuda is present and that the correct cuda versions are used
assert !cudaSupport || cudatoolkit != null; assert !cudaSupport || cudatoolkit != null;
assert cudnn == null || cudatoolkit != null; assert cudnn == null || cudatoolkit != null;
@ -38,7 +36,7 @@ assert !cudaSupport || (let majorIs = lib.versions.major cudatoolkit.version;
in majorIs == "9" || majorIs == "10" || majorIs == "11"); in majorIs == "9" || majorIs == "10" || majorIs == "11");
# confirm that cudatoolkits are sync'd across dependencies # confirm that cudatoolkits are sync'd across dependencies
assert !(openMPISupport && cudaSupport) || openmpi.cudatoolkit == cudatoolkit; assert !(MPISupport && cudaSupport) || mpi.cudatoolkit == cudatoolkit;
assert !cudaSupport || magma.cudatoolkit == cudatoolkit; assert !cudaSupport || magma.cudatoolkit == cudatoolkit;
let let
@ -224,7 +222,7 @@ in buildPythonPackage rec {
typing-extensions typing-extensions
# the following are required for tensorboard support # the following are required for tensorboard support
pillow six future tensorflow-tensorboard protobuf pillow six future tensorflow-tensorboard protobuf
] ++ lib.optionals openMPISupport [ openmpi ] ] ++ lib.optionals MPISupport [ mpi ]
++ lib.optionals (pythonOlder "3.7") [ dataclasses ]; ++ lib.optionals (pythonOlder "3.7") [ dataclasses ];
checkInputs = [ hypothesis ninja psutil ]; checkInputs = [ hypothesis ninja psutil ];

4
pkgs/development/python-modules/tensorflow/default.nix
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@ -11,7 +11,7 @@
# Common deps # Common deps
, git, pybind11, which, binutils, glibcLocales, cython, perl , git, pybind11, which, binutils, glibcLocales, cython, perl
# Common libraries # Common libraries
, jemalloc, openmpi, gast, grpc, sqlite, boringssl, jsoncpp , jemalloc, mpi, gast, grpc, sqlite, boringssl, jsoncpp
, curl, snappy, flatbuffers-core, lmdb-core, icu, double-conversion, libpng, libjpeg_turbo, giflib , curl, snappy, flatbuffers-core, lmdb-core, icu, double-conversion, libpng, libjpeg_turbo, giflib
# Upsteam by default includes cuda support since tensorflow 1.15. We could do # Upsteam by default includes cuda support since tensorflow 1.15. We could do
# that in nix as well. It would make some things easier and less confusing, but # that in nix as well. It would make some things easier and less confusing, but
@ -129,7 +129,7 @@ let
buildInputs = [ buildInputs = [
jemalloc jemalloc
openmpi mpi
glibcLocales glibcLocales
git git

10
pkgs/development/r-modules/default.nix
View File

@ -237,7 +237,7 @@ let
BayesSAE = [ pkgs.gsl_1 ]; BayesSAE = [ pkgs.gsl_1 ];
BayesVarSel = [ pkgs.gsl_1 ]; BayesVarSel = [ pkgs.gsl_1 ];
BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ]; BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
bigGP = [ pkgs.openmpi ]; bigGP = [ pkgs.mpi ];
bio3d = [ pkgs.zlib ]; bio3d = [ pkgs.zlib ];
BiocCheck = [ pkgs.which ]; BiocCheck = [ pkgs.which ];
Biostrings = [ pkgs.zlib ]; Biostrings = [ pkgs.zlib ];
@ -284,8 +284,8 @@ let
n1qn1 = [ pkgs.gfortran ]; n1qn1 = [ pkgs.gfortran ];
odbc = [ pkgs.unixODBC ]; odbc = [ pkgs.unixODBC ];
pander = [ pkgs.pandoc pkgs.which ]; pander = [ pkgs.pandoc pkgs.which ];
pbdMPI = [ pkgs.openmpi ]; pbdMPI = [ pkgs.mpi ];
pbdPROF = [ pkgs.openmpi ]; pbdPROF = [ pkgs.mpi ];
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ]; pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
pdftools = [ pkgs.poppler.dev ]; pdftools = [ pkgs.poppler.dev ];
phytools = [ pkgs.which ]; phytools = [ pkgs.which ];
@ -309,14 +309,14 @@ let
RGtk2 = [ pkgs.gtk2.dev ]; RGtk2 = [ pkgs.gtk2.dev ];
rhdf5 = [ pkgs.zlib ]; rhdf5 = [ pkgs.zlib ];
Rhdf5lib = [ pkgs.zlib ]; Rhdf5lib = [ pkgs.zlib ];
Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.openmpi pkgs.pcre.dev ]; Rhpc = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.mpi pkgs.pcre.dev ];
Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ]; Rhtslib = [ pkgs.zlib.dev pkgs.automake pkgs.autoconf pkgs.bzip2.dev pkgs.lzma.dev pkgs.curl.dev ];
rjags = [ pkgs.jags ]; rjags = [ pkgs.jags ];
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ]; rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
Rlibeemd = [ pkgs.gsl_1 ]; Rlibeemd = [ pkgs.gsl_1 ];
rmatio = [ pkgs.zlib.dev ]; rmatio = [ pkgs.zlib.dev ];
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ]; Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
Rmpi = [ pkgs.openmpi ]; Rmpi = [ pkgs.mpi ];
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ]; RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
RNetCDF = [ pkgs.netcdf pkgs.udunits ]; RNetCDF = [ pkgs.netcdf pkgs.udunits ];
RODBC = [ pkgs.libiodbc ]; RODBC = [ pkgs.libiodbc ];

6
pkgs/development/tools/poetry2nix/poetry2nix/overrides.nix
View File

@ -245,7 +245,7 @@ self: super:
horovod = super.horovod.overridePythonAttrs ( horovod = super.horovod.overridePythonAttrs (
old: { old: {
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.openmpi ]; propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.mpi ];
} }
); );
@ -528,14 +528,14 @@ self: super:
{ } { }
{ {
mpi = { mpi = {
mpicc = "${pkgs.openmpi.outPath}/bin/mpicc"; mpicc = "${pkgs.mpi.outPath}/bin/mpicc";
}; };
} }
); );
}; };
in in
{ {
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.openmpi ]; propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.mpi ];
enableParallelBuilding = true; enableParallelBuilding = true;
preBuild = '' preBuild = ''
ln -sf ${cfg} mpi.cfg ln -sf ${cfg} mpi.cfg

11
pkgs/tools/misc/hdf5/default.nix
View File

@ -5,13 +5,14 @@
, gfortran ? null , gfortran ? null
, zlib ? null , zlib ? null
, szip ? null , szip ? null
, mpi ? null , mpiSupport ? false
, mpi
, enableShared ? !stdenv.hostPlatform.isStatic , enableShared ? !stdenv.hostPlatform.isStatic
}: }:
# cpp and mpi options are mutually exclusive # cpp and mpi options are mutually exclusive
# (--enable-unsupported could be used to force the build) # (--enable-unsupported could be used to force the build)
assert !cpp || mpi == null; assert !cpp || !mpiSupport;
let inherit (lib) optional optionals; in let inherit (lib) optional optionals; in
@ -24,7 +25,7 @@ stdenv.mkDerivation rec {
}; };
passthru = { passthru = {
mpiSupport = (mpi != null); inherit mpiSupport;
inherit mpi; inherit mpi;
}; };
@ -38,13 +39,13 @@ stdenv.mkDerivation rec {
propagatedBuildInputs = [] propagatedBuildInputs = []
++ optional (zlib != null) zlib ++ optional (zlib != null) zlib
++ optional (mpi != null) mpi; ++ optional mpiSupport mpi;
configureFlags = [] configureFlags = []
++ optional cpp "--enable-cxx" ++ optional cpp "--enable-cxx"
++ optional (gfortran != null) "--enable-fortran" ++ optional (gfortran != null) "--enable-fortran"
++ optional (szip != null) "--with-szlib=${szip}" ++ optional (szip != null) "--with-szlib=${szip}"
++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"] ++ optionals mpiSupport ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
++ optional enableShared "--enable-shared"; ++ optional enableShared "--enable-shared";
patches = [ patches = [

4
pkgs/tools/misc/hpcg/default.nix
View File

@ -1,4 +1,4 @@
{ lib, stdenv, fetchurl, openmpi } : { lib, stdenv, fetchurl, mpi } :
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "hpcg"; pname = "hpcg";
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
enableParallelBuilding = true; enableParallelBuilding = true;
buildInputs = [ openmpi ]; buildInputs = [ mpi ];
makeFlags = [ "arch=Linux_MPI" ]; makeFlags = [ "arch=Linux_MPI" ];

4
pkgs/tools/system/ior/default.nix
View File

@ -1,4 +1,4 @@
{ lib, stdenv, fetchFromGitHub, openmpi, perl, autoreconfHook }: { lib, stdenv, fetchFromGitHub, mpi, perl, autoreconfHook }:
stdenv.mkDerivation rec { stdenv.mkDerivation rec {
pname = "ior"; pname = "ior";
@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
}; };
nativeBuildInputs = [ autoreconfHook ]; nativeBuildInputs = [ autoreconfHook ];
buildInputs = [ openmpi perl ]; buildInputs = [ mpi perl ];
enableParallelBuilding = true; enableParallelBuilding = true;

39
pkgs/top-level/all-packages.nix
View File

@ -4975,12 +4975,11 @@ in
hdf5 = callPackage ../tools/misc/hdf5 { hdf5 = callPackage ../tools/misc/hdf5 {
gfortran = null; gfortran = null;
szip = null; szip = null;
mpi = null;
}; };
hdf5-mpi = appendToName "mpi" (hdf5.override { hdf5-mpi = appendToName "mpi" (hdf5.override {
szip = null; szip = null;
mpi = pkgs.openmpi; mpiSupport = true;
}); });
hdf5-cpp = appendToName "cpp" (hdf5.override { hdf5-cpp = appendToName "cpp" (hdf5.override {
@ -7216,6 +7215,8 @@ in
openmpi = callPackage ../development/libraries/openmpi { }; openmpi = callPackage ../development/libraries/openmpi { };
mpi = openmpi; # this attribute should used to build MPI applications
ucx = callPackage ../development/libraries/ucx {}; ucx = callPackage ../development/libraries/ucx {};
openmodelica = callPackage ../applications/science/misc/openmodelica { openmodelica = callPackage ../applications/science/misc/openmodelica {
@ -22092,9 +22093,7 @@ in
fractal = callPackage ../applications/networking/instant-messengers/fractal { }; fractal = callPackage ../applications/networking/instant-messengers/fractal { };
freecad = libsForQt5.callPackage ../applications/graphics/freecad { freecad = libsForQt5.callPackage ../applications/graphics/freecad { };
mpi = openmpi;
};
freemind = callPackage ../applications/misc/freemind { freemind = callPackage ../applications/misc/freemind {
jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731 jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
@ -22480,7 +22479,7 @@ in
hpcg = callPackage ../tools/misc/hpcg/default.nix { }; hpcg = callPackage ../tools/misc/hpcg/default.nix { };
hpl = callPackage ../tools/misc/hpl { mpi = openmpi; }; hpl = callPackage ../tools/misc/hpl { };
hpmyroom = libsForQt5.callPackage ../applications/networking/hpmyroom { }; hpmyroom = libsForQt5.callPackage ../applications/networking/hpmyroom { };
@ -27254,15 +27253,11 @@ in
quantum-espresso = callPackage ../applications/science/chemistry/quantum-espresso { }; quantum-espresso = callPackage ../applications/science/chemistry/quantum-espresso { };
quantum-espresso-mpi = callPackage ../applications/science/chemistry/quantum-espresso { quantum-espresso-mpi = callPackage ../applications/science/chemistry/quantum-espresso { useMpi = true; };
mpi = openmpi;
};
siesta = callPackage ../applications/science/chemistry/siesta { }; siesta = callPackage ../applications/science/chemistry/siesta { };
siesta-mpi = callPackage ../applications/science/chemistry/siesta { siesta-mpi = callPackage ../applications/science/chemistry/siesta { useMpi = true; };
mpi = openmpi;
};
### SCIENCE/GEOMETRY ### SCIENCE/GEOMETRY
@ -27393,7 +27388,7 @@ in
}; };
neuron-mpi = appendToName "mpi" (neuron.override { neuron-mpi = appendToName "mpi" (neuron.override {
mpi = pkgs.openmpi; useMpi = true;
}); });
neuron-full = neuron-mpi.override { inherit python; }; neuron-full = neuron-mpi.override { inherit python; };
@ -27445,7 +27440,7 @@ in
raxml = callPackage ../applications/science/biology/raxml { }; raxml = callPackage ../applications/science/biology/raxml { };
raxml-mpi = appendToName "mpi" (raxml.override { raxml-mpi = appendToName "mpi" (raxml.override {
mpi = true; useMpi = true;
}); });
sambamba = callPackage ../applications/science/biology/sambamba { }; sambamba = callPackage ../applications/science/biology/sambamba { };
@ -27567,9 +27562,7 @@ in
planarity = callPackage ../development/libraries/science/math/planarity { }; planarity = callPackage ../development/libraries/science/math/planarity { };
scalapack = callPackage ../development/libraries/science/math/scalapack { scalapack = callPackage ../development/libraries/science/math/scalapack { };
mpi = openmpi;
};
rankwidth = callPackage ../development/libraries/science/math/rankwidth { }; rankwidth = callPackage ../development/libraries/science/math/rankwidth { };
@ -27599,9 +27592,7 @@ in
petsc = callPackage ../development/libraries/science/math/petsc { }; petsc = callPackage ../development/libraries/science/math/petsc { };
parmetis = callPackage ../development/libraries/science/math/parmetis { parmetis = callPackage ../development/libraries/science/math/parmetis { };
mpi = openmpi;
};
QuadProgpp = callPackage ../development/libraries/science/math/QuadProgpp { }; QuadProgpp = callPackage ../development/libraries/science/math/QuadProgpp { };
@ -27631,17 +27622,13 @@ in
### SCIENCE/MOLECULAR-DYNAMICS ### SCIENCE/MOLECULAR-DYNAMICS
dl-poly-classic-mpi = callPackage ../applications/science/molecular-dynamics/dl-poly-classic { dl-poly-classic-mpi = callPackage ../applications/science/molecular-dynamics/dl-poly-classic { };
mpi = openmpi;
};
lammps = callPackage ../applications/science/molecular-dynamics/lammps { lammps = callPackage ../applications/science/molecular-dynamics/lammps {
fftw = fftw; fftw = fftw;
}; };
lammps-mpi = lowPrio (lammps.override { lammps-mpi = lowPrio (lammps.override { withMPI = true; });
mpi = openmpi;
});
gromacs = callPackage ../applications/science/molecular-dynamics/gromacs { gromacs = callPackage ../applications/science/molecular-dynamics/gromacs {
singlePrec = true; singlePrec = true;

5
pkgs/top-level/python-packages.nix
View File

@ -2184,7 +2184,6 @@ in {
fenics = callPackage ../development/libraries/science/math/fenics { fenics = callPackage ../development/libraries/science/math/fenics {
inherit (pkgs) pkg-config; inherit (pkgs) pkg-config;
mpi = pkgs.openmpi;
pytest = self.pytest_4; pytest = self.pytest_4;
}; };
@ -3486,7 +3485,7 @@ in {
labelbox = callPackage ../development/python-modules/labelbox { }; labelbox = callPackage ../development/python-modules/labelbox { };
lammps-cython = callPackage ../development/python-modules/lammps-cython { mpi = pkgs.openmpi; }; lammps-cython = callPackage ../development/python-modules/lammps-cython { mpi = pkgs.mpi; };
langcodes = callPackage ../development/python-modules/langcodes { }; langcodes = callPackage ../development/python-modules/langcodes { };
@ -4120,7 +4119,7 @@ in {
mpd = callPackage ../development/python-modules/mpd { }; mpd = callPackage ../development/python-modules/mpd { };
mpi4py = callPackage ../development/python-modules/mpi4py { mpi = pkgs.openmpi; }; mpi4py = callPackage ../development/python-modules/mpi4py { mpi = pkgs.mpi; };
mplleaflet = callPackage ../development/python-modules/mplleaflet { }; mplleaflet = callPackage ../development/python-modules/mplleaflet { };