mirror of
https://github.com/ilyakooo0/nixpkgs.git
synced 2024-09-19 03:29:17 +03:00
Merge pull request #108983 from markuskowa/dev-mpi
Use mpi attribute consistently to provide a default MPI implementation
This commit is contained in:
commit
2f34b4b883
@ -291,5 +291,40 @@ stdenv.mkDerivation {
|
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}
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</programlisting>
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</section>
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<section xml:id="sec-overlays-alternatives-mpi">
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<title>Switching the MPI implementation</title>
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<para>
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All programs that are built with
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<link xlink:href="https://en.wikipedia.org/wiki/Message_Passing_Interface">MPI</link>
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support use the generic attribute <varname>mpi</varname>
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as an input. At the moment Nixpkgs natively provides two different
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MPI implementations:
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<itemizedlist>
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<listitem>
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<para>
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<link xlink:href="https://www.open-mpi.org/">Open MPI</link>
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(default), attribute name <varname>openmpi</varname>
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</para>
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</listitem>
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<listitem>
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<para>
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<link xlink:href="https://www.mpich.org/">MPICH</link>,
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attribute name <varname>mpich</varname>
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</para>
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</listitem>
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</itemizedlist>
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</para>
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<para>
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To provide MPI enabled applications that use <literal>MPICH</literal>, instead
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of the default <literal>Open MPI</literal>, simply use the following overlay:
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</para>
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<programlisting>
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self: super:
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{
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mpi = self.mpich;
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}
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</programlisting>
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</section>
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</section>
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</chapter>
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|
@ -418,6 +418,26 @@ http://some.json-exporter.host:7979/probe?target=https://example.com/some/json/e
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SDK licenses if your project requires it. See the androidenv documentation for more details.
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</para>
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</listitem>
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<listitem>
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<para>
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The attribute <varname>mpi</varname> is now consistently used to
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provide a default, system-wide MPI implementation.
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The default implementation is openmpi, which has been used before by
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all derivations affects by this change.
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Note that all packages that have used <varname>mpi ? null</varname> in the input
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for optional MPI builds, have been changed to the boolean input paramater
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<varname>useMpi</varname> to enable building with MPI.
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Building all packages with <varname>mpich</varname> instead
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of the default <varname>openmpi</varname> can now be achived like this:
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<programlisting>
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self: super:
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{
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mpi = super.mpich;
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}
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</programlisting>
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</para>
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</listitem>
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<listitem>
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<para>
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The Searx module has been updated with the ability to configure the
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|
@ -1,6 +1,6 @@
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{ boost, cmake, fetchFromGitHub, ffmpeg, qtbase, qtx11extras,
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qttools, qtxmlpatterns, qtsvg, gdal, gfortran, libXt, makeWrapper,
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mkDerivation, ninja, openmpi, python3, lib, stdenv, tbb, libGLU, libGL }:
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mkDerivation, ninja, mpi, python3, lib, stdenv, tbb, libGLU, libGL }:
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mkDerivation rec {
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pname = "paraview";
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@ -65,7 +65,7 @@ mkDerivation rec {
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buildInputs = [
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libGLU libGL
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libXt
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openmpi
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mpi
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tbb
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boost
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ffmpeg
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|
@ -1,4 +1,4 @@
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{ gccStdenv, fetchurl, zlib, openmpi }:
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{ gccStdenv, fetchurl, zlib, mpi }:
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gccStdenv.mkDerivation rec {
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version = "3.7.2";
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@ -9,7 +9,7 @@ gccStdenv.mkDerivation rec {
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sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v";
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};
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buildInputs = [ zlib openmpi ];
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buildInputs = [ zlib mpi ];
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setSourceRoot = ''sourceRoot=$(echo */src)'';
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buildFlags = [ "thread" "mpis" ];
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preInstall = "mkdir -p $out/man/man1";
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|
@ -8,7 +8,8 @@
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, readline
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, which
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, python ? null
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, mpi ? null
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, useMpi ? false
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, mpi
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, iv
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}:
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@ -17,7 +18,8 @@ stdenv.mkDerivation rec {
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version = "7.5";
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nativeBuildInputs = [ which pkg-config automake autoconf libtool ];
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buildInputs = [ ncurses readline python mpi iv ];
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buildInputs = [ ncurses readline python iv ]
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++ lib.optional useMpi mpi;
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src = fetchurl {
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url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz";
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@ -54,7 +56,7 @@ stdenv.mkDerivation rec {
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configureFlags = with lib;
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[ "--with-readline=${readline}" "--with-iv=${iv}" ]
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++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ]
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++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
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++ (if useMpi then ["--with-mpi" "--with-paranrn"]
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else ["--without-mpi"]);
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@ -84,4 +86,3 @@ stdenv.mkDerivation rec {
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platforms = platforms.x86_64 ++ platforms.i686;
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};
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}
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|
@ -1,7 +1,7 @@
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{ lib, stdenv
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, fetchFromGitHub
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, pkgs
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, mpi ? false
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, useMpi ? false
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, mpi
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}:
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stdenv.mkDerivation rec {
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@ -15,16 +15,16 @@ stdenv.mkDerivation rec {
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sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh";
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};
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buildInputs = lib.optionals mpi [ pkgs.openmpi ];
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buildInputs = lib.optionals useMpi [ mpi ];
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# TODO darwin, AVX and AVX2 makefile targets
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buildPhase = if mpi then ''
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buildPhase = if useMpi then ''
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make -f Makefile.MPI.gcc
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'' else ''
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make -f Makefile.SSE3.PTHREADS.gcc
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'';
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installPhase = if mpi then ''
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installPhase = if useMpi then ''
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mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin
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'' else ''
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mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin
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|
@ -1,6 +1,6 @@
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{ lib, stdenv, fetchFromGitLab, cmake, gfortran, perl
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, openblas, hdf5-cpp, python3, texlive
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, armadillo, openmpi, globalarrays, openssh
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, armadillo, mpi, globalarrays, openssh
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, makeWrapper, fetchpatch
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} :
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@ -33,7 +33,7 @@ in stdenv.mkDerivation {
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hdf5-cpp
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python
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armadillo
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openmpi
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mpi
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globalarrays
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openssh
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];
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|
@ -1,6 +1,7 @@
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{ lib, stdenv, fetchurl
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, gfortran, fftw, blas, lapack
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, mpi ? null
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, useMpi ? false
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, mpi
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}:
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stdenv.mkDerivation rec {
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@ -21,9 +22,9 @@ stdenv.mkDerivation rec {
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'';
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buildInputs = [ fftw blas lapack gfortran ]
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++ (lib.optionals (mpi != null) [ mpi ]);
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++ (lib.optionals useMpi [ mpi ]);
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configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ];
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configureFlags = if useMpi then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ];
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makeFlags = [ "all" ];
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|
@ -1,6 +1,7 @@
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{ lib, stdenv, fetchurl
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, gfortran, blas, lapack
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, mpi ? null, scalapack
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, gfortran, blas, lapack, scalapack
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, useMpi ? false
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, mpi
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}:
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stdenv.mkDerivation {
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@ -17,7 +18,7 @@ stdenv.mkDerivation {
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};
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buildInputs = [ blas lapack gfortran ]
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++ (lib.optionals (mpi != null) [ mpi scalapack ]);
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++ lib.optionals useMpi [ mpi scalapack ];
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enableParallelBuilding = true;
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@ -29,7 +30,7 @@ stdenv.mkDerivation {
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cp gfortran.make arch.make
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'';
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preBuild = if (mpi != null) then ''
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preBuild = if useMpi then ''
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makeFlagsArray=(
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CC="mpicc" FC="mpifort"
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FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="."
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|
@ -11,16 +11,15 @@
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, cmake
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, octave
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, gl2ps
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, mpi
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, withQcsxcad ? true
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, withMPI ? false
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, withHyp2mat ? true
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, qcsxcad ? null
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, openmpi ? null
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, hyp2mat ? null
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}:
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assert withQcsxcad -> qcsxcad != null;
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assert withMPI -> openmpi != null;
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assert withHyp2mat -> hyp2mat != null;
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stdenv.mkDerivation {
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@ -50,7 +49,7 @@ stdenv.mkDerivation {
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csxcad
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(octave.override { inherit hdf5; }) ]
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++ lib.optionals withQcsxcad [ qcsxcad ]
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++ lib.optionals withMPI [ openmpi ]
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++ lib.optionals withMPI [ mpi ]
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++ lib.optionals withHyp2mat [ hyp2mat ];
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postFixup = ''
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|
@ -1,5 +1,5 @@
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{ lib, stdenv, fetchgit, fetchFromGitHub, cmake
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, openblas, blas, lapack, opencv3, libzip, boost, protobuf, openmpi
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, openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi
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, onebitSGDSupport ? false
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, cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11
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, cudnnSupport ? cudaSupport, cudnn
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@ -33,7 +33,7 @@ in stdenv.mkDerivation rec {
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# Force OpenMPI to use g++ in PATH.
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OMPI_CXX = "g++";
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buildInputs = [ openblas opencv3 libzip boost protobuf openmpi ]
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buildInputs = [ openblas opencv3 libzip boost protobuf mpi ]
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++ lib.optional cudaSupport cudatoolkit
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++ lib.optional cudnnSupport cudnn;
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@ -43,7 +43,7 @@ in stdenv.mkDerivation rec {
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"--with-openblas=${openblas}"
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"--with-boost=${boost.dev}"
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"--with-protobuf=${protobuf}"
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"--with-mpi=${openmpi}"
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"--with-mpi=${mpi}"
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"--cuda=${if cudaSupport then "yes" else "no"}"
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# FIXME
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"--asgd=no"
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|
@ -1,4 +1,4 @@
|
||||
{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, openmpi, petsc, python3 }:
|
||||
{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, mpi, petsc, python3 }:
|
||||
|
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stdenv.mkDerivation rec {
|
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name = "getdp-${version}";
|
||||
@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ cmake gfortran ];
|
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buildInputs = [ blas lapack openmpi petsc python3 ];
|
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buildInputs = [ blas lapack mpi petsc python3 ];
|
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|
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meta = with lib; {
|
||||
description = "A General Environment for the Treatment of Discrete Problems";
|
||||
|
@ -1,11 +1,11 @@
|
||||
{ lib, stdenv, fetchurl, bison, openmpi, flex, zlib}:
|
||||
{ lib, stdenv, fetchurl, bison, mpi, flex, zlib}:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
version = "6.0.4";
|
||||
pname = "scotch";
|
||||
src_name = "scotch_${version}";
|
||||
|
||||
buildInputs = [ bison openmpi flex zlib ];
|
||||
buildInputs = [ bison mpi flex zlib ];
|
||||
|
||||
src = fetchurl {
|
||||
url = "https://gforge.inria.fr/frs/download.php/file/34618/${src_name}.tar.gz";
|
||||
|
@ -3,10 +3,10 @@
|
||||
, cmake
|
||||
, hwloc
|
||||
, fftw
|
||||
, openmpi
|
||||
, perl
|
||||
, singlePrec ? true
|
||||
, mpiEnabled ? false
|
||||
, mpi
|
||||
, cpuAcceleration ? null
|
||||
}:
|
||||
|
||||
@ -33,7 +33,7 @@ in stdenv.mkDerivation rec {
|
||||
|
||||
nativeBuildInputs = [ cmake ];
|
||||
buildInputs = [ fftw perl hwloc ]
|
||||
++ (lib.optionals mpiEnabled [ openmpi ]);
|
||||
++ (lib.optionals mpiEnabled [ mpi ]);
|
||||
|
||||
cmakeFlags = [
|
||||
"-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"
|
||||
|
@ -1,6 +1,7 @@
|
||||
{ lib, stdenv, fetchFromGitHub
|
||||
, libpng, gzip, fftw, blas, lapack
|
||||
, mpi ? null
|
||||
, withMPI ? false
|
||||
, mpi
|
||||
}:
|
||||
let packages = [
|
||||
"asphere" "body" "class2" "colloid" "compress" "coreshell"
|
||||
@ -8,7 +9,6 @@ let packages = [
|
||||
"opt" "peri" "qeq" "replica" "rigid" "shock" "snap" "srd" "user-reaxc"
|
||||
];
|
||||
lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64";
|
||||
withMPI = (mpi != null);
|
||||
in
|
||||
stdenv.mkDerivation rec {
|
||||
# LAMMPS has weird versioning converted to ISO 8601 format
|
||||
|
@ -1,4 +1,4 @@
|
||||
{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, openmpi, blas, liblapack, qt4, qwt6_qt4, pkg-config }:
|
||||
{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, qt4, qwt6_qt4, pkg-config }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "elmerfem";
|
||||
@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
|
||||
hardeningDisable = [ "format" ];
|
||||
|
||||
nativeBuildInputs = [ cmake pkg-config git ];
|
||||
buildInputs = [ gfortran openmpi blas liblapack qt4 qwt6_qt4 ];
|
||||
buildInputs = [ gfortran mpi blas liblapack qt4 qwt6_qt4 ];
|
||||
|
||||
preConfigure = ''
|
||||
patchShebangs ./
|
||||
|
@ -14,7 +14,8 @@
|
||||
, enableNumpy ? false
|
||||
, taggedLayout ? ((enableRelease && enableDebug) || (enableSingleThreaded && enableMultiThreaded) || (enableShared && enableStatic))
|
||||
, patches ? []
|
||||
, mpi ? null
|
||||
, useMpi ? false
|
||||
, mpi
|
||||
, extraB2Args ? []
|
||||
|
||||
# Attributes inherit from specific versions
|
||||
@ -94,7 +95,7 @@ let
|
||||
++ optional (variant == "release") "debug-symbols=off"
|
||||
++ optional (toolset != null) "toolset=${toolset}"
|
||||
++ 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") [
|
||||
"threadapi=win32"
|
||||
] ++ extraB2Args
|
||||
@ -140,7 +141,7 @@ stdenv.mkDerivation {
|
||||
substituteInPlace tools/build/src/tools/clang-darwin.jam \
|
||||
--replace '@rpath/$(<[1]:D=)' "$out/lib/\$(<[1]:D=)";
|
||||
fi;
|
||||
'' + optionalString (mpi != null) ''
|
||||
'' + optionalString useMpi ''
|
||||
cat << EOF >> user-config.jam
|
||||
using mpi : ${mpi}/bin/mpiCC ;
|
||||
EOF
|
||||
|
@ -1,5 +1,5 @@
|
||||
{ lib, stdenv, fetchpatch, fetchFromGitHub, autoreconfHook
|
||||
, blas, gfortran, openssh, openmpi
|
||||
, blas, gfortran, openssh, mpi
|
||||
} :
|
||||
|
||||
let
|
||||
@ -17,7 +17,7 @@ in stdenv.mkDerivation {
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ autoreconfHook ];
|
||||
buildInputs = [ openmpi blas gfortran openssh ];
|
||||
buildInputs = [ mpi blas gfortran openssh ];
|
||||
|
||||
preConfigure = ''
|
||||
configureFlagsArray+=( "--enable-i8" \
|
||||
|
@ -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 {
|
||||
pname = "precice";
|
||||
@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
|
||||
NIX_CFLAGS_COMPILE = lib.optional stdenv.isDarwin [ "-D_GNU_SOURCE" ];
|
||||
|
||||
nativeBuildInputs = [ cmake gcc ];
|
||||
buildInputs = [ boost eigen libxml2 openmpi python3 python3.pkgs.numpy ];
|
||||
buildInputs = [ boost eigen libxml2 mpi python3 python3.pkgs.numpy ];
|
||||
|
||||
meta = {
|
||||
description = "preCICE stands for Precise Code Interaction Coupling Environment";
|
||||
|
@ -36,6 +36,9 @@ stdenv.mkDerivation rec {
|
||||
# make sure the test starts even if we have less than 4 cores
|
||||
export OMPI_MCA_rmaps_base_oversubscribe=1
|
||||
|
||||
# Fix to make mpich run in a sandbox
|
||||
export HYDRA_IFACE=lo
|
||||
|
||||
# Run single threaded
|
||||
export OMP_NUM_THREADS=1
|
||||
|
||||
|
@ -3,7 +3,7 @@
|
||||
, pkgs
|
||||
, numpy
|
||||
, scipy
|
||||
, openmpi
|
||||
, mpi
|
||||
, enum34
|
||||
, protobuf
|
||||
, pip
|
||||
@ -17,8 +17,8 @@ in
|
||||
buildPythonPackage {
|
||||
inherit (cntk) name version src;
|
||||
|
||||
nativeBuildInputs = [ swig openmpi ];
|
||||
buildInputs = [ cntk openmpi ];
|
||||
nativeBuildInputs = [ swig mpi ];
|
||||
buildInputs = [ cntk mpi ];
|
||||
propagatedBuildInputs = [ numpy scipy enum34 protobuf pip ];
|
||||
|
||||
CNTK_LIB_PATH = "${cntk}/lib";
|
||||
@ -28,7 +28,7 @@ buildPythonPackage {
|
||||
|
||||
postPatch = ''
|
||||
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
|
||||
# compatibility by providing a package.
|
||||
|
@ -1,7 +1,7 @@
|
||||
{ stdenv, lib, fetchFromGitHub, fetchpatch, buildPythonPackage, python,
|
||||
cudaSupport ? false, cudatoolkit ? null, cudnn ? null, nccl ? null, magma ? null,
|
||||
mklDnnSupport ? true, useSystemNccl ? true,
|
||||
openMPISupport ? false, openmpi ? null,
|
||||
MPISupport ? false, mpi,
|
||||
buildDocs ? false,
|
||||
cudaArchList ? null,
|
||||
|
||||
@ -29,8 +29,6 @@
|
||||
|
||||
isPy3k, pythonOlder }:
|
||||
|
||||
assert !openMPISupport || openmpi != null;
|
||||
|
||||
# assert that everything needed for cuda is present and that the correct cuda versions are used
|
||||
assert !cudaSupport || 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");
|
||||
|
||||
# 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;
|
||||
|
||||
let
|
||||
@ -224,7 +222,7 @@ in buildPythonPackage rec {
|
||||
typing-extensions
|
||||
# the following are required for tensorboard support
|
||||
pillow six future tensorflow-tensorboard protobuf
|
||||
] ++ lib.optionals openMPISupport [ openmpi ]
|
||||
] ++ lib.optionals MPISupport [ mpi ]
|
||||
++ lib.optionals (pythonOlder "3.7") [ dataclasses ];
|
||||
|
||||
checkInputs = [ hypothesis ninja psutil ];
|
||||
|
@ -11,7 +11,7 @@
|
||||
# Common deps
|
||||
, git, pybind11, which, binutils, glibcLocales, cython, perl
|
||||
# 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
|
||||
# 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
|
||||
@ -129,7 +129,7 @@ let
|
||||
|
||||
buildInputs = [
|
||||
jemalloc
|
||||
openmpi
|
||||
mpi
|
||||
glibcLocales
|
||||
git
|
||||
|
||||
|
@ -237,7 +237,7 @@ let
|
||||
BayesSAE = [ pkgs.gsl_1 ];
|
||||
BayesVarSel = [ pkgs.gsl_1 ];
|
||||
BayesXsrc = [ pkgs.readline.dev pkgs.ncurses ];
|
||||
bigGP = [ pkgs.openmpi ];
|
||||
bigGP = [ pkgs.mpi ];
|
||||
bio3d = [ pkgs.zlib ];
|
||||
BiocCheck = [ pkgs.which ];
|
||||
Biostrings = [ pkgs.zlib ];
|
||||
@ -284,8 +284,8 @@ let
|
||||
n1qn1 = [ pkgs.gfortran ];
|
||||
odbc = [ pkgs.unixODBC ];
|
||||
pander = [ pkgs.pandoc pkgs.which ];
|
||||
pbdMPI = [ pkgs.openmpi ];
|
||||
pbdPROF = [ pkgs.openmpi ];
|
||||
pbdMPI = [ pkgs.mpi ];
|
||||
pbdPROF = [ pkgs.mpi ];
|
||||
pbdZMQ = lib.optionals stdenv.isDarwin [ pkgs.which ];
|
||||
pdftools = [ pkgs.poppler.dev ];
|
||||
phytools = [ pkgs.which ];
|
||||
@ -309,14 +309,14 @@ let
|
||||
RGtk2 = [ pkgs.gtk2.dev ];
|
||||
rhdf5 = [ 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 ];
|
||||
rjags = [ pkgs.jags ];
|
||||
rJava = [ pkgs.zlib pkgs.bzip2.dev pkgs.icu pkgs.lzma.dev pkgs.pcre.dev pkgs.jdk pkgs.libzip ];
|
||||
Rlibeemd = [ pkgs.gsl_1 ];
|
||||
rmatio = [ pkgs.zlib.dev ];
|
||||
Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
|
||||
Rmpi = [ pkgs.openmpi ];
|
||||
Rmpi = [ pkgs.mpi ];
|
||||
RMySQL = [ pkgs.zlib pkgs.libmysqlclient pkgs.openssl.dev ];
|
||||
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
|
||||
RODBC = [ pkgs.libiodbc ];
|
||||
|
@ -245,7 +245,7 @@ self: super:
|
||||
|
||||
horovod = super.horovod.overridePythonAttrs (
|
||||
old: {
|
||||
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.openmpi ];
|
||||
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.mpi ];
|
||||
}
|
||||
);
|
||||
|
||||
@ -528,14 +528,14 @@ self: super:
|
||||
{ }
|
||||
{
|
||||
mpi = {
|
||||
mpicc = "${pkgs.openmpi.outPath}/bin/mpicc";
|
||||
mpicc = "${pkgs.mpi.outPath}/bin/mpicc";
|
||||
};
|
||||
}
|
||||
);
|
||||
};
|
||||
in
|
||||
{
|
||||
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.openmpi ];
|
||||
propagatedBuildInputs = old.propagatedBuildInputs ++ [ pkgs.mpi ];
|
||||
enableParallelBuilding = true;
|
||||
preBuild = ''
|
||||
ln -sf ${cfg} mpi.cfg
|
||||
|
@ -5,13 +5,14 @@
|
||||
, gfortran ? null
|
||||
, zlib ? null
|
||||
, szip ? null
|
||||
, mpi ? null
|
||||
, mpiSupport ? false
|
||||
, mpi
|
||||
, enableShared ? !stdenv.hostPlatform.isStatic
|
||||
}:
|
||||
|
||||
# cpp and mpi options are mutually exclusive
|
||||
# (--enable-unsupported could be used to force the build)
|
||||
assert !cpp || mpi == null;
|
||||
assert !cpp || !mpiSupport;
|
||||
|
||||
let inherit (lib) optional optionals; in
|
||||
|
||||
@ -24,7 +25,7 @@ stdenv.mkDerivation rec {
|
||||
};
|
||||
|
||||
passthru = {
|
||||
mpiSupport = (mpi != null);
|
||||
inherit mpiSupport;
|
||||
inherit mpi;
|
||||
};
|
||||
|
||||
@ -38,13 +39,13 @@ stdenv.mkDerivation rec {
|
||||
|
||||
propagatedBuildInputs = []
|
||||
++ optional (zlib != null) zlib
|
||||
++ optional (mpi != null) mpi;
|
||||
++ optional mpiSupport mpi;
|
||||
|
||||
configureFlags = []
|
||||
++ optional cpp "--enable-cxx"
|
||||
++ optional (gfortran != null) "--enable-fortran"
|
||||
++ optional (szip != null) "--with-szlib=${szip}"
|
||||
++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
|
||||
++ optionals mpiSupport ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
|
||||
++ optional enableShared "--enable-shared";
|
||||
|
||||
patches = [
|
||||
|
@ -1,4 +1,4 @@
|
||||
{ lib, stdenv, fetchurl, openmpi } :
|
||||
{ lib, stdenv, fetchurl, mpi } :
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "hpcg";
|
||||
@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
buildInputs = [ openmpi ];
|
||||
buildInputs = [ mpi ];
|
||||
|
||||
makeFlags = [ "arch=Linux_MPI" ];
|
||||
|
||||
|
@ -1,4 +1,4 @@
|
||||
{ lib, stdenv, fetchFromGitHub, openmpi, perl, autoreconfHook }:
|
||||
{ lib, stdenv, fetchFromGitHub, mpi, perl, autoreconfHook }:
|
||||
|
||||
stdenv.mkDerivation rec {
|
||||
pname = "ior";
|
||||
@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
|
||||
};
|
||||
|
||||
nativeBuildInputs = [ autoreconfHook ];
|
||||
buildInputs = [ openmpi perl ];
|
||||
buildInputs = [ mpi perl ];
|
||||
|
||||
enableParallelBuilding = true;
|
||||
|
||||
|
@ -4975,12 +4975,11 @@ in
|
||||
hdf5 = callPackage ../tools/misc/hdf5 {
|
||||
gfortran = null;
|
||||
szip = null;
|
||||
mpi = null;
|
||||
};
|
||||
|
||||
hdf5-mpi = appendToName "mpi" (hdf5.override {
|
||||
szip = null;
|
||||
mpi = pkgs.openmpi;
|
||||
mpiSupport = true;
|
||||
});
|
||||
|
||||
hdf5-cpp = appendToName "cpp" (hdf5.override {
|
||||
@ -7220,6 +7219,8 @@ in
|
||||
|
||||
openmpi = callPackage ../development/libraries/openmpi { };
|
||||
|
||||
mpi = openmpi; # this attribute should used to build MPI applications
|
||||
|
||||
ucx = callPackage ../development/libraries/ucx {};
|
||||
|
||||
openmodelica = callPackage ../applications/science/misc/openmodelica {
|
||||
@ -22101,9 +22102,7 @@ in
|
||||
|
||||
fractal = callPackage ../applications/networking/instant-messengers/fractal { };
|
||||
|
||||
freecad = libsForQt5.callPackage ../applications/graphics/freecad {
|
||||
mpi = openmpi;
|
||||
};
|
||||
freecad = libsForQt5.callPackage ../applications/graphics/freecad { };
|
||||
|
||||
freemind = callPackage ../applications/misc/freemind {
|
||||
jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
|
||||
@ -22489,7 +22488,7 @@ in
|
||||
|
||||
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 { };
|
||||
|
||||
@ -27263,15 +27262,11 @@ in
|
||||
|
||||
quantum-espresso = callPackage ../applications/science/chemistry/quantum-espresso { };
|
||||
|
||||
quantum-espresso-mpi = callPackage ../applications/science/chemistry/quantum-espresso {
|
||||
mpi = openmpi;
|
||||
};
|
||||
quantum-espresso-mpi = callPackage ../applications/science/chemistry/quantum-espresso { useMpi = true; };
|
||||
|
||||
siesta = callPackage ../applications/science/chemistry/siesta { };
|
||||
|
||||
siesta-mpi = callPackage ../applications/science/chemistry/siesta {
|
||||
mpi = openmpi;
|
||||
};
|
||||
siesta-mpi = callPackage ../applications/science/chemistry/siesta { useMpi = true; };
|
||||
|
||||
### SCIENCE/GEOMETRY
|
||||
|
||||
@ -27402,7 +27397,7 @@ in
|
||||
};
|
||||
|
||||
neuron-mpi = appendToName "mpi" (neuron.override {
|
||||
mpi = pkgs.openmpi;
|
||||
useMpi = true;
|
||||
});
|
||||
|
||||
neuron-full = neuron-mpi.override { inherit python; };
|
||||
@ -27454,7 +27449,7 @@ in
|
||||
raxml = callPackage ../applications/science/biology/raxml { };
|
||||
|
||||
raxml-mpi = appendToName "mpi" (raxml.override {
|
||||
mpi = true;
|
||||
useMpi = true;
|
||||
});
|
||||
|
||||
sambamba = callPackage ../applications/science/biology/sambamba { };
|
||||
@ -27576,9 +27571,7 @@ in
|
||||
|
||||
planarity = callPackage ../development/libraries/science/math/planarity { };
|
||||
|
||||
scalapack = callPackage ../development/libraries/science/math/scalapack {
|
||||
mpi = openmpi;
|
||||
};
|
||||
scalapack = callPackage ../development/libraries/science/math/scalapack { };
|
||||
|
||||
rankwidth = callPackage ../development/libraries/science/math/rankwidth { };
|
||||
|
||||
@ -27608,9 +27601,7 @@ in
|
||||
|
||||
petsc = callPackage ../development/libraries/science/math/petsc { };
|
||||
|
||||
parmetis = callPackage ../development/libraries/science/math/parmetis {
|
||||
mpi = openmpi;
|
||||
};
|
||||
parmetis = callPackage ../development/libraries/science/math/parmetis { };
|
||||
|
||||
QuadProgpp = callPackage ../development/libraries/science/math/QuadProgpp { };
|
||||
|
||||
@ -27640,17 +27631,13 @@ in
|
||||
|
||||
### SCIENCE/MOLECULAR-DYNAMICS
|
||||
|
||||
dl-poly-classic-mpi = callPackage ../applications/science/molecular-dynamics/dl-poly-classic {
|
||||
mpi = openmpi;
|
||||
};
|
||||
dl-poly-classic-mpi = callPackage ../applications/science/molecular-dynamics/dl-poly-classic { };
|
||||
|
||||
lammps = callPackage ../applications/science/molecular-dynamics/lammps {
|
||||
fftw = fftw;
|
||||
};
|
||||
|
||||
lammps-mpi = lowPrio (lammps.override {
|
||||
mpi = openmpi;
|
||||
});
|
||||
lammps-mpi = lowPrio (lammps.override { withMPI = true; });
|
||||
|
||||
gromacs = callPackage ../applications/science/molecular-dynamics/gromacs {
|
||||
singlePrec = true;
|
||||
|
@ -2188,7 +2188,6 @@ in {
|
||||
|
||||
fenics = callPackage ../development/libraries/science/math/fenics {
|
||||
inherit (pkgs) pkg-config;
|
||||
mpi = pkgs.openmpi;
|
||||
pytest = self.pytest_4;
|
||||
};
|
||||
|
||||
@ -3490,7 +3489,7 @@ in {
|
||||
|
||||
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 { };
|
||||
|
||||
@ -4124,7 +4123,7 @@ in {
|
||||
|
||||
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 { };
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user