diff options
Diffstat (limited to 'pkgs/applications/science')
13 files changed, 38 insertions, 36 deletions
diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 0e2aa1c1a7915..ba55898e4f9d2 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/pkgs/applications/science/biology/migrate/default.nix @@ -1,4 +1,4 @@ -{ gccStdenv, fetchurl, zlib, openmpi }: +{ gccStdenv, fetchurl, zlib, mpi }: gccStdenv.mkDerivation rec { version = "3.7.2"; @@ -9,7 +9,7 @@ gccStdenv.mkDerivation rec { sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v"; }; - buildInputs = [ zlib openmpi ]; + buildInputs = [ zlib mpi ]; setSourceRoot = ''sourceRoot=$(echo */src)''; buildFlags = [ "thread" "mpis" ]; preInstall = "mkdir -p $out/man/man1"; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 154965b15214f..7bfef3a82fed8 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -8,7 +8,8 @@ , readline , which , python ? null -, mpi ? null +, useMpi ? false +, mpi , iv }: @@ -17,7 +18,8 @@ stdenv.mkDerivation rec { version = "7.5"; nativeBuildInputs = [ which pkg-config automake autoconf libtool ]; - buildInputs = [ ncurses readline python mpi iv ]; + buildInputs = [ ncurses readline python iv ] + ++ lib.optional useMpi mpi; src = fetchurl { url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz"; @@ -54,7 +56,7 @@ stdenv.mkDerivation rec { configureFlags = with lib; [ "--with-readline=${readline}" "--with-iv=${iv}" ] ++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ] - ++ (if mpi != null then ["--with-mpi" "--with-paranrn"] + ++ (if useMpi then ["--with-mpi" "--with-paranrn"] else ["--without-mpi"]); @@ -84,4 +86,3 @@ stdenv.mkDerivation rec { platforms = platforms.x86_64 ++ platforms.i686; }; } - diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index 4f9b5aca1b2d1..6e747e318f574 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -1,7 +1,7 @@ { lib, stdenv , fetchFromGitHub -, pkgs -, mpi ? false +, useMpi ? false +, mpi }: stdenv.mkDerivation rec { @@ -15,16 +15,16 @@ stdenv.mkDerivation rec { sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"; }; - buildInputs = lib.optionals mpi [ pkgs.openmpi ]; + buildInputs = lib.optionals useMpi [ mpi ]; # TODO darwin, AVX and AVX2 makefile targets - buildPhase = if mpi then '' + buildPhase = if useMpi then '' make -f Makefile.MPI.gcc '' else '' make -f Makefile.SSE3.PTHREADS.gcc ''; - installPhase = if mpi then '' + installPhase = if useMpi then '' mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin '' else '' mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin diff --git a/pkgs/applications/science/chemistry/openmolcas/default.nix b/pkgs/applications/science/chemistry/openmolcas/default.nix index 1297e595b9a8e..4bd88456b8f6e 100644 --- a/pkgs/applications/science/chemistry/openmolcas/default.nix +++ b/pkgs/applications/science/chemistry/openmolcas/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchFromGitLab, cmake, gfortran, perl , openblas, hdf5-cpp, python3, texlive -, armadillo, openmpi, globalarrays, openssh +, armadillo, mpi, globalarrays, openssh , makeWrapper, fetchpatch } : @@ -33,7 +33,7 @@ in stdenv.mkDerivation { hdf5-cpp python armadillo - openmpi + mpi globalarrays openssh ]; diff --git a/pkgs/applications/science/chemistry/quantum-espresso/default.nix b/pkgs/applications/science/chemistry/quantum-espresso/default.nix index c7b1f90104682..6d70e9f984f64 100644 --- a/pkgs/applications/science/chemistry/quantum-espresso/default.nix +++ b/pkgs/applications/science/chemistry/quantum-espresso/default.nix @@ -1,6 +1,7 @@ { lib, stdenv, fetchurl , gfortran, fftw, blas, lapack -, mpi ? null +, useMpi ? false +, mpi }: stdenv.mkDerivation rec { @@ -21,9 +22,9 @@ stdenv.mkDerivation rec { ''; buildInputs = [ fftw blas lapack gfortran ] - ++ (lib.optionals (mpi != null) [ mpi ]); + ++ (lib.optionals useMpi [ mpi ]); -configureFlags = if (mpi != null) then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; +configureFlags = if useMpi then [ "LD=${mpi}/bin/mpif90" ] else [ "LD=${gfortran}/bin/gfortran" ]; makeFlags = [ "all" ]; diff --git a/pkgs/applications/science/chemistry/siesta/default.nix b/pkgs/applications/science/chemistry/siesta/default.nix index 0df953f710673..02ff4c1ca4404 100644 --- a/pkgs/applications/science/chemistry/siesta/default.nix +++ b/pkgs/applications/science/chemistry/siesta/default.nix @@ -1,6 +1,7 @@ { lib, stdenv, fetchurl -, gfortran, blas, lapack -, mpi ? null, scalapack +, gfortran, blas, lapack, scalapack +, useMpi ? false +, mpi }: stdenv.mkDerivation { @@ -17,7 +18,7 @@ stdenv.mkDerivation { }; buildInputs = [ blas lapack gfortran ] - ++ (lib.optionals (mpi != null) [ mpi scalapack ]); + ++ lib.optionals useMpi [ mpi scalapack ]; enableParallelBuilding = true; @@ -29,7 +30,7 @@ stdenv.mkDerivation { cp gfortran.make arch.make ''; - preBuild = if (mpi != null) then '' + preBuild = if useMpi then '' makeFlagsArray=( CC="mpicc" FC="mpifort" FPPFLAGS="-DMPI" MPI_INTERFACE="libmpi_f90.a" MPI_INCLUDE="." diff --git a/pkgs/applications/science/electronics/openems/default.nix b/pkgs/applications/science/electronics/openems/default.nix index e1063f8e26cf0..64afe3222c2d1 100644 --- a/pkgs/applications/science/electronics/openems/default.nix +++ b/pkgs/applications/science/electronics/openems/default.nix @@ -11,16 +11,15 @@ , cmake , octave , gl2ps +, mpi , withQcsxcad ? true , withMPI ? false , withHyp2mat ? true , qcsxcad ? null -, openmpi ? null , hyp2mat ? null }: assert withQcsxcad -> qcsxcad != null; -assert withMPI -> openmpi != null; assert withHyp2mat -> hyp2mat != null; stdenv.mkDerivation { @@ -50,7 +49,7 @@ stdenv.mkDerivation { csxcad (octave.override { inherit hdf5; }) ] ++ lib.optionals withQcsxcad [ qcsxcad ] - ++ lib.optionals withMPI [ openmpi ] + ++ lib.optionals withMPI [ mpi ] ++ lib.optionals withHyp2mat [ hyp2mat ]; postFixup = '' diff --git a/pkgs/applications/science/math/cntk/default.nix b/pkgs/applications/science/math/cntk/default.nix index a348210179e20..e15e2a43d7744 100644 --- a/pkgs/applications/science/math/cntk/default.nix +++ b/pkgs/applications/science/math/cntk/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchgit, fetchFromGitHub, cmake -, openblas, blas, lapack, opencv3, libzip, boost, protobuf, openmpi +, openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi , onebitSGDSupport ? false , cudaSupport ? false, addOpenGLRunpath, cudatoolkit, nvidia_x11 , cudnnSupport ? cudaSupport, cudnn @@ -33,7 +33,7 @@ in stdenv.mkDerivation rec { # Force OpenMPI to use g++ in PATH. OMPI_CXX = "g++"; - buildInputs = [ openblas opencv3 libzip boost protobuf openmpi ] + buildInputs = [ openblas opencv3 libzip boost protobuf mpi ] ++ lib.optional cudaSupport cudatoolkit ++ lib.optional cudnnSupport cudnn; @@ -43,7 +43,7 @@ in stdenv.mkDerivation rec { "--with-openblas=${openblas}" "--with-boost=${boost.dev}" "--with-protobuf=${protobuf}" - "--with-mpi=${openmpi}" + "--with-mpi=${mpi}" "--cuda=${if cudaSupport then "yes" else "no"}" # FIXME "--asgd=no" diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index 915c7e1147f1f..39d9c866caef8 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, openmpi, petsc, python3 }: +{ lib, stdenv, fetchurl, cmake, gfortran, blas, lapack, mpi, petsc, python3 }: stdenv.mkDerivation rec { name = "getdp-${version}"; @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ cmake gfortran ]; - buildInputs = [ blas lapack openmpi petsc python3 ]; + buildInputs = [ blas lapack mpi petsc python3 ]; meta = with lib; { description = "A General Environment for the Treatment of Discrete Problems"; diff --git a/pkgs/applications/science/math/scotch/default.nix b/pkgs/applications/science/math/scotch/default.nix index 6f8753ff38ac0..b6613f25cbc7c 100644 --- a/pkgs/applications/science/math/scotch/default.nix +++ b/pkgs/applications/science/math/scotch/default.nix @@ -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"; diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index c40faddbbf946..bdec2ccc669f7 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -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}" diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 123afef03e86a..51ce64115ea56 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -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 diff --git a/pkgs/applications/science/physics/elmerfem/default.nix b/pkgs/applications/science/physics/elmerfem/default.nix index 6fa25ce66aeb7..5033b28bd3b3a 100644 --- a/pkgs/applications/science/physics/elmerfem/default.nix +++ b/pkgs/applications/science/physics/elmerfem/default.nix @@ -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 ./ |