Unverified Commit 250b695f authored by Nick Cao's avatar Nick Cao Committed by GitHub
Browse files

petsc: refactor inputs, configureFlags; add tests, petscPackages scope (#392392)

parents effac2a6 26d320d7

pkgs/by-name/pe/petsc/package.nix

+132 −75
Original line number Diff line number Diff line 
{

  lib,

  newScope,

  stdenv,

  fetchzip,

  gfortran,

  replaceVars,

  python3,

  python3Packages,

  blas,

  lapack,

  zlib, # propagated by p4est but required by petsc

  bash,

  pkg-config,

  gfortran,

  bison,

  mpi, # generic mpi dependency

  mpiCheckPhaseHook,

  bash,

  python3,

  python3Packages,



  # Build options

  petsc-optimized ? true,

  petsc-scalar-type ? "real",

  petsc-precision ? "double",

  debug ? false,

  scalarType ? "real",

  precision ? "double",

  mpiSupport ? true,

  fortranSupport ? true,

  pythonSupport ? false, # petsc python binding

  withExamples ? false,

  withFullDeps ? false, # full External libraries support
@@ -26,41 +27,88 @@ 
  # External libraries options

  withHdf5 ? withCommonDeps,

  withMetis ? withCommonDeps,

  withScalapack ? withFullDeps,

  withZlib ? (withP4est || withPtscotch),

  withScalapack ? withCommonDeps && mpiSupport,

  withParmetis ? withFullDeps, # parmetis is unfree

  withPtscotch ? withFullDeps,

  withMumps ? withFullDeps,

  withPtscotch ? withCommonDeps && mpiSupport,

  withMumps ? withCommonDeps,

  withP4est ? withFullDeps,

  withHypre ? withCommonDeps && mpiSupport,

  withFftw ? withCommonDeps,

  withSuperLu ? withCommonDeps,

  withSuitesparse ? withCommonDeps,



  # External libraries

  hdf5-fortran-mpi,

  blas,

  lapack,

  hdf5,

  metis,

  parmetis,

  scotch,

  scalapack,

  mumps_par,

  pkg-config,

  mumps,

  p4est,

  zlib, # propagated by p4est but required by petsc

  hypre,

  fftw,

  superlu,

  suitesparse,



  # Used in passthru.tests

  petsc,

}:

assert withFullDeps -> withCommonDeps;



# This version of PETSc does not support a non-MPI p4est build

assert withP4est -> (p4est.mpiSupport && mpiSupport);

assert withP4est -> (mpiSupport && withZlib);



# Package parmetis depend on metis and mpi support

assert withParmetis -> (withMetis && mpiSupport);



assert withPtscotch -> mpiSupport;

assert withPtscotch -> (mpiSupport && withZlib);

assert withScalapack -> mpiSupport;

assert withMumps -> withScalapack;

assert (withMumps && mpiSupport) -> withScalapack;

assert withHypre -> mpiSupport;



stdenv.mkDerivation rec {

let

  petscPackages = lib.makeScope newScope (self: {

    inherit

      # global override options

      mpiSupport

      fortranSupport

      pythonSupport

      precision

      ;

    enableMpi = self.mpiSupport;



    petscPackages = self;

    # external libraries

    mpi = self.callPackage mpi.override { };

    blas = self.callPackage blas.override { };

    lapack = self.callPackage lapack.override { };

    hdf5 = self.callPackage hdf5.override {

      fortran = gfortran;

      cppSupport = !mpiSupport;

    };

    metis = self.callPackage metis.override { };

    parmetis = self.callPackage parmetis.override { };

    scotch = self.callPackage scotch.override { };

    scalapack = self.callPackage scalapack.override { };

    mumps = self.callPackage mumps.override { };

    p4est = self.callPackage p4est.override { };

    hypre = self.callPackage hypre.override { };

    fftw = self.callPackage fftw.override { };

    superlu = self.callPackage superlu.override { };

    suitesparse = self.callPackage suitesparse.override { };

  });

in

stdenv.mkDerivation (finalAttrs: {

  pname = "petsc";

  version = "3.22.4";

  version = "3.23.0";



  src = fetchzip {

    url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz";

    hash = "sha256-8WV1ylXytkhiNa7YpWSOIpSvzLCCjdVVe5SiGfhicas=";

    url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${finalAttrs.version}.tar.gz";

    hash = "sha256-OcI4iyDOR0YTVV+JoOhbfutoW00EmfapNaMnD/JJFsI=";

  };



  strictDeps = true;
@@ -70,6 +118,7 @@ stdenv.mkDerivation rec { 
      python3

      gfortran

      pkg-config

      bison

    ]

    ++ lib.optional mpiSupport mpi

    ++ lib.optionals pythonSupport [
@@ -79,16 +128,21 @@ stdenv.mkDerivation rec { 


  buildInputs =

    [

      blas

      lapack

      petscPackages.blas

      petscPackages.lapack

    ]

    ++ lib.optional withHdf5 hdf5-fortran-mpi

    ++ lib.optional withP4est p4est

    ++ lib.optional withMetis metis

    ++ lib.optional withParmetis parmetis

    ++ lib.optional withPtscotch scotch

    ++ lib.optional withScalapack scalapack

    ++ lib.optional withMumps mumps_par;

    ++ lib.optional withZlib zlib

    ++ lib.optional withHdf5 petscPackages.hdf5

    ++ lib.optional withP4est petscPackages.p4est

    ++ lib.optional withMetis petscPackages.metis

    ++ lib.optional withParmetis petscPackages.parmetis

    ++ lib.optional withPtscotch petscPackages.scotch

    ++ lib.optional withScalapack petscPackages.scalapack

    ++ lib.optional withMumps petscPackages.mumps

    ++ lib.optional withHypre petscPackages.hypre

    ++ lib.optional withSuperLu petscPackages.superlu

    ++ lib.optional withFftw petscPackages.fftw

    ++ lib.optional withSuitesparse petscPackages.suitesparse;



  propagatedBuildInputs = lib.optional pythonSupport python3Packages.numpy;
@@ -109,57 +163,39 @@ stdenv.mkDerivation rec { 
    [

      "--with-blas=1"

      "--with-lapack=1"

      "--with-scalar-type=${petsc-scalar-type}"

      "--with-precision=${petsc-precision}"

      "--with-scalar-type=${scalarType}"

      "--with-precision=${precision}"

      "--with-mpi=${if mpiSupport then "1" else "0"}"

    ]

    ++ lib.optional pythonSupport "--with-petsc4py=1"

    ++ lib.optionals mpiSupport [

      "--CC=mpicc"

      "--with-cxx=mpicxx"

      "--with-fc=mpif90"

    ]

    ++ lib.optionals withMetis [

      "--with-metis=1"

      "--with-metis-dir=${metis}"

    ]

    ++ lib.optionals withParmetis [

      "--with-parmetis=1"

      "--with-parmetis-dir=${parmetis}"

    ]

    ++ lib.optionals withPtscotch [

      "--with-ptscotch=1"

      "--with-ptscotch-include=${lib.getDev scotch}/include"

      "--with-ptscotch-lib=[-L${lib.getLib scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"

    ]

    ++ lib.optionals withScalapack [

      "--with-scalapack=1"

      "--with-scalapack-dir=${scalapack}"

    ]

    ++ lib.optionals withMumps [

      "--with-mumps=1"

      "--with-mumps-dir=${mumps_par}"

    ]

    ++ lib.optionals withP4est [

      "--with-p4est=1"

      "--with-zlib-include=${lib.getDev zlib}/include"

      "--with-zlib-lib=[-L${lib.getLib zlib}/lib,-lz]"

    ]

    ++ lib.optionals withHdf5 [

      "--with-hdf5=1"

      "--with-hdf5-fortran-bindings=1"

      "--with-hdf5-include=${lib.getDev hdf5-fortran-mpi}/include"

      "--with-hdf5-lib=[-L${lib.getLib hdf5-fortran-mpi}/lib,-lhdf5]"

    ]

    ++ lib.optionals petsc-optimized [

    ++ lib.optionals (!debug) [

      "--with-debugging=0"

      "COPTFLAGS=-O3"

      "FOPTFLAGS=-O3"

      "CXXOPTFLAGS=-O3"

      "CXXFLAGS=-O3"

    ];

    ]

    ++ lib.optional (!fortranSupport) "--with-fortran-bindings=0"

    ++ lib.optional pythonSupport "--with-petsc4py=1"

    ++ lib.optional withMetis "--with-metis=1"

    ++ lib.optional withParmetis "--with-parmetis=1"

    ++ lib.optional withPtscotch "--with-ptscotch=1"

    ++ lib.optional withScalapack "--with-scalapack=1"

    ++ lib.optional withMumps "--with-mumps=1"

    ++ lib.optional (withMumps && !mpiSupport) "--with-mumps-serial=1"

    ++ lib.optional withP4est "--with-p4est=1"

    ++ lib.optional withZlib "--with-zlib=1"

    ++ lib.optional withHdf5 "--with-hdf5=1"

    ++ lib.optional withHypre "--with-hypre=1"

    ++ lib.optional withSuperLu "--with-superlu=1"

    ++ lib.optional withFftw "--with-fftw=1"

    ++ lib.optional withSuitesparse "--with-suitesparse=1";



  hardeningDisable = lib.optionals (!petsc-optimized) [

  hardeningDisable = lib.optionals debug [

    "fortify"

    "fortify3"

  ];
@@ -198,19 +234,40 @@ stdenv.mkDerivation rec { 
  pythonImportsCheck = [ "petsc4py" ];



  passthru = {

    inherit mpiSupport pythonSupport;

    inherit

      mpiSupport

      pythonSupport

      fortranSupport

      ;

    petscPackages = petscPackages.overrideScope (

      final: prev: {

        petsc = finalAttrs.finalPackage;

      }

    );

    tests =

      {

        serial = petsc.override {

          mpiSupport = false;

        };

      }

      // lib.optionalAttrs stdenv.hostPlatform.isLinux {

        fullDeps = petsc.override {

          withFullDeps = true;

          withParmetis = false;

        };

      };

  };



  setupHook = ./setup-hook.sh;



  meta = with lib; {

  meta = {

    description = "Portable Extensible Toolkit for Scientific computation";

    homepage = "https://petsc.org/release/";

    license = licenses.bsd2;

    license = lib.licenses.bsd2;

    platforms = lib.platforms.unix;

    maintainers = with maintainers; [

    maintainers = with lib.maintainers; [

      cburstedde

      qbisi

    ];

  };

}
 
})

pkgs/by-name/sl/slepc/package.nix

+2 −8
Original line number Diff line number Diff line
@@ -2,7 +2,6 @@ 
  lib,

  stdenv,

  fetchFromGitLab,

  sowing,

  python3,

  python3Packages,

  arpack-mpi,
@@ -17,13 +16,13 @@ assert petsc.mpiSupport; 
assert pythonSupport -> petsc.pythonSupport;

stdenv.mkDerivation (finalAttrs: {

  pname = "slepc";

  version = "3.22.2";

  version = "3.23.0";



  src = fetchFromGitLab {

    owner = "slepc";

    repo = "slepc";

    tag = "v${finalAttrs.version}";

    hash = "sha256-a5DmsA7NAlhrEaS43TYPk7vtDfhXLEP+5sftu2A9Yt4=";

    hash = "sha256-Z9CVZQ/Ezb1S2EkTb9amAPxaN4tiUnKrbvQIc3BnVuU=";

  };



  postPatch = ''
@@ -33,11 +32,6 @@ stdenv.mkDerivation (finalAttrs: { 
      "slepc.prefixdir,'${python3.sitePackages}'"



    patchShebangs lib/slepc/bin



    # Use system bfort

    substituteInPlace config/packages/sowing.py \

      --replace-fail "bfort = os.path.join(archdir,'bin','bfort')" \

      "bfort = '${sowing}/bin/bfort'"

  '';



  # Usually this project is being built as part of a `petsc` build or as part of