commit 7bf025e6aef44ed98bd72e58fcbdf505116bdd4e · pyrox.dev/nixpkgs

+22

pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch

···

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       diff --git a/config/BuildSystem/config/packages/petsc4py.py b/config/BuildSystem/config/packages/petsc4py.py

     

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       index 4a58243..831aa04 100644

     

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       --- a/config/BuildSystem/config/packages/petsc4py.py

     

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       +++ b/config/BuildSystem/config/packages/petsc4py.py

     

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       @@ -37,7 +37,7 @@ class Configure(config.package.Package):

     

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          def Install(self):

     

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            import os

     

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       -    installLibPath = os.path.join(self.installDir, 'lib')

     

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       +    installLibPath = os.path.join(self.installDir, 'lib', '@PYTHON_SITEPACKAGES@')

     

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            if self.setCompilers.isDarwin(self.log):

     

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              apple = 'You may need to\n (csh/tcsh) setenv MACOSX_DEPLOYMENT_TARGET 10.X\n (sh/bash) MACOSX_DEPLOYMENT_TARGET=10.X; export MACOSX_DEPLOYMENT_TARGET\nbefore running make on PETSc'

     

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            else:

     

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       @@ -70,7 +70,7 @@ class Configure(config.package.Package):

     

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              newdir += 'NUMPY_INCLUDE="'+numpy_include+'" '

     

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       +
        

     

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            self.addDefine('HAVE_PETSC4PY',1)

     

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       -    self.addDefine('PETSC4PY_INSTALL_PATH','"'+os.path.join(self.installdir.dir,'lib')+'"')

     

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       +    self.addDefine('PETSC4PY_INSTALL_PATH','"'+installLibPath+'"')

     

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            self.addMakeMacro('PETSC4PY','yes')

     

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            self.addMakeRule('petsc4pybuild','', \

     

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                               ['@echo "*** Building petsc4py ***"',\

+124 -57

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

···

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         fetchzip,

     

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         cctools,

     

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         gfortran,

     

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         replaceVars,

     

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         python3,

     

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         python3Packages,

     

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         blas,

     

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         lapack,

     

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         mpiSupport ? true,

     

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         zlib, # propagated by p4est but required by petsc

     

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         mpi, # generic mpi dependency

     

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         mpiCheckPhaseHook,

     

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         petsc-withp4est ? false,

     

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         hdf5-support ? false,

     

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       -
         hdf5,

     

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       +
       

     

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         # Build options

     

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         petsc-optimized ? true,

     

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         petsc-scalar-type ? "real",

     

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         petsc-precision ? "double",

     

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         mpiSupport ? true,

     

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         withPetsc4py ? false, # petsc python binding

     

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         withFullDeps ? false, # full External libraries support

     

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         # External libraries options

     

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         withHdf5 ? true,

     

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         withMetis ? withFullDeps,

     

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         withParmetis ? false, # parmetis is unfree and should be enabled manualy

     

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         withPtscotch ? withFullDeps,

     

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         withScalapack ? withFullDeps,

     

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         withMumps ? withFullDeps,

     

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         withP4est ? withFullDeps,

     

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       +
       

     

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         # External libraries

     

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         hdf5-fortran-mpi,

     

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         metis,

     

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         parmetis,

     

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       -
         withParmetis ? false,

     

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         scotch,

     

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         scalapack,

     

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         mumps_par,

     

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         pkg-config,

     

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         p4est,

     

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       -
         zlib, # propagated by p4est but required by petsc

     

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         petsc-optimized ? false,

     

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         petsc-scalar-type ? "real",

     

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         petsc-precision ? "double",

     

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       }:

     

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

     

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       -
       assert petsc-withp4est -> p4est.mpiSupport;

     

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

     

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       +
       

     

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       # Package parmetis depend on metis and mpi support

     

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       assert withParmetis -> (withMetis && mpiSupport);

     

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       assert withPtscotch -> mpiSupport;

     

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       assert withScalapack -> mpiSupport;

     

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       assert withMumps -> withScalapack;

     

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       stdenv.mkDerivation rec {

     

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         pname = "petsc";

     
···

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         };

     

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         strictDeps = true;

     

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       -
         nativeBuildInputs = [

     

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           python3

     

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           gfortran

     

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           pkg-config

     

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       -
         ] ++ lib.optional mpiSupport mpi;

     

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         buildInputs = [

     

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           blas

     

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           lapack

     

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       -
         ] ++ lib.optional hdf5-support hdf5 ++ lib.optional petsc-withp4est p4est ++ lib.optionals withParmetis [ metis parmetis ];

     

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         nativeBuildInputs =

     

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           [

     

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             python3

     

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             gfortran

     

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             pkg-config

     

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           ]

     

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           ++ lib.optional mpiSupport mpi

     

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           ++ lib.optionals withPetsc4py [

     

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             python3Packages.setuptools

     

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             python3Packages.cython

     

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           ];

     

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         buildInputs =

     

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           [

     

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             blas

     

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             lapack

     

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           ]

     

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           ++ lib.optional withHdf5 hdf5-fortran-mpi

     

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           ++ lib.optional withP4est p4est

     

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           ++ lib.optional withMetis metis

     

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           ++ lib.optional withParmetis parmetis

     

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           ++ lib.optional withPtscotch scotch

     

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           ++ lib.optional withScalapack scalapack

     

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           ++ lib.optional withMumps mumps_par;

     

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         prePatch = lib.optionalString stdenv.hostPlatform.isDarwin ''

     

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           substituteInPlace config/install.py \

     

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             --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool

     

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         '';

     

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         propagatedBuildInputs = lib.optional withPetsc4py python3Packages.numpy;

     

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         configureFlags = [

     

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           "--with-blas=1"

     

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           "--with-lapack=1"

     

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

     

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

     

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

     

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         ] ++ lib.optionals mpiSupport [

     

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           "--CC=mpicc"

     

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           "--with-cxx=mpicxx"

     

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           "--with-fc=mpif90"

     

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         ] ++ lib.optionals (mpiSupport && withParmetis) [

     

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           "--with-metis=1"

     

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

     

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           "--with-parmetis=1"

     

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

     

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         ] ++ lib.optionals petsc-optimized [

     

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           "--with-debugging=0"

     

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           "COPTFLAGS=-O3"

     

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           "FOPTFLAGS=-O3"

     

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           "CXXOPTFLAGS=-O3"

     

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           "CXXFLAGS=-O3"

     

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         patches = [

     

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           (replaceVars ./fix-petsc4py-install-prefix.patch {

     

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             PYTHON_SITEPACKAGES = python3.sitePackages;

     

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           })

     

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         ];

     

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         preConfigure = ''

     

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           patchShebangs ./lib/petsc/bin

     

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         '' + lib.optionalString petsc-withp4est ''

     

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           configureFlagsArray+=(

     

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         postPatch =

     

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           ''

     

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             patchShebangs ./lib/petsc/bin

     

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           ''

     

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           + lib.optionalString stdenv.hostPlatform.isDarwin ''

     

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             substituteInPlace config/install.py \

     

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               --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool

     

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           '';

     

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         configureFlags =

     

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           [

     

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             "--with-blas=1"

     

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             "--with-lapack=1"

     

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

     

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

     

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

     

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           ]

     

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           ++ lib.optional withPetsc4py "--with-petsc4py=1"

     

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           ++ lib.optionals mpiSupport [

     

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             "--CC=mpicc"

     

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             "--with-cxx=mpicxx"

     

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             "--with-fc=mpif90"

     

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           ]

     

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           ++ lib.optionals withMetis [

     

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             "--with-metis=1"

     

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

     

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           ]

     

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           ++ lib.optionals withParmetis [

     

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             "--with-parmetis=1"

     

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

     

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           ]

     

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           ++ lib.optionals withPtscotch [

     

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             "--with-ptscotch=1"

     

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

     

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

     

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           ]

     

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           ++ lib.optionals withScalapack [

     

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             "--with-scalapack=1"

     

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

     

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           ]

     

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           ++ lib.optionals withMumps [

     

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             "--with-mumps=1"

     

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

     

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           ]

     

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           ++ lib.optionals withP4est [

     

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             "--with-p4est=1"

     

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             "--with-zlib-include=${zlib.dev}/include"

     

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             "--with-zlib-lib=-L${zlib}/lib -lz"

     

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           )

     

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         '' + lib.optionalString hdf5-support ''

     

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           configureFlagsArray+=(

     

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

     

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

     

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           ]

     

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           ++ lib.optionals withHdf5 [

     

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             "--with-hdf5=1"

     

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

     

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             "--with-hdf5-include=${hdf5.dev}/include"

     

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             "--with-hdf5-lib=-L${hdf5}/lib -lhdf5"

     

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           )

     

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         '';

     

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

     

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

     

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           ]

     

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           ++ lib.optionals petsc-optimized [

     

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             "--with-debugging=0"

     

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             "COPTFLAGS=-O3"

     

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             "FOPTFLAGS=-O3"

     

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             "CXXOPTFLAGS=-O3"

     

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             "CXXFLAGS=-O3"

     

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           ];

     

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

     

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           "fortify"

-9

pkgs/top-level/all-packages.nix

···

       17025
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       17026
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         ### SCIENCE/PROGRAMMING

     

       17027
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       17028
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       -
         ### SCIENCE/GEOLOGY

     

       17029
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         pflotran = callPackage ../by-name/pf/pflotran/package.nix {

     

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           petsc = petsc.override {

     

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             hdf5-support = true;

     

       17032
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             hdf5 = hdf5-fortran-mpi;

     

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             petsc-optimized = true;

     

       17034
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       -
           };

     

       17035
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       -
         };

     

       17036
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       -
       

     

       17037
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         ### SCIENCE/LOGIC

     

       17038
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       17039
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         abella = callPackage ../applications/science/logic/abella {

pkgs/top-level/python-packages.nix

···

       10348
       10348
        
       

     

       10349
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         pesq = callPackage ../development/python-modules/pesq { };

     

       10350
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       10351
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       +
         petsc4py = toPythonModule (pkgs.petsc.override {

     

       10352
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       +
           python3 = python;

     

       10353
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       +
           python3Packages = self;

     

       10354
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           withPetsc4py = true;

     

       10355
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           withFullDeps = true;

     

       10356
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       +
         });

     

       10357
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       +
       

     

       10351
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         pex = callPackage ../development/python-modules/pex { };

     

       10352
       10359
        
       

     

       10353
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         pexif = callPackage ../development/python-modules/pexif { };