Unverified Commit 23b9ffb1 authored by Markus Kowalewski's avatar Markus Kowalewski Committed by GitHub
Browse files

gromacs: 2024.5 -> 2025.0 (#382385)

parents ba752ffe 8bad41cc

pkgs/applications/science/molecular-dynamics/gromacs/default.nix

+99 −72
Original line number Diff line number Diff line 
{ lib

, stdenv

, fetchurl

, cmake

, hwloc

, fftw

, perl

, blas

, lapack

, llvmPackages

, mpi

, cudaPackages

, plumed

, singlePrec ? true

, config

, enableCuda ? config.cudaSupport

, enableMpi ? false

, enablePlumed ? false

, cpuAcceleration ? null

{

  lib,

  stdenv,

  fetchurl,

  cmake,

  hwloc,

  fftw,

  perl,

  blas,

  lapack,

  llvmPackages,

  mpi,

  cudaPackages,

  plumed,

  singlePrec ? true,

  config,

  enableCuda ? config.cudaSupport,

  enableMpi ? false,

  enablePlumed ? false,

  cpuAcceleration ? null,

}:





# CUDA is only implemented for single precission

assert enableCuda -> singlePrec;
@@ -30,11 +30,19 @@ let 
  # The possible values are defined in CMakeLists.txt:

  # AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256

  # AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD

  SIMD = x: if (cpuAcceleration != null) then x else

    if stdenv.hostPlatform.system == "i686-linux" then "SSE2" else

    if stdenv.hostPlatform.system == "x86_64-linux" then "SSE4.1" else

    if stdenv.hostPlatform.system == "x86_64-darwin" then "SSE4.1" else

    if stdenv.hostPlatform.system == "aarch64-linux" then "ARM_NEON_ASIMD" else

  SIMD =

    x:

    if (cpuAcceleration != null) then

      x

    else if stdenv.hostPlatform.system == "i686-linux" then

      "SSE2"

    else if stdenv.hostPlatform.system == "x86_64-linux" then

      "SSE4.1"

    else if stdenv.hostPlatform.system == "x86_64-darwin" then

      "SSE4.1"

    else if stdenv.hostPlatform.system == "aarch64-linux" then

      "ARM_NEON_ASIMD"

    else

      "None";



  source =
@@ -45,11 +53,12 @@ let 
      }

    else

      {

        version = "2024.5";

        hash = "sha256-/s8GsYbN25Qs+0LujaXz6yuZk+aswKLxjRSsCwFEJPM=";

        version = "2025.0";

        hash = "sha256-onrTWmRilbvsEpq+aE2dA9Hi4L12sNYl6QVXRqrvroI=";

      };



in stdenv.mkDerivation rec {

in

stdenv.mkDerivation rec {

  pname = "gromacs";

  version = source.version;
@@ -58,58 +67,73 @@ in stdenv.mkDerivation rec { 
    inherit (source) hash;

  };



  patches = [ ./pkgconfig.patch ];

  patches = [ (if enablePlumed then ./pkgconfig-2024.patch else ./pkgconfig-2025.patch) ];



  postPatch = lib.optionalString enablePlumed ''

    plumed patch -p -e gromacs-${source.version}

  '';



  outputs = [ "out" "dev" "man" ];

  outputs = [

    "out"

    "dev"

    "man"

  ];



  nativeBuildInputs =

    [ cmake ]

    ++ lib.optional enablePlumed plumed

    ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];



  buildInputs = [

  buildInputs =

    [

      fftw

      perl

      hwloc

      blas

      lapack

  ] ++ lib.optional enableMpi mpi

    ]

    ++ lib.optional enableMpi mpi

    ++ lib.optionals enableCuda [

      cudaPackages.cuda_cccl

      cudaPackages.cuda_cudart

      cudaPackages.libcufft

      cudaPackages.cuda_profiler_api

  ] ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;

    ]

    ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;



  propagatedBuildInputs = lib.optional enableMpi mpi;

  propagatedUserEnvPkgs = lib.optional enableMpi mpi;



  cmakeFlags = [

  cmakeFlags =

    [

      (lib.cmakeBool "GMX_HWLOC" true)

      "-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"

      "-DGMX_OPENMP:BOOL=TRUE"

      "-DBUILD_SHARED_LIBS=ON"

  ] ++ (

    if singlePrec then [

    ]

    ++ (

      if singlePrec then

        [

          "-DGMX_DOUBLE=OFF"

    ] else [

        ]

      else

        [

          "-DGMX_DOUBLE=ON"

          "-DGMX_DEFAULT_SUFFIX=OFF"

        ]

  ) ++ (

    if enableMpi

      then [

    )

    ++ (

      if enableMpi then

        [

          "-DGMX_MPI:BOOL=TRUE"

          "-DGMX_THREAD_MPI:BOOL=FALSE"

        ]

     else [

      else

        [

          "-DGMX_MPI:BOOL=FALSE"

        ]

  ) ++ lib.optionals enableCuda [

    )

    ++ lib.optionals enableCuda [

      "-DGMX_GPU=CUDA"

      (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString)
@@ -145,6 +169,9 @@ in stdenv.mkDerivation rec { 
      See: https://www.gromacs.org/about.html for details.

    '';

    platforms = platforms.unix;

    maintainers = with maintainers; [ sheepforce markuskowa ];

    maintainers = with maintainers; [

      sheepforce

      markuskowa

    ];

  };

}

pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig-2025.patch

0 → 100644
+36 −0
Original line number Diff line number Diff line 
diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in

index 646787cb53..d26e84de8f 100644

--- a/src/external/muparser/muparser.pc.in

+++ b/src/external/muparser/muparser.pc.in

@@ -1,11 +1,9 @@

-prefix=@CMAKE_INSTALL_PREFIX@

-exec_prefix=${prefix}

-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@

-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@

-

-Name: @PACKAGE_NAME@

-Description: Mathematical expressions parser library

-Version: @MUPARSER_VERSION@

-Requires:

-Libs: -L${libdir} -lmuparser

-Cflags: -I${includedir} @PKG_CONFIG_FLAGS@

+libdir=@CMAKE_INSTALL_FULL_LIBDIR@

+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@

+

+Name: @PACKAGE_NAME@

+Description: Mathematical expressions parser library

+Version: @MUPARSER_VERSION@

+Requires:

+Libs: -L${libdir} -lmuparser

+Cflags: -I${includedir} @PKG_CONFIG_FLAGS@

diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein

index af9b5a6dc0..5f58d549bf 100644

--- a/src/gromacs/libgromacs.pc.cmakein

+++ b/src/gromacs/libgromacs.pc.cmakein

@@ -1,5 +1,4 @@

-prefix=@CMAKE_INSTALL_PREFIX@

-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@

+libdir=@CMAKE_INSTALL_FULL_LIBDIR

 

 Name: libgromacs@GMX_LIBS_SUFFIX@

 Description: Gromacs library