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gromacs: 2024.5 -> 2025.0 (#382385)

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This commit is contained in:
Markus Kowalewski
2025-02-17 11:01:06 +01:00
committed by GitHub
parent ba752ffe4f 8bad41cc0f
commit 23b9ffb1e4
3 changed files with 134 additions and 71 deletions
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pkgs/applications/science/molecular-dynamics/gromacs/default.nix
+98 -71
View File
@@ -1,25 +1,25 @@
{ 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;
@@ -30,12 +30,20 @@ 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
"None";
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 =
if enablePlumed then
@@ -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;
@@ -58,64 +67,79 @@ 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-${source.version}
'';
outputs = [ "out" "dev" "man" ];
outputs = [
"out"
"dev"
"man"
];
nativeBuildInputs =
[ cmake ]
++ lib.optional enablePlumed plumed
++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
buildInputs = [
fftw
perl
hwloc
blas
lapack
] ++ lib.optional enableMpi mpi
++ lib.optionals enableCuda [
cudaPackages.cuda_cccl
cudaPackages.cuda_cudart
cudaPackages.libcufft
cudaPackages.cuda_profiler_api
] ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;
buildInputs =
[
fftw
perl
hwloc
blas
lapack
]
++ lib.optional enableMpi mpi
++ lib.optionals enableCuda [
cudaPackages.cuda_cccl
cudaPackages.cuda_cudart
cudaPackages.libcufft
cudaPackages.cuda_profiler_api
]
++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;
propagatedBuildInputs = lib.optional enableMpi mpi;
propagatedUserEnvPkgs = lib.optional enableMpi mpi;
cmakeFlags = [
(lib.cmakeBool "GMX_HWLOC" true)
"-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"
"-DGMX_OPENMP:BOOL=TRUE"
"-DBUILD_SHARED_LIBS=ON"
] ++ (
if singlePrec then [
"-DGMX_DOUBLE=OFF"
] else [
"-DGMX_DOUBLE=ON"
"-DGMX_DEFAULT_SUFFIX=OFF"
cmakeFlags =
[
(lib.cmakeBool "GMX_HWLOC" true)
"-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"
"-DGMX_OPENMP:BOOL=TRUE"
"-DBUILD_SHARED_LIBS=ON"
]
) ++ (
if enableMpi
then [
"-DGMX_MPI:BOOL=TRUE"
"-DGMX_THREAD_MPI:BOOL=FALSE"
]
else [
"-DGMX_MPI:BOOL=FALSE"
]
) ++ lib.optionals enableCuda [
"-DGMX_GPU=CUDA"
(lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString)
++ (
if singlePrec then
[
"-DGMX_DOUBLE=OFF"
]
else
[
"-DGMX_DOUBLE=ON"
"-DGMX_DEFAULT_SUFFIX=OFF"
]
)
++ (
if enableMpi then
[
"-DGMX_MPI:BOOL=TRUE"
"-DGMX_THREAD_MPI:BOOL=FALSE"
]
else
[
"-DGMX_MPI:BOOL=FALSE"
]
)
++ lib.optionals enableCuda [
"-DGMX_GPU=CUDA"
(lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString)
# Gromacs seems to ignore and override the normal variables, so we add this ad hoc:
(lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" cmakeCudaArchitecturesString)
];
# Gromacs seems to ignore and override the normal variables, so we add this ad hoc:
(lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" cmakeCudaArchitecturesString)
];
postInstall = ''
moveToOutput share/cmake $dev
@@ -145,6 +169,9 @@ in stdenv.mkDerivation rec {
See: https://www.gromacs.org/about.html for details.
'';
platforms = platforms.unix;
maintainers = with maintainers; [ sheepforce markuskowa ];
maintainers = with maintainers; [
sheepforce
markuskowa
];
};
}
pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig.patch → pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig-2024.patch
View File
pkgs/applications/science/molecular-dynamics/gromacs/pkgconfig-2025.patch
+36
View File
@@ -0,0 +1,36 @@
diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
index 646787cb53..d26e84de8f 100644
--- a/src/external/muparser/muparser.pc.in
+++ b/src/external/muparser/muparser.pc.in
@@ -1,11 +1,9 @@
-prefix=@CMAKE_INSTALL_PREFIX@
-exec_prefix=${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