Add gromacs
This commit is contained in:
parent
44cc60fcd8
commit
c4b74a7cd8
@ -59,6 +59,8 @@ let
|
|||||||
tampi = callPackage ./pkgs/tampi/default.nix { };
|
tampi = callPackage ./pkgs/tampi/default.nix { };
|
||||||
upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
|
upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
|
||||||
wxparaver = callPackage ./pkgs/paraver/default.nix { };
|
wxparaver = callPackage ./pkgs/paraver/default.nix { };
|
||||||
|
|
||||||
|
gromacs = callPackage ./pkgs/gromacs/default.nix { enableSYCL = true; };
|
||||||
};
|
};
|
||||||
|
|
||||||
tests = rec {
|
tests = rec {
|
||||||
|
|||||||
188
pkgs/gromacs/default.nix
Normal file
188
pkgs/gromacs/default.nix
Normal file
@ -0,0 +1,188 @@
|
|||||||
|
{
|
||||||
|
lib,
|
||||||
|
stdenv,
|
||||||
|
fetchurl,
|
||||||
|
cmake,
|
||||||
|
hwloc,
|
||||||
|
fftw,
|
||||||
|
perl,
|
||||||
|
blas,
|
||||||
|
lapack,
|
||||||
|
llvmPackages,
|
||||||
|
intelPackages ? null,
|
||||||
|
mpi,
|
||||||
|
cudaPackages,
|
||||||
|
plumed,
|
||||||
|
singlePrec ? true,
|
||||||
|
config,
|
||||||
|
enableSYCL ? false,
|
||||||
|
enableCuda ? config.cudaSupport,
|
||||||
|
enableMpi ? false,
|
||||||
|
enablePlumed ? false,
|
||||||
|
cpuAcceleration ? null,
|
||||||
|
}:
|
||||||
|
|
||||||
|
# CUDA is only implemented for single precission
|
||||||
|
assert enableCuda -> singlePrec;
|
||||||
|
|
||||||
|
assert !(enableSYCL && enableCuda);
|
||||||
|
|
||||||
|
assert enableSYCL -> intelPackages != null;
|
||||||
|
|
||||||
|
let
|
||||||
|
inherit (cudaPackages.flags) cmakeCudaArchitecturesString;
|
||||||
|
|
||||||
|
# Select reasonable defaults for all major platforms
|
||||||
|
# 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";
|
||||||
|
|
||||||
|
source =
|
||||||
|
if enablePlumed then
|
||||||
|
{
|
||||||
|
version = "2024.2";
|
||||||
|
hash = "sha256-gCp+M18uiVdw9XsVnk7DaOuw/yzm2sz3BsboAlw2hSs=";
|
||||||
|
}
|
||||||
|
else
|
||||||
|
{
|
||||||
|
version = "2025.3";
|
||||||
|
hash = "sha256-i9/KAmjz8Qp8o8BuWbYvc+oCQgxnIRwP85EvMteDPGU=";
|
||||||
|
};
|
||||||
|
|
||||||
|
stdenv' =
|
||||||
|
if enableSYCL then intelPackages.stdenv else stdenv;
|
||||||
|
|
||||||
|
in
|
||||||
|
stdenv'.mkDerivation rec {
|
||||||
|
pname = "gromacs";
|
||||||
|
version = source.version;
|
||||||
|
|
||||||
|
src = fetchurl {
|
||||||
|
url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz";
|
||||||
|
inherit (source) hash;
|
||||||
|
};
|
||||||
|
|
||||||
|
patches = [ (if enablePlumed then ./pkgconfig-2024.patch else ./pkgconfig-2025.patch) ];
|
||||||
|
|
||||||
|
postPatch = lib.optionalString enablePlumed ''
|
||||||
|
plumed patch -p -e gromacs-${source.version}
|
||||||
|
'';
|
||||||
|
|
||||||
|
outputs = [
|
||||||
|
"out"
|
||||||
|
"dev"
|
||||||
|
"man"
|
||||||
|
];
|
||||||
|
|
||||||
|
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;
|
||||||
|
|
||||||
|
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"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
++ (
|
||||||
|
if enableMpi then
|
||||||
|
[
|
||||||
|
"-DGMX_MPI:BOOL=TRUE"
|
||||||
|
"-DGMX_THREAD_MPI:BOOL=FALSE"
|
||||||
|
]
|
||||||
|
else
|
||||||
|
[
|
||||||
|
"-DGMX_MPI:BOOL=FALSE"
|
||||||
|
]
|
||||||
|
)
|
||||||
|
++ (lib.optionals enableSYCL [
|
||||||
|
"-DGMX_GPU=SYCL"
|
||||||
|
])
|
||||||
|
++ 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)
|
||||||
|
];
|
||||||
|
|
||||||
|
postInstall = ''
|
||||||
|
moveToOutput share/cmake $dev
|
||||||
|
'';
|
||||||
|
|
||||||
|
meta = with lib; {
|
||||||
|
homepage = "https://www.gromacs.org";
|
||||||
|
license = licenses.lgpl21Plus;
|
||||||
|
description = "Molecular dynamics software package";
|
||||||
|
longDescription = ''
|
||||||
|
GROMACS is a versatile package to perform molecular dynamics,
|
||||||
|
i.e. simulate the Newtonian equations of motion for systems
|
||||||
|
with hundreds to millions of particles.
|
||||||
|
|
||||||
|
It is primarily designed for biochemical molecules like
|
||||||
|
proteins, lipids and nucleic acids that have a lot of
|
||||||
|
complicated bonded interactions, but since GROMACS is
|
||||||
|
extremely fast at calculating the nonbonded interactions (that
|
||||||
|
usually dominate simulations) many groups are also using it
|
||||||
|
for research on non-biological systems, e.g. polymers.
|
||||||
|
|
||||||
|
GROMACS supports all the usual algorithms you expect from a
|
||||||
|
modern molecular dynamics implementation, (check the online
|
||||||
|
reference or manual for details), but there are also quite a
|
||||||
|
few features that make it stand out from the competition.
|
||||||
|
|
||||||
|
See: https://www.gromacs.org/about.html for details.
|
||||||
|
'';
|
||||||
|
platforms = platforms.unix;
|
||||||
|
maintainers = with maintainers; [
|
||||||
|
sheepforce
|
||||||
|
markuskowa
|
||||||
|
];
|
||||||
|
};
|
||||||
|
}
|
||||||
24
pkgs/gromacs/pkgconfig-2024.patch
Normal file
24
pkgs/gromacs/pkgconfig-2024.patch
Normal file
@ -0,0 +1,24 @@
|
|||||||
|
diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
|
||||||
|
index 646787cb53..9b97ad57f7 100644
|
||||||
|
--- a/src/external/muparser/muparser.pc.in
|
||||||
|
+++ b/src/external/muparser/muparser.pc.in
|
||||||
|
@@ -1,7 +1,5 @@
|
||||||
|
-prefix=@CMAKE_INSTALL_PREFIX@
|
||||||
|
-exec_prefix=${prefix}
|
||||||
|
-libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
|
||||||
|
-includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
|
||||||
|
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
|
||||||
|
+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
|
||||||
|
|
||||||
|
Name: @PACKAGE_NAME@
|
||||||
|
Description: Mathematical expressions parser library
|
||||||
|
diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
|
||||||
|
index ec1ed6684e..ca1105474a 100644
|
||||||
|
--- a/src/gromacs/libgromacs.pc.cmakein
|
||||||
|
+++ b/src/gromacs/libgromacs.pc.cmakein
|
||||||
|
@@ -1,4 +1,4 @@
|
||||||
|
-libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@
|
||||||
|
+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
|
||||||
|
|
||||||
|
Name: libgromacs@GMX_LIBS_SUFFIX@
|
||||||
|
Description: Gromacs library
|
||||||
36
pkgs/gromacs/pkgconfig-2025.patch
Normal file
36
pkgs/gromacs/pkgconfig-2025.patch
Normal 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
|
||||||
Loading…
x
Reference in New Issue
Block a user