1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
{ lib, stdenv, fetchurl, cmake, hwloc, fftw, perl, blas, lapack, mpi, cudatoolkit
, singlePrec ? true
, config
, enableMpi ? false
, enableCuda ? config.cudaSupport
, cpuAcceleration ? null
}:
let
# 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";
in stdenv.mkDerivation rec {
pname = "gromacs";
version = "2023.3";
src = fetchurl {
url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz";
sha256 = "sha256-Tsj40MevdrE/j9FtuOLBIOdJ3kOa6VVNn2U/gS140cs=";
};
patches = [ ./pkgconfig.patch ];
outputs = [ "out" "dev" "man" ];
nativeBuildInputs = [ cmake ];
buildInputs = [
fftw
perl
hwloc
blas
lapack
] ++ lib.optional enableMpi mpi
++ lib.optional enableCuda cudatoolkit
;
propagatedBuildInputs = lib.optional enableMpi mpi;
propagatedUserEnvPkgs = lib.optional enableMpi mpi;
cmakeFlags = [
"-DGMX_SIMD:STRING=${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.optional enableCuda "-DGMX_GPU=CUDA";
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 ];
};
}
|