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
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
|
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import llnl.util.cpu
class Gromacs(CMakePackage):
"""GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
dynamics package primarily designed for simulations of proteins, lipids
and nucleic acids. It was originally developed in the Biophysical
Chemistry department of University of Groningen, and is now maintained
by contributors in universities and research centers across the world.
GROMACS is one of the fastest and most popular software packages
available and can run on CPUs as well as GPUs. It is free, open source
released under the GNU General Public License. Starting from version 4.6,
GROMACS is released under the GNU Lesser General Public License.
"""
homepage = 'http://www.gromacs.org'
url = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
git = 'https://github.com/gromacs/gromacs.git'
maintainers = ['junghans', 'marvinbernhardt']
version('master', branch='master')
version('2020.4', sha256='5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6')
version('2020.3', sha256='903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9')
version('2020.2', sha256='7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3')
version('2020.1', sha256='e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf')
version('2020', sha256='477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01')
version('2019.6', sha256='bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358')
version('2019.5', sha256='438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a')
version('2019.4', sha256='ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867')
version('2019.3', sha256='4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573')
version('2019.2', sha256='bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e')
version('2019.1', sha256='b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec')
version('2019', sha256='c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b')
version('2018.8', sha256='776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf')
version('2018.5', sha256='32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8')
version('2018.4', sha256='6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891')
version('2018.3', sha256='4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291')
version('2018.2', sha256='4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857')
version('2018.1', sha256='4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd')
version('2018', sha256='deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9')
version('2016.6', sha256='bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7')
version('2016.5', sha256='57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c')
version('2016.4', sha256='4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264')
version('2016.3', sha256='7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27')
version('5.1.5', sha256='c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e')
version('5.1.4', sha256='0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc')
version('5.1.2', sha256='39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304')
version('4.5.5', sha256='e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba')
variant('mpi', default=True, description='Activate MPI support')
variant('shared', default=True,
description='Enables the build of shared libraries')
variant(
'double', default=False,
description='Produces a double precision version of the executables')
variant('plumed', default=False, description='Enable PLUMED support')
variant('cuda', default=False, description='Enable CUDA support')
variant('opencl', default=False, description='Enable OpenCL support')
variant('nosuffix', default=False, description='Disable default suffixes')
variant('build_type', default='RelWithDebInfo',
description='The build type to build',
values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel',
'Reference', 'RelWithAssert', 'Profile'))
variant('mdrun_only', default=False,
description='Enables the build of a cut-down version'
' of libgromacs and/or the mdrun program')
variant('openmp', default=True,
description='Enables OpenMP at configure time')
variant('double_precision', default=False,
description='GMX_RELAXED_DOUBLE_PRECISION for Fujitsu PRIMEHPC')
variant('hwloc', default=True,
description='Use the hwloc portable hardware locality library')
variant('lapack', default=False,
description='Enables an external LAPACK library')
depends_on('mpi', when='+mpi')
# define matching plumed versions
depends_on('plumed@2.6.0:2.6.9+mpi', when='@2020.2+plumed+mpi')
depends_on('plumed@2.6.0:2.6.9~mpi', when='@2020.2+plumed~mpi')
depends_on('plumed@2.6.0:2.6.9+mpi', when='@2019.6+plumed+mpi')
depends_on('plumed@2.6.0:2.6.9~mpi', when='@2019.6+plumed~mpi')
depends_on('plumed@2.5.0:2.5.9+mpi', when='@2019.4+plumed+mpi')
depends_on('plumed@2.5.0:2.5.9~mpi', when='@2019.4+plumed~mpi')
depends_on('plumed@2.5.0:2.5.9+mpi', when='@2018.6+plumed+mpi')
depends_on('plumed@2.5.0:2.5.9~mpi', when='@2018.6+plumed~mpi')
depends_on('plumed+mpi', when='+plumed+mpi')
depends_on('plumed~mpi', when='+plumed~mpi')
depends_on('fftw-api@3')
depends_on('mkl', when='fft=mkl')
depends_on('cmake@2.8.8:3.99.99', type='build')
depends_on('cmake@3.4.3:3.99.99', type='build', when='@2018:')
depends_on('cmake@3.13.0:3.99.99', type='build', when='@master')
depends_on('cmake@3.13.0:3.99.99', type='build', when='%fj')
depends_on('cuda', when='+cuda')
depends_on('lapack', when='+lapack')
# TODO: openmpi constraint; remove when concretizer is fixed
depends_on('hwloc@:1.999', when='+hwloc')
patch('gmxDetectCpu-cmake-3.14.patch', when='@2018:2019.3^cmake@3.14.0:')
patch('gmxDetectSimd-cmake-3.14.patch', when='@:2017.99^cmake@3.14.0:')
def patch(self):
if '+plumed' in self.spec:
self.spec['plumed'].package.apply_patch(self)
if self.spec.satisfies('%nvhpc'):
# Disable obsolete workaround
filter_file('ifdef __PGI', 'if 0', 'src/gromacs/fileio/xdrf.h')
def cmake_args(self):
options = []
if self.spec.satisfies('@2020:'):
options.append('-DGMX_INSTALL_LEGACY_API=ON')
if '+mpi' in self.spec:
options.append('-DGMX_MPI:BOOL=ON')
if '+double' in self.spec:
options.append('-DGMX_DOUBLE:BOOL=ON')
if '+nosuffix' in self.spec:
options.append('-DGMX_DEFAULT_SUFFIX:BOOL=OFF')
if '~shared' in self.spec:
options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
if '+hwloc' in self.spec:
options.append('-DGMX_HWLOC:BOOL=ON')
else:
options.append('-DGMX_HWLOC:BOOL=OFF')
if '+cuda' in self.spec or '+opencl' in self.spec:
options.append('-DGMX_GPU:BOOL=ON')
else:
options.append('-DGMX_GPU:BOOL=OFF')
if '+cuda' in self.spec:
options.append('-DCUDA_TOOLKIT_ROOT_DIR:STRING=' +
self.spec['cuda'].prefix)
if '+opencl' in self.spec:
options.append('-DGMX_USE_OPENCL=on')
if '+lapack' in self.spec:
options.append('-DGMX_EXTERNAL_LAPACK:BOOL=ON')
if self.spec['lapack'].libs:
options.append('-DLAPACK_LIBRARIES={0}'.format(
self.spec['lapack'].libs.joined(';')))
else:
options.append('-DGMX_EXTERNAL_LAPACK:BOOL=OFF')
# Activate SIMD based on properties of the target
target = self.spec.target
if target >= llnl.util.cpu.targets['zen2']:
# AMD Family 17h (EPYC Rome)
options.append('-DGMX_SIMD=AVX2_256')
elif target >= llnl.util.cpu.targets['zen']:
# AMD Family 17h (EPYC Naples)
options.append('-DGMX_SIMD=AVX2_128')
elif target >= llnl.util.cpu.targets['bulldozer']:
# AMD Family 15h
options.append('-DGMX_SIMD=AVX_128_FMA')
elif 'vsx' in target:
# IBM Power 7 and beyond
options.append('-DGMX_SIMD=IBM_VSX')
elif target.family == llnl.util.cpu.targets['aarch64']:
# ARMv8
if self.spec.satisfies('%nvhpc'):
options.append('-DGMX_SIMD=None')
else:
options.append('-DGMX_SIMD=ARM_NEON_ASIMD')
elif target == llnl.util.cpu.targets['mic_knl']:
# Intel KNL
options.append('-DGMX_SIMD=AVX_512_KNL')
elif target.vendor == 'GenuineIntel':
# Other Intel architectures
simd_features = [
('sse2', 'SSE2'),
('sse4_1', 'SSE4.1'),
('avx', 'AVX_256'),
('axv128', 'AVX2_128'),
('avx2', 'AVX2_256'),
('avx512', 'AVX_512'),
]
# Workaround NVIDIA compiler bug when avx512 is enabled
if (self.spec.satisfies('%nvhpc') and
('avx512', 'AVX_512') in simd_features):
simd_features.remove(('avx512', 'AVX_512'))
for feature, flag in reversed(simd_features):
if feature in target:
options.append('-DGMX_SIMD:STRING={0}'.format(flag))
break
else:
# Fall back to this for unknown microarchitectures
options.append('-DGMX_SIMD:STRING=None')
# Use the 'rtdscp' assembly instruction only on
# appropriate architectures
options.append(self.define(
'GMX_USE_RDTSCP', str(target.family) in ('x86_64', 'x86')
))
if '+mdrun_only' in self.spec:
options.append('-DGMX_BUILD_MDRUN_ONLY:BOOL=ON')
else:
options.append('-DGMX_BUILD_MDRUN_ONLY:BOOL=OFF')
if '~openmp' in self.spec:
options.append('-DGMX_OPENMP:BOOL=OFF')
else:
options.append('-DGMX_OPENMP:BOOL=ON')
if '+double_precision' in self.spec:
options.append('-DGMX_RELAXED_DOUBLE_PRECISION:BOOL=ON')
else:
options.append('-DGMX_RELAXED_DOUBLE_PRECISION:BOOL=OFF')
if '^mkl' in self.spec:
# fftw-api@3 is provided by intel-mkl or intel-parllel-studio
# we use the mkl interface of gromacs
options.append('-DGMX_FFT_LIBRARY=mkl')
options.append('-DMKL_INCLUDE_DIR={0}'.
format(self.spec['mkl'].headers.directories[0]))
# The 'blas' property provides a minimal set of libraries
# that is sufficient for fft. Using full mkl fails the cmake test
options.append('-DMKL_LIBRARIES={0}'.
format(self.spec['blas'].libs.joined(';')))
else:
# we rely on the fftw-api@3
options.append('-DGMX_FFT_LIBRARY=fftw3')
return options
|