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
|
# 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 platform
import sys
import os
from spack import *
import llnl.util.tty as tty
class Namd(MakefilePackage):
"""NAMDis a parallel molecular dynamics code designed for
high-performance simulation of large biomolecular systems."""
homepage = "http://www.ks.uiuc.edu/Research/namd/"
url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd())
git = "https://charm.cs.illinois.edu/gerrit/namd.git"
manual_download = True
version("master", branch="master")
version('2.15a1', branch="master", tag='release-2-15-alpha-1')
version('2.14', sha256='34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235',
preferred=True)
version('2.13', '9e3323ed856e36e34d5c17a7b0341e38')
version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9')
variant('fftw', default='3', values=('none', '2', '3', 'mkl'),
description='Enable the use of FFTW/FFTW3/MKL FFT')
variant('interface', default='none', values=('none', 'tcl', 'python'),
description='Enables TCL and/or python interface')
# init_tcl_pointers() declaration and implementation are inconsistent
# "src/colvarproxy_namd.C", line 482: error: inherited member is not
# allowed
patch('inherited-member.patch', when='@:2.13')
patch('inherited-member-2.14.patch', when='@2.14:')
depends_on('charmpp@6.10.1:', when="@2.14:")
depends_on('charmpp@6.8.2', when="@2.13")
depends_on('charmpp@6.7.1', when="@2.12")
depends_on('fftw@:2.99', when="fftw=2")
depends_on('fftw@3:', when="fftw=3")
depends_on('intel-mkl', when="fftw=mkl")
depends_on('tcl', when='interface=tcl')
depends_on('tcl', when='interface=python')
depends_on('python', when='interface=python')
def _copy_arch_file(self, lib):
config_filename = 'arch/{0}.{1}'.format(self.arch, lib)
copy('arch/Linux-x86_64.{0}'.format(lib),
config_filename)
if lib == 'tcl':
filter_file(r'-ltcl8\.5',
'-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)),
config_filename)
def _append_option(self, opts, lib):
if lib != 'python':
self._copy_arch_file(lib)
spec = self.spec
opts.extend([
'--with-{0}'.format(lib),
'--{0}-prefix'.format(lib), spec[lib].prefix
])
@property
def arch(self):
plat = sys.platform
if plat.startswith("linux"):
plat = "linux"
march = platform.machine()
return '{0}-{1}'.format(plat, march)
@property
def build_directory(self):
return '{0}-spack'.format(self.arch)
def _edit_arch_generic(self, spec, prefix):
"""Generic arch makefile generation"""
m64 = '-m64 ' if not spec.satisfies('arch=aarch64:') else ''
with working_dir('arch'):
with open('{0}.arch'.format(self.build_directory), 'w') as fh:
# this options are take from the default provided
# configuration files
# https://github.com/UIUC-PPL/charm/pull/2778
archopt = spec.target.optimization_flags(
spec.compiler.name, spec.compiler.version)
if self.spec.satisfies('^charmpp@:6.10.1'):
optims_opts = {
'gcc': m64 + '-O3 -fexpensive-optimizations \
-ffast-math -lpthread ' + archopt,
'intel': '-O2 -ip -qopenmp-simd' + archopt}
else:
optims_opts = {
'gcc': m64 + '-O3 -fexpensive-optimizations \
-ffast-math ' + archopt,
'intel': '-O2 -ip ' + archopt}
optim_opts = optims_opts[self.compiler.name] \
if self.compiler.name in optims_opts else ''
fh.write('\n'.join([
'NAMD_ARCH = {0}'.format(self.arch),
'CHARMARCH = {0}'.format(self.spec['charmpp'].charmarch),
'CXX = {0.cxx} {0.cxx11_flag}'.format(
self.compiler),
'CXXOPTS = {0}'.format(optim_opts),
'CC = {0}'.format(self.compiler.cc),
'COPTS = {0}'.format(optim_opts),
''
]))
def _edit_arch_target_based(self, spec, prefix):
"""Try to use target base arch file return True if succeed"""
if spec.version < Version("2.14"):
return False
found_special_opt = False
with working_dir('arch'):
arch_filename = '{0}.arch'.format(self.build_directory)
replace = [
[
r"^CHARMARCH = .*$",
'CHARMARCH = {0}'.format(self.spec['charmpp'].charmarch)
],
[
r"^NAMD_ARCH = .*$",
'NAMD_ARCH = {0}'.format(self.arch)
]
]
# Optimizations for skylake_avx512
if spec.platform == "linux" and \
self.compiler.name == "intel" and \
'avx512' in spec.target and \
spec.target >= 'skylake_avx512':
if spec.version >= Version("2.15") and \
os.path.exists("Linux-AVX512-icc.arch"):
tty.info("Building binaries with AVX512-tile optimization")
copy("Linux-AVX512-icc.arch", arch_filename)
elif spec.version >= Version("2.14") and \
os.path.exists("Linux-SKX-icc.arch"):
tty.info("Building binaries with Skylake-X"
"AVX512 optimization")
copy("Linux-SKX-icc.arch", arch_filename)
else:
return False
replace.append([
r"^CXX = icpc",
'CXX = {0}'.format(self.compiler.cxx)
])
replace.append([
r"^CC = icc",
'CC = {0}'.format(self.compiler.cc)
])
found_special_opt = True
if found_special_opt:
for pattern, replacement in replace:
filter_file(pattern, replacement, arch_filename)
return found_special_opt
def _edit_arch(self, spec, prefix):
"""Try to use target base arch file, if not make generic"""
if not self._edit_arch_target_based(spec, prefix):
self._edit_arch_generic(spec, prefix)
def edit(self, spec, prefix):
self._edit_arch(spec, prefix)
self._copy_arch_file('base')
opts = ['--charm-base', spec['charmpp'].prefix]
fftw_version = spec.variants['fftw'].value
if fftw_version == 'none':
opts.append('--without-fftw')
elif fftw_version == 'mkl':
self._append_option(opts, 'mkl')
else:
_fftw = 'fftw{0}'.format('' if fftw_version == '2' else '3')
self._copy_arch_file(_fftw)
opts.extend(['--with-{0}'.format(_fftw),
'--fftw-prefix', spec['fftw'].prefix])
interface_type = spec.variants['interface'].value
if interface_type != 'none':
self._append_option(opts, 'tcl')
if interface_type == 'python':
self._append_option(opts, 'python')
else:
opts.extend([
'--without-tcl',
'--without-python'
])
config = Executable('./config')
config(self.build_directory, *opts)
# patch Make.config if needed
# spack install charmpp straight to prefix
# (not to $(CHARMBASE)/$(CHARMARCH))
if not os.path.exists(join_path(
self.spec['charmpp'].prefix, self.spec['charmpp'].charmarch)):
filter_file(r"^CHARM = \$\(CHARMBASE\)/\$\(CHARMARCH\)",
"CHARM = $(CHARMBASE)",
join_path(self.build_directory, "Make.config"))
def install(self, spec, prefix):
with working_dir(self.build_directory):
mkdirp(prefix.bin)
install('namd2', prefix.bin)
# I'm not sure this is a good idea or if an autoload of the charm
# module would not be better.
install('charmrun', prefix.bin)
|