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# 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('2020.3', 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('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('rdtscp', default=True,
description='Enable RDTSCP instruction usage')
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')
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', when='~cuda')
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')
# 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)
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:
options.append('-DGMX_GPU:BOOL=ON')
options.append('-DCUDA_TOOLKIT_ROOT_DIR:STRING=' +
self.spec['cuda'].prefix)
else:
options.append('-DGMX_GPU:BOOL=OFF')
# Activate SIMD based on properties of the target
target = self.spec.target
if target >= llnl.util.cpu.targets['bulldozer']:
# AMD Family 15h
options.append('-DGMX_SIMD=AVX_128_FMA')
elif target >= llnl.util.cpu.targets['zen']:
# AMD Family 17h
options.append('-DGMX_SIMD=AVX2_128')
elif target >= llnl.util.cpu.targets['power7']:
# IBM Power 7 and beyond
options.append('-DGMX_SIMD=IBM_VSX')
elif target.family == llnl.util.cpu.targets['aarch64']:
# ARMv8
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'),
]
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')
if '-rdtscp' in self.spec:
options.append('-DGMX_USE_RDTSCP:BOOL=OFF')
else:
options.append('-DGMX_USE_RDTSCP:BOOL=ON')
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
|
