# 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