9414b11490
* Clarify relaxed double precision option This is only intended for use on the Fujitsu PRIMEHPC platform * Fix typo * Shorten line to keep linter happy
287 lines
13 KiB
Python
287 lines
13 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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class Gromacs(CMakePackage):
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"""GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
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dynamics package primarily designed for simulations of proteins, lipids
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and nucleic acids. It was originally developed in the Biophysical
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Chemistry department of University of Groningen, and is now maintained
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by contributors in universities and research centers across the world.
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GROMACS is one of the fastest and most popular software packages
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available and can run on CPUs as well as GPUs. It is free, open source
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released under the GNU General Public License. Starting from version 4.6,
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GROMACS is released under the GNU Lesser General Public License.
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"""
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homepage = 'http://www.gromacs.org'
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url = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
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git = 'https://github.com/gromacs/gromacs.git'
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maintainers = ['junghans', 'marvinbernhardt']
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version('master', branch='master')
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version('2021', sha256='efa78ab8409b0f5bf0fbca174fb8fbcf012815326b5c71a9d7c385cde9a8f87b')
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version('2020.5', sha256='7b6aff647f7c8ee1bf12204d02cef7c55f44402a73195bd5f42cf11850616478')
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version('2020.4', sha256='5519690321b5500c7951aaf53ff624042c3edd1a5f5d6dd1f2d802a3ecdbf4e6')
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version('2020.3', sha256='903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9')
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version('2020.2', sha256='7465e4cd616359d84489d919ec9e4b1aaf51f0a4296e693c249e83411b7bd2f3')
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version('2020.1', sha256='e1666558831a3951c02b81000842223698016922806a8ce152e8f616e29899cf')
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version('2020', sha256='477e56142b3dcd9cb61b8f67b24a55760b04d1655e8684f979a75a5eec40ba01')
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version('2019.6', sha256='bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358')
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version('2019.5', sha256='438061a4a2d45bbb5cf5c3aadd6c6df32d2d77ce8c715f1c8ffe56156994083a')
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version('2019.4', sha256='ba4366eedfc8a1dbf6bddcef190be8cd75de53691133f305a7f9c296e5ca1867')
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version('2019.3', sha256='4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573')
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version('2019.2', sha256='bcbf5cc071926bc67baa5be6fb04f0986a2b107e1573e15fadcb7d7fc4fb9f7e')
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version('2019.1', sha256='b2c37ed2fcd0e64c4efcabdc8ee581143986527192e6e647a197c76d9c4583ec')
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version('2019', sha256='c5b281a5f0b5b4eeb1f4c7d4dc72f96985b566561ca28acc9c7c16f6ee110d0b')
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version('2018.8', sha256='776923415df4bc78869d7f387c834141fdcda930b2e75be979dc59ecfa6ebecf')
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version('2018.5', sha256='32261df6f7ec4149fc0508f9af416953d056e281590359838c1ed6644ba097b8')
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version('2018.4', sha256='6f2ee458c730994a8549d6b4f601ecfc9432731462f8bd4ffa35d330d9aaa891')
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version('2018.3', sha256='4423a49224972969c52af7b1f151579cea6ab52148d8d7cbae28c183520aa291')
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version('2018.2', sha256='4bdde8120c510b6543afb4b18f82551fddb11851f7edbd814aa24022c5d37857')
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version('2018.1', sha256='4d3533340499323fece83b4a2d4251fa856376f2426c541e00b8e6b4c0d705cd')
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version('2018', sha256='deb5d0b749a52a0c6083367b5f50a99e08003208d81954fb49e7009e1b1fd0e9')
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version('2016.6', sha256='bac0117d2cad21f9b94fe5b854fb9ae7435b098a6da4e732ee745f18e52473d7')
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version('2016.5', sha256='57db26c6d9af84710a1e0c47a1f5bf63a22641456448dcd2eeb556ebd14e0b7c')
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version('2016.4', sha256='4be9d3bfda0bdf3b5c53041e0b8344f7d22b75128759d9bfa9442fe65c289264')
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version('2016.3', sha256='7bf00e74a9d38b7cef9356141d20e4ba9387289cbbfd4d11be479ef932d77d27')
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version('5.1.5', sha256='c25266abf07690ecad16ed3996899b1d489cbb1ef733a1befb3b5c75c91a703e')
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version('5.1.4', sha256='0f3793d8f1f0be747cf9ebb0b588fb2b2b5dc5acc32c3046a7bee2d2c03437bc')
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version('5.1.2', sha256='39d6f1d7ae8ba38cea6089da40676bfa4049a49903d21551abc030992a58f304')
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version('4.5.5', sha256='e0605e4810b0d552a8761fef5540c545beeaf85893f4a6e21df9905a33f871ba')
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variant('mpi', default=True, description='Activate MPI support')
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variant('shared', default=True,
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description='Enables the build of shared libraries')
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variant(
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'double', default=False,
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description='Produces a double precision version of the executables')
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variant('plumed', default=False, description='Enable PLUMED support')
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variant('cuda', default=False, description='Enable CUDA support')
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variant('opencl', default=False, description='Enable OpenCL support')
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variant('sycl', default=False, description='Enable SYCL support')
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variant('nosuffix', default=False, description='Disable default suffixes')
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variant('build_type', default='RelWithDebInfo',
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description='The build type to build',
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values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel',
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'Reference', 'RelWithAssert', 'Profile'))
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variant('mdrun_only', default=False,
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description='Enables the build of a cut-down version'
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' of libgromacs and/or the mdrun program')
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variant('openmp', default=True,
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description='Enables OpenMP at configure time')
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variant('relaxed_double_precision', default=False,
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description='GMX_RELAXED_DOUBLE_PRECISION, use only for Fujitsu PRIMEHPC')
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variant('hwloc', default=True,
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description='Use the hwloc portable hardware locality library')
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variant('lapack', default=False,
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description='Enables an external LAPACK library')
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variant('blas', default=False,
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description='Enables an external BLAS library')
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variant('cycle_subcounters', default=False,
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description='Enables cycle subcounters')
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depends_on('mpi', when='+mpi')
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# define matching plumed versions
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depends_on('plumed@2.6.0:2.6.9+mpi', when='@2020.2+plumed+mpi')
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depends_on('plumed@2.6.0:2.6.9~mpi', when='@2020.2+plumed~mpi')
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depends_on('plumed@2.6.0:2.6.9+mpi', when='@2019.6+plumed+mpi')
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depends_on('plumed@2.6.0:2.6.9~mpi', when='@2019.6+plumed~mpi')
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depends_on('plumed@2.5.0:2.5.9+mpi', when='@2019.4+plumed+mpi')
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depends_on('plumed@2.5.0:2.5.9~mpi', when='@2019.4+plumed~mpi')
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depends_on('plumed@2.5.0:2.5.9+mpi', when='@2018.6+plumed+mpi')
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depends_on('plumed@2.5.0:2.5.9~mpi', when='@2018.6+plumed~mpi')
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depends_on('plumed+mpi', when='+plumed+mpi')
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depends_on('plumed~mpi', when='+plumed~mpi')
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depends_on('fftw-api@3')
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depends_on('cmake@2.8.8:3.99.99', type='build')
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depends_on('cmake@3.4.3:3.99.99', type='build', when='@2018:')
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depends_on('cmake@3.13.0:3.99.99', type='build', when='@master')
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depends_on('cmake@3.13.0:3.99.99', type='build', when='%fj')
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depends_on('cuda', when='+cuda')
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depends_on('sycl', when='+sycl')
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depends_on('lapack', when='+lapack')
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depends_on('blas', when='+blas')
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depends_on('hwloc', when='+hwloc')
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patch('gmxDetectCpu-cmake-3.14.patch', when='@2018:2019.3^cmake@3.14.0:')
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patch('gmxDetectSimd-cmake-3.14.patch', when='@:2017.99^cmake@3.14.0:')
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def patch(self):
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if '+plumed' in self.spec:
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self.spec['plumed'].package.apply_patch(self)
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if self.spec.satisfies('%nvhpc'):
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# Disable obsolete workaround
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filter_file('ifdef __PGI', 'if 0', 'src/gromacs/fileio/xdrf.h')
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def cmake_args(self):
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options = []
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if self.spec.satisfies('@2020:'):
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options.append('-DGMX_INSTALL_LEGACY_API=ON')
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if '+mpi' in self.spec:
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options.append('-DGMX_MPI:BOOL=ON')
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# Ensures gmxapi builds properly
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options.extend([
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'-DCMAKE_C_COMPILER=%s' % self.spec['mpi'].mpicc,
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'-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx,
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'-DCMAKE_Fortran_COMPILER=%s' % self.spec['mpi'].mpifc,
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])
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if '+double' in self.spec:
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options.append('-DGMX_DOUBLE:BOOL=ON')
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if '+nosuffix' in self.spec:
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options.append('-DGMX_DEFAULT_SUFFIX:BOOL=OFF')
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if '~shared' in self.spec:
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options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
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options.append('-DGMXAPI:BOOL=OFF')
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if '+hwloc' in self.spec:
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options.append('-DGMX_HWLOC:BOOL=ON')
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else:
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options.append('-DGMX_HWLOC:BOOL=OFF')
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if self.version >= Version('2021'):
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if '+cuda' in self.spec:
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options.append('-DGMX_GPU:STRING=CUDA')
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elif '+opencl' in self.spec:
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options.append('-DGMX_GPU:STRING=OpenCL')
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elif '+sycl' in self.spec:
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options.append('-DGMX_GPU:STRING=SYCL')
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else:
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options.append('-DGMX_GPU:STRING=OFF')
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else:
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if '+cuda' in self.spec or '+opencl' in self.spec:
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options.append('-DGMX_GPU:BOOL=ON')
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else:
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options.append('-DGMX_GPU:BOOL=OFF')
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if '+cuda' in self.spec:
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options.append('-DCUDA_TOOLKIT_ROOT_DIR:STRING=' +
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self.spec['cuda'].prefix)
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if '+opencl' in self.spec:
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options.append('-DGMX_USE_OPENCL=on')
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if '+lapack' in self.spec:
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options.append('-DGMX_EXTERNAL_LAPACK:BOOL=ON')
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if self.spec['lapack'].libs:
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options.append('-DGMX_LAPACK_USER={0}'.format(
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self.spec['lapack'].libs.joined(';')))
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else:
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options.append('-DGMX_EXTERNAL_LAPACK:BOOL=OFF')
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if '+blas' in self.spec:
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options.append('-DGMX_EXTERNAL_BLAS:BOOL=ON')
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if self.spec['blas'].libs:
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options.append('-DGMX_BLAS_USER={0}'.format(
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self.spec['blas'].libs.joined(';')))
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else:
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options.append('-DGMX_EXTERNAL_BLAS:BOOL=OFF')
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# Activate SIMD based on properties of the target
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target = self.spec.target
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if target >= 'zen2':
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# AMD Family 17h (EPYC Rome)
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options.append('-DGMX_SIMD=AVX2_256')
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elif target >= 'zen':
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# AMD Family 17h (EPYC Naples)
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options.append('-DGMX_SIMD=AVX2_128')
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elif target >= 'bulldozer':
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# AMD Family 15h
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options.append('-DGMX_SIMD=AVX_128_FMA')
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elif 'vsx' in target:
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# IBM Power 7 and beyond
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options.append('-DGMX_SIMD=IBM_VSX')
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elif target.family == 'aarch64':
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# ARMv8
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if self.spec.satisfies('%nvhpc'):
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options.append('-DGMX_SIMD=None')
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else:
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options.append('-DGMX_SIMD=ARM_NEON_ASIMD')
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elif target == 'mic_knl':
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# Intel KNL
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options.append('-DGMX_SIMD=AVX_512_KNL')
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else:
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# Other architectures
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simd_features = [
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('sse2', 'SSE2'),
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('sse4_1', 'SSE4.1'),
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('avx', 'AVX_256'),
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('axv128', 'AVX2_128'),
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('avx2', 'AVX2_256'),
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('avx512', 'AVX_512'),
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]
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# Workaround NVIDIA compiler bug when avx512 is enabled
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if (self.spec.satisfies('%nvhpc') and
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('avx512', 'AVX_512') in simd_features):
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simd_features.remove(('avx512', 'AVX_512'))
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for feature, flag in reversed(simd_features):
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if feature in target:
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options.append('-DGMX_SIMD:STRING={0}'.format(flag))
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break
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# Fall back
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options.append('-DGMX_SIMD:STRING=None')
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# Use the 'rtdscp' assembly instruction only on
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# appropriate architectures
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options.append(self.define(
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'GMX_USE_RDTSCP', str(target.family) in ('x86_64', 'x86')
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))
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if '+mdrun_only' in self.spec:
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options.append('-DGMX_BUILD_MDRUN_ONLY:BOOL=ON')
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else:
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options.append('-DGMX_BUILD_MDRUN_ONLY:BOOL=OFF')
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if '~openmp' in self.spec:
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options.append('-DGMX_OPENMP:BOOL=OFF')
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else:
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options.append('-DGMX_OPENMP:BOOL=ON')
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if '+relaxed_double_precision' in self.spec:
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options.append('-DGMX_RELAXED_DOUBLE_PRECISION:BOOL=ON')
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else:
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options.append('-DGMX_RELAXED_DOUBLE_PRECISION:BOOL=OFF')
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if '+cycle_subcounters' in self.spec:
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options.append('-DGMX_CYCLE_SUBCOUNTERS:BOOL=ON')
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else:
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options.append('-DGMX_CYCLE_SUBCOUNTERS:BOOL=OFF')
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if '^mkl' in self.spec:
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# fftw-api@3 is provided by intel-mkl or intel-parllel-studio
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# we use the mkl interface of gromacs
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options.append('-DGMX_FFT_LIBRARY=mkl')
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options.append('-DMKL_INCLUDE_DIR={0}'.
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format(self.spec['mkl'].headers.directories[0]))
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# The 'blas' property provides a minimal set of libraries
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# that is sufficient for fft. Using full mkl fails the cmake test
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options.append('-DMKL_LIBRARIES={0}'.
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format(self.spec['blas'].libs.joined(';')))
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else:
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# we rely on the fftw-api@3
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options.append('-DGMX_FFT_LIBRARY=fftw3')
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if '^amdfftw' in self.spec:
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options.append('-DGMX_FFT_LIBRARY=fftw3')
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options.append(
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'-DFFTWF_INCLUDE_DIRS={0}'.
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format(self.spec['amdfftw'].headers.directories[0])
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)
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options.append('-DFFTWF_LIBRARIES={0}'.
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format(self.spec['amdfftw'].libs.joined(';')))
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return options
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