# Copyright 2013-2022 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 os import platform import sys import llnl.util.tty as tty from spack import * class Namd(MakefilePackage, CudaPackage): """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" homepage = "https://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', 'amdfftw'), description='Enable the use of FFTW/FFTW3/MKL FFT/AMDFFTW') 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-2.13.patch', when='@2.13') patch('inherited-member-2.14.patch', when='@2.14') # Handle change in python-config for python@3.8: patch('namd-python38.patch', when='interface=python ^python@3.8:') 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', when="fftw=2") depends_on('fftw@3:', when="fftw=3") depends_on('amdfftw', when="fftw=amdfftw") 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') # https://www.ks.uiuc.edu/Research/namd/2.12/features.html # https://www.ks.uiuc.edu/Research/namd/2.13/features.html # https://www.ks.uiuc.edu/Research/namd/2.14/features.html depends_on('cuda@6.5.14:7.5.18', when='@2.12 +cuda') depends_on('cuda@8.0.61:', when='@2.13: +cuda') 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, 'aocc': m64 + '-O3 -ffp-contract=fast -ffast-math \ -fopenmp ' + archopt} else: optims_opts = { 'gcc': m64 + '-O3 -fexpensive-optimizations \ -ffast-math -lpthread ' + archopt, 'intel': '-O2 -ip ' + archopt, 'aocc': m64 + '-O3 -ffp-contract=fast \ -ffast-math ' + 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') elif fftw_version == 'amdfftw': self._copy_arch_file('fftw3') opts.extend(['--with-fftw3', '--fftw-prefix', spec['amdfftw'].prefix]) 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' ]) if '+cuda' in spec: self._append_option(opts, 'cuda') filter_file('^CUDADIR=.*$', 'CUDADIR={0}'.format(spec['cuda'].prefix), join_path('arch', self.arch + '.cuda')) 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)