diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/namd/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/namd/package.py | 281 |
1 files changed, 144 insertions, 137 deletions
diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py index 54cc100af0..ec3723b27c 100644 --- a/var/spack/repos/builtin/packages/namd/package.py +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -17,70 +17,77 @@ class Namd(MakefilePackage, CudaPackage): 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" + 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') + 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') + 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:') + patch("namd-python38.patch", when="interface=python ^python@3.8:") - depends_on('charmpp@6.10.1:6', when="@2.14:") - depends_on('charmpp@6.8.2', when="@2.13") - depends_on('charmpp@6.7.1', when="@2.12") + depends_on("charmpp@6.10.1:6", 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("fftw@:2", when="fftw=2") + depends_on("fftw@3:", when="fftw=3") - depends_on('amdfftw', when="fftw=amdfftw") + depends_on("amdfftw", when="fftw=amdfftw") - depends_on('intel-mkl', when="fftw=mkl") + depends_on("intel-mkl", when="fftw=mkl") - depends_on('tcl', when='interface=tcl') + depends_on("tcl", when="interface=tcl") - depends_on('tcl', when='interface=python') - depends_on('python', when='interface=python') + 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') + 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) + 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': + if lib != "python": self._copy_arch_file(lib) spec = self.spec - opts.extend([ - '--with-{0}'.format(lib), - '--{0}-prefix'.format(lib), spec[lib].prefix - ]) + opts.extend(["--with-{0}".format(lib), "--{0}-prefix".format(lib), spec[lib].prefix]) @property def arch(self): @@ -88,51 +95,64 @@ class Namd(MakefilePackage, CudaPackage): if plat.startswith("linux"): plat = "linux" march = platform.machine() - return '{0}-{1}'.format(plat, march) + return "{0}-{1}".format(plat, march) @property def build_directory(self): - return '{0}-spack'.format(self.arch) + 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: + 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) + archopt = spec.target.optimization_flags(spec.compiler.name, spec.compiler.version) - if self.spec.satisfies('^charmpp@:6.10.1'): + 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} + "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), - '' - ])) + "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""" @@ -140,45 +160,32 @@ class Namd(MakefilePackage, CudaPackage): return False found_special_opt = False - with working_dir('arch'): - arch_filename = '{0}.arch'.format(self.build_directory) + 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) - ] + [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"): + 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") + 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) - ]) + 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: @@ -195,61 +202,61 @@ class Namd(MakefilePackage, CudaPackage): 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]) + 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') + _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]) + 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') + interface_type = spec.variants["interface"].value + if interface_type != "none": + self._append_option(opts, "tcl") - if interface_type == 'python': - self._append_option(opts, 'python') + if interface_type == "python": + self._append_option(opts, "python") else: - opts.extend([ - '--without-tcl', - '--without-python' - ]) + opts.extend(["--without-tcl", "--without-python"]) - if '+cuda' in spec: - self._append_option(opts, 'cuda') - filter_file('^CUDADIR=.*$', - 'CUDADIR={0}'.format(spec['cuda'].prefix), - join_path('arch', self.arch + '.cuda')) + if "+cuda" in spec: + self._append_option(opts, "cuda") + filter_file( + "^CUDADIR=.*$", + "CUDADIR={0}".format(spec["cuda"].prefix), + join_path("arch", self.arch + ".cuda"), + ) - config = Executable('./config') + config = 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")) + 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) + 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) + install("charmrun", prefix.bin) |