diff options
| -rw-r--r-- | lib/spack/spack/util/prefix.py | 23 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/charm/package.py | 36 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/intel-mpi/package.py | 7 | ||||
| -rw-r--r-- | var/spack/repos/builtin/packages/namd/package.py | 151 |
4 files changed, 195 insertions, 22 deletions
diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py index e39b81a4c6..ca880c53b7 100644 --- a/lib/spack/spack/util/prefix.py +++ b/lib/spack/spack/util/prefix.py @@ -60,17 +60,18 @@ class Prefix(str): def __new__(cls, path): s = super(Prefix, cls).__new__(cls, path) - s.bin = join_path(s, 'bin') - s.bin64 = join_path(s, 'bin64') - s.sbin = join_path(s, 'sbin') - s.etc = join_path(s, 'etc') - s.include = join_path(s, 'include') - s.lib = join_path(s, 'lib') - s.lib64 = join_path(s, 'lib64') - s.libexec = join_path(s, 'libexec') - s.share = join_path(s, 'share') - s.doc = join_path(s.share, 'doc') - s.info = join_path(s.share, 'info') + s.bin = join_path(s, 'bin') + s.bin64 = join_path(s, 'bin64') + s.sbin = join_path(s, 'sbin') + s.etc = join_path(s, 'etc') + s.include = join_path(s, 'include') + s.include64 = join_path(s, 'include64') + s.lib = join_path(s, 'lib') + s.lib64 = join_path(s, 'lib64') + s.libexec = join_path(s, 'libexec') + s.share = join_path(s, 'share') + s.doc = join_path(s.share, 'doc') + s.info = join_path(s.share, 'info') s.man = join_path(s, 'man') s.man1 = join_path(s.man, 'man1') diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py index 3e84394da8..9f08d820d2 100644 --- a/var/spack/repos/builtin/packages/charm/package.py +++ b/var/spack/repos/builtin/packages/charm/package.py @@ -115,29 +115,43 @@ class Charm(Package): # We assume that Spack's compiler wrappers make this work. If # not, then we need to query the compiler vendor from Spack # here. - compiler = "gcc" - - options = [compiler, - "--with-production", # Note: turn this into a variant - "-j%d" % make_jobs, - "--destination=%s" % prefix] - if "+mpi" in spec: - options.append("--basedir=%s" % spec["mpi"].prefix) + compiler = os.path.basename(self.compiler.cc) + + options = [compiler] + if compiler == 'icc': + options.append('ifort') + + options.extend([ + "--with-production", # Note: turn this into a variant + "-j%d" % make_jobs, + "--destination=%s" % prefix]) + + if 'backend=mpi' in spec: + # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir + # cannot be used + options.extend([ + '--incdir={0}'.format(incdir) + for incdir in spec["mpi"].headers.directories + ]) + options.extend([ + '--libdir={0}'.format(libdir) + for libdir in spec["mpi"].libs.directories + ]) if "+papi" in spec: options.extend(["papi", "--basedir=%s" % spec["papi"].prefix]) if "+smp" in spec: - if "+multicore" in spec: + if 'backend=multicore' in spec: # This is a Charm++ limitation; it would lead to a # build error raise InstallError("Cannot combine +smp with +multicore") options.append("smp") if "+tcp" in spec: - if "+net" not in spec: + if 'backend=net' not in spec: # This is a Charm++ limitation; it would lead to a # build error raise InstallError( "The +tcp variant requires " - "the +net communication mechanism") + "the backend=net communication mechanism") options.append("tcp") if "+shared" in spec: options.append("--build-shared") diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py index 0336f426be..68610d7afe 100644 --- a/var/spack/repos/builtin/packages/intel-mpi/package.py +++ b/var/spack/repos/builtin/packages/intel-mpi/package.py @@ -54,6 +54,13 @@ class IntelMpi(IntelInstaller): libraries, root=self.prefix.lib64, shared=True, recurse=True ) + @property + def mpi_headers(self): + # recurse from self.prefix will find too many things for all the + # supported sub-architectures like 'mic' + return find_headers( + 'mpi', root=self.prefix.include64, recurse=False) + def install(self, spec, prefix): self.intel_prefix = prefix IntelInstaller.install(self, spec, prefix) diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py new file mode 100644 index 0000000000..160d508004 --- /dev/null +++ b/var/spack/repos/builtin/packages/namd/package.py @@ -0,0 +1,151 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import platform +import shutil +import sys +import os +from spack import * + + +class Namd(MakefilePackage): + """NAMDis a parallel molecular dynamics code designed for + high-performance simulation of large biomolecular systems.""" + + homepage = "http://www.ks.uiuc.edu/Research/namd/" + url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd()) + + version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9') + + variant('fftw', default='3', values=('none', '2', '3', 'mkl'), + description='Enable the use of FFTW/FFTW3/MKL FFT') + + variant('interface', default='none', values=('none', 'tcl', 'python'), + description='Enables TCL and/or python interface') + + depends_on('charm') + + depends_on('fftw@:2.99', when="fftw=2") + depends_on('fftw@3:', when="fftw=3") + + 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') + + def _copy_arch_file(self, lib): + config_filename = 'arch/{0}.{1}'.format(self.arch, lib) + shutil.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(self, spec, prefix): + 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 + optims_opts = { + 'gcc': '-m64 -O3 -fexpensive-optimizations -ffast-math', + 'intel': '-O2 -ip' + } + + 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 = ', + '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), + '' + ])) + + self._copy_arch_file('base') + + opts = ['--charm-base', spec['charm'].prefix] + fftw_version = spec.variants['fftw'].value + if fftw_version == 'none': + opts.append('--without-fftw') + elif fftw_version == 'mkl': + self._append_option(opts, 'mkl') + 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' + ]) + + config = Executable('./config') + + config(self.build_directory, *opts) + + 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) |