Adding package namd (#4321)
* Initial version of the namd package * Modified charm to consider compile against intel/intel-mpi * Correction of namd to compile with intel-mkl and intel compiler * Adding inclue64 in the prefix * adding property for the build directory * removing useless function build
This commit is contained in:
Nicolas Richart
Adam J. Stewart
parent
bc2c4a14c2
commit
f06c23ef42
4 changed files with 194 additions and 21 deletions
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@ -60,17 +60,18 @@ class Prefix(str):
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def __new__(cls, path):
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s = super(Prefix, cls).__new__(cls, path)
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s.bin = join_path(s, 'bin')
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s.bin64 = join_path(s, 'bin64')
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s.sbin = join_path(s, 'sbin')
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s.etc = join_path(s, 'etc')
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s.include = join_path(s, 'include')
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s.lib = join_path(s, 'lib')
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s.lib64 = join_path(s, 'lib64')
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s.libexec = join_path(s, 'libexec')
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s.share = join_path(s, 'share')
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s.doc = join_path(s.share, 'doc')
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s.info = join_path(s.share, 'info')
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s.bin = join_path(s, 'bin')
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s.bin64 = join_path(s, 'bin64')
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s.sbin = join_path(s, 'sbin')
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s.etc = join_path(s, 'etc')
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s.include = join_path(s, 'include')
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s.include64 = join_path(s, 'include64')
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s.lib = join_path(s, 'lib')
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s.lib64 = join_path(s, 'lib64')
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s.libexec = join_path(s, 'libexec')
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s.share = join_path(s, 'share')
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s.doc = join_path(s.share, 'doc')
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s.info = join_path(s.share, 'info')
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s.man = join_path(s, 'man')
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s.man1 = join_path(s.man, 'man1')
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@ -115,29 +115,43 @@ def install(self, spec, prefix):
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# We assume that Spack's compiler wrappers make this work. If
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# not, then we need to query the compiler vendor from Spack
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# here.
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compiler = "gcc"
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compiler = os.path.basename(self.compiler.cc)
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options = [compiler,
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"--with-production", # Note: turn this into a variant
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"-j%d" % make_jobs,
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"--destination=%s" % prefix]
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if "+mpi" in spec:
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options.append("--basedir=%s" % spec["mpi"].prefix)
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options = [compiler]
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if compiler == 'icc':
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options.append('ifort')
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options.extend([
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"--with-production", # Note: turn this into a variant
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"-j%d" % make_jobs,
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"--destination=%s" % prefix])
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if 'backend=mpi' in spec:
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# in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
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# cannot be used
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options.extend([
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'--incdir={0}'.format(incdir)
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for incdir in spec["mpi"].headers.directories
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])
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options.extend([
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'--libdir={0}'.format(libdir)
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for libdir in spec["mpi"].libs.directories
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])
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if "+papi" in spec:
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options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
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if "+smp" in spec:
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if "+multicore" in spec:
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if 'backend=multicore' in spec:
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# This is a Charm++ limitation; it would lead to a
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# build error
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raise InstallError("Cannot combine +smp with +multicore")
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options.append("smp")
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if "+tcp" in spec:
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if "+net" not in spec:
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if 'backend=net' not in spec:
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# This is a Charm++ limitation; it would lead to a
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# build error
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raise InstallError(
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"The +tcp variant requires "
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"the +net communication mechanism")
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"the backend=net communication mechanism")
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options.append("tcp")
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if "+shared" in spec:
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options.append("--build-shared")
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@ -54,6 +54,13 @@ def mpi_libs(self):
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libraries, root=self.prefix.lib64, shared=True, recurse=True
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)
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@property
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def mpi_headers(self):
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# recurse from self.prefix will find too many things for all the
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# supported sub-architectures like 'mic'
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return find_headers(
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'mpi', root=self.prefix.include64, recurse=False)
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def install(self, spec, prefix):
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self.intel_prefix = prefix
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IntelInstaller.install(self, spec, prefix)
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151
var/spack/repos/builtin/packages/namd/package.py
Normal file
151
var/spack/repos/builtin/packages/namd/package.py
Normal file
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@ -0,0 +1,151 @@
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the LICENSE file for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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import platform
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import shutil
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import sys
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import os
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from spack import *
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class Namd(MakefilePackage):
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"""NAMDis a parallel molecular dynamics code designed for
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high-performance simulation of large biomolecular systems."""
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homepage = "http://www.ks.uiuc.edu/Research/namd/"
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url = "file://{0}/NAMD_2.12_Source.tar.gz".format(os.getcwd())
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version('2.12', '2a1191909b1ab03bf0205971ad4d8ee9')
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variant('fftw', default='3', values=('none', '2', '3', 'mkl'),
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description='Enable the use of FFTW/FFTW3/MKL FFT')
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variant('interface', default='none', values=('none', 'tcl', 'python'),
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description='Enables TCL and/or python interface')
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depends_on('charm')
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depends_on('fftw@:2.99', when="fftw=2")
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depends_on('fftw@3:', when="fftw=3")
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depends_on('intel-mkl', when="fftw=mkl")
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depends_on('tcl', when='interface=tcl')
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depends_on('tcl', when='interface=python')
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depends_on('python', when='interface=python')
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def _copy_arch_file(self, lib):
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config_filename = 'arch/{0}.{1}'.format(self.arch, lib)
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shutil.copy('arch/Linux-x86_64.{0}'.format(lib),
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config_filename)
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if lib == 'tcl':
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filter_file(r'-ltcl8\.5',
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'-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)),
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config_filename)
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def _append_option(self, opts, lib):
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if lib != 'python':
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self._copy_arch_file(lib)
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spec = self.spec
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opts.extend([
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'--with-{0}'.format(lib),
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'--{0}-prefix'.format(lib), spec[lib].prefix
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])
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@property
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def arch(self):
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plat = sys.platform
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if plat.startswith("linux"):
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plat = "linux"
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march = platform.machine()
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return '{0}-{1}'.format(plat, march)
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@property
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def build_directory(self):
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return '{0}-spack'.format(self.arch)
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def edit(self, spec, prefix):
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with working_dir('arch'):
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with open('{0}.arch'.format(self.build_directory), 'w') as fh:
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# this options are take from the default provided
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# configuration files
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optims_opts = {
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'gcc': '-m64 -O3 -fexpensive-optimizations -ffast-math',
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'intel': '-O2 -ip'
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}
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optim_opts = optims_opts[self.compiler.name] \
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if self.compiler.name in optims_opts else ''
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fh.write('\n'.join([
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'NAMD_ARCH = {0}'.format(self.arch),
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'CHARMARCH = ',
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'CXX = {0.cxx} {0.cxx11_flag}'.format(
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self.compiler),
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'CXXOPTS = {0}'.format(optim_opts),
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'CC = {0}'.format(self.compiler.cc),
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'COPTS = {0}'.format(optim_opts),
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''
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]))
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self._copy_arch_file('base')
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opts = ['--charm-base', spec['charm'].prefix]
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fftw_version = spec.variants['fftw'].value
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if fftw_version == 'none':
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opts.append('--without-fftw')
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elif fftw_version == 'mkl':
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self._append_option(opts, 'mkl')
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else:
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_fftw = 'fftw{0}'.format('' if fftw_version == '2' else '3')
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self._copy_arch_file(_fftw)
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opts.extend(['--with-{0}'.format(_fftw),
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'--fftw-prefix', spec['fftw'].prefix])
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interface_type = spec.variants['interface'].value
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if interface_type != 'none':
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self._append_option(opts, 'tcl')
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if interface_type == 'python':
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self._append_option(opts, 'python')
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else:
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opts.extend([
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'--without-tcl',
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'--without-python'
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])
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config = Executable('./config')
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config(self.build_directory, *opts)
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def install(self, spec, prefix):
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with working_dir(self.build_directory):
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mkdirp(prefix.bin)
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install('namd2', prefix.bin)
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# I'm not sure this is a good idea or if an autoload of the charm
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# module would not be better.
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install('charmrun', prefix.bin)
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