diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py
index e39b81a4c6f10b0a4e190c0a83f73231d66d89bf..ca880c53b75e7ae24f45d56fc0149b836a9ad787 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 3e84394da8a5bcb79609a83a63f73bf7413ff6f0..9f08d820d2213b8087926e2c5e8014fcdb737b2a 100644
--- a/var/spack/repos/builtin/packages/charm/package.py
+++ b/var/spack/repos/builtin/packages/charm/package.py
@@ -115,29 +115,43 @@ def install(self, spec, prefix):
# 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 0336f426be72ad07d1ed9adcd7a6524723573a4c..68610d7afe7e6f8dc45d064cd164ce51ebd423dd 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 @@ def mpi_libs(self):
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 0000000000000000000000000000000000000000..160d508004fd17d938558a9e0132af7b376d3677
--- /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)