Adding NEURON simulator package (#5097)

* Adding NEURON package widely used in computational neuroscience community

* flake8 fixes

* Add rx3d variant

* Addressed review comments from Adam

* Addressed 2nd review comments

* Added check for +mpi on bg-q

* Filter spack compiler wrappers in NEURON scripts
Add gcc march=native flag to make front-end build robust

* Make develop as preferred version due to bug in long filename handlings in <= v7.4

* Avoid use of gcc in cross compiling environment
Use arch specific options on cray and bg-q arch

* Simplify cross compiling build:
    - v7.5 added and no longer need develop as preferred version
    - legacy cray related options removed
    - cross compiling args reduced
    - python arguments reduced as neuron finds proper libraries

* Simplify bg-q configurations

* Cleanup and unify arch options

* Make sure to add commonly available packages as dependency

* Arch path added to dependent_environment as nrniv needed at runtime

* Support for Power 8 architecture

* Fix python3 on OS X

* flake8 fix

* remove unnecessary conflcist directives

1 files changed, 224 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py
new file mode 100644
index 0000000000..245d2d2902
--- /dev/null
+++ b/var/spack/repos/builtin/packages/neuron/package.py
@@ -0,0 +1,224 @@
+##############################################################################
+# 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 NOTICE and LICENSE files 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 os
+from spack import *
+
+
+class Neuron(Package):
+
+    """NEURON is a simulation environment for modeling individual
+    and networks of neurons. NEURON models individual neurons via
+    the use of sections that are automatically subdivided into individual
+    compartments, instead of requiring the user to manually create
+    compartments. The primary scripting language is hoc but a Python
+    interface is also available."""
+
+    homepage = "https://www.neuron.yale.edu/"
+    url      = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.5/nrn-7.5.tar.gz"
+    github   = "https://github.com/nrnhines/nrn"
+
+    version('7.5', '1641ae7a7cd02728e5ae4c8aa93b3749')
+    version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf')
+    version('7.3', '993e539cb8bf102ca52e9fefd644ab61')
+    version('7.2', '5486709b6366add932e3a6d141c4f7ad')
+    version('develop', git=github)
+
+    variant('mpi',           default=True,  description='Enable MPI parallelism')
+    variant('python',        default=True,  description='Enable python')
+    variant('shared',        default=False, description='Build shared libraries')
+    variant('cross-compile', default=False, description='Build for cross-compile environment')
+    variant('multisend',     default=True,  description="Enable multi-send spike exchange")
+    variant('rx3d',          default=False, description="Enable cython translated 3-d rxd")
+
+    depends_on('flex',       type='build')
+    depends_on('bison',      type='build')
+    depends_on('automake',   type='build')
+    depends_on('automake',   type='build')
+    depends_on('autoconf',   type='build')
+    depends_on('libtool',    type='build')
+    depends_on('pkg-config', type='build')
+
+    depends_on('mpi',         when='+mpi')
+    depends_on('python@2.6:', when='+python')
+    depends_on('ncurses',     when='~cross-compile')
+
+    def patch(self):
+        # aclocal need complete include path (especially on os x)
+        pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkg-config'].prefix)
+        libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)
+        newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)
+        filter_file(r'aclocal -I m4', r'%s' % newpath, "build.sh")
+
+    def get_arch_options(self, spec):
+        options = []
+
+        if spec.satisfies('+cross-compile'):
+            options.extend(['cross_compiling=yes',
+                            '--without-memacs',
+                            '--without-nmodl'])
+
+        # need to enable bg-q arch
+        if 'bgq' in self.spec.architecture:
+            options.extend(['--enable-bluegeneQ',
+                            '--host=powerpc64'])
+
+        # on os-x disable building carbon 'click' utility
+        if 'darwin' in self.spec.architecture:
+            options.append('macdarwin=no')
+
+        return options
+
+    def get_arch_dir(self):
+        if 'bgq' in self.spec.architecture:
+            arch = 'powerpc64'
+        elif 'cray' in self.spec.architecture:
+            arch = 'x86_64'
+        elif 'ppc64le' in self.spec.architecture:
+            arch = 'powerpc64le'
+        else:
+            arch = self.spec.architecture.target
+
+        return arch
+
+    def get_python_options(self, spec):
+        options = []
+
+        if spec.satisfies('+python'):
+            python_exec = spec['python'].command.path
+            py_inc = spec['python'].headers.directories[0]
+            py_lib = spec['python'].prefix.lib
+
+            if not os.path.isdir(py_lib):
+                py_lib = spec['python'].prefix.lib64
+
+            options.extend(['--with-nrnpython=%s' % python_exec,
+                            '--disable-pysetup',
+                            'PYINCDIR=%s' % py_inc,
+                            'PYLIBDIR=%s' % py_lib])
+
+            if spec.satisfies('~cross-compile'):
+                options.append('PYTHON_BLD=%s' % python_exec)
+
+        else:
+            options.append('--without-nrnpython')
+
+        return options
+
+    def get_compiler_options(self, spec):
+        flags = '-O2 -g'
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-O3 -qtune=qp -qarch=qp -q64 -qstrict -qnohot -g'
+
+        if self.spec.satisfies('%pgi'):
+            flags += ' ' + self.compiler.pic_flag
+
+        return ['CFLAGS=%s' % flags,
+                'CXXFLAGS=%s' % flags]
+
+    def build_nmodl(self, spec, prefix):
+        # build components for front-end arch in cross compiling environment
+        options = ['--prefix=%s' % prefix,
+                   '--with-nmodl-only',
+                   '--without-x']
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-qarch=ppc64'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        if 'cray' in self.spec.architecture:
+            flags = '-target-cpu=x86_64 -target-network=none'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        configure = Executable(join_path(self.stage.source_path, 'configure'))
+        configure(*options)
+        make()
+        make('install')
+
+    def install(self, spec, prefix):
+
+        options = ['--prefix=%s' % prefix,
+                   '--without-iv',
+                   '--without-x',
+                   '--without-readline']
+
+        if spec.satisfies('+multisend'):
+            options.append('--with-multisend')
+
+        if spec.satisfies('~rx3d'):
+            options.append('--disable-rx3d')
+
+        if spec.satisfies('+mpi'):
+            options.extend(['MPICC=%s' % spec['mpi'].mpicc,
+                            'MPICXX=%s' % spec['mpi'].mpicxx,
+                            '--with-paranrn'])
+        else:
+            options.append('--without-paranrn')
+
+        if spec.satisfies('~shared'):
+            options.extend(['--disable-shared',
+                            'linux_nrnmech=no'])
+
+        options.extend(self.get_arch_options(spec))
+        options.extend(self.get_python_options(spec))
+        options.extend(self.get_compiler_options(spec))
+
+        build = Executable('./build.sh')
+        build()
+
+        with working_dir('build', create=True):
+            if spec.satisfies('+cross-compile'):
+                self.build_nmodl(spec, prefix)
+            srcpath = self.stage.source_path
+            configure = Executable(join_path(srcpath, 'configure'))
+            configure(*options)
+            make('VERBOSE=1')
+            make('install')
+
+    @run_after('install')
+    def filter_compilers(self):
+        """run after install to avoid spack compiler wrappers
+        getting embded into nrnivmodl script"""
+
+        arch = self.get_arch_dir()
+        nrnmakefile = join_path(self.prefix, arch, 'bin/nrniv_makefile')
+
+        kwargs = {
+            'backup': False,
+            'string': True
+        }
+
+        filter_file(env['CC'],  self.compiler.cc, nrnmakefile, **kwargs)
+        filter_file(env['CXX'], self.compiler.cxx, nrnmakefile, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        arch = self.get_arch_dir()
+        run_env.prepend_path('PATH', join_path(self.prefix, arch, 'bin'))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        arch = self.get_arch_dir()
+        spack_env.prepend_path('PATH', join_path(self.prefix, arch, 'bin'))