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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class Neuron(Package):
"""NEURON is a simulation environment for single and networks of neurons.
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"
git = "https://github.com/nrnhines/nrn.git"
version('develop', branch='master')
version('7.5', sha256='67642216a969fdc844da1bd56643edeed5e9f9ab8c2a3049dcbcbcccba29c336')
version('7.4', sha256='1403ba16b2b329d2376f4bf007d96e6bf2992fa850f137f1068ad5b22b432de6')
version('7.3', sha256='71cff5962966c5cd5d685d90569598a17b4b579d342126b31e2d431128cc8832')
version('7.2', sha256='c777d73a58ff17a073e8ea25f140cb603b8b5f0df3c361388af7175e44d85b0e')
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('pkgconfig', type='build')
depends_on('mpi', when='+mpi')
depends_on('python@2.6:', when='+python')
depends_on('ncurses', when='~cross-compile')
conflicts('~shared', when='+python')
filter_compiler_wrappers('*/bin/nrniv_makefile')
def get_neuron_archdir(self):
"""Determine the architecture-specific neuron base directory.
Instead of recreating the logic of the neuron's configure
we dynamically find the architecture-specific directory by
looking for a specific binary.
"""
file_list = find(self.prefix, '*/bin/nrniv_makefile')
# check needed as when initially evaluated the prefix is empty
if file_list:
neuron_archdir = os.path.dirname(os.path.dirname(file_list[0]))
else:
neuron_archdir = self.prefix
return neuron_archdir
def patch(self):
# aclocal need complete include path (especially on os x)
pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkgconfig'].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_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')
def setup_environment(self, spack_env, run_env):
neuron_archdir = self.get_neuron_archdir()
run_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
run_env.prepend_path(
'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
neuron_archdir = self.get_neuron_archdir()
spack_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
spack_env.prepend_path(
'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
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