62927654dd
We'd like to use a consistent checksum scheme everywhere so that we can:
a) incorporate archive checksums into our specs and have a
consistent hashing algorithm across all specs.
b) index mirrors with a consistent type of checksum, and not one that
is dependent on how spack packages are written.
- [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
203 lines
7.6 KiB
Python
203 lines
7.6 KiB
Python
# 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'))
|