203 lines
7.4 KiB
Python
203 lines
7.4 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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from spack import *
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class Neuron(Package):
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"""NEURON is a simulation environment for single and networks of neurons.
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NEURON is a simulation environment for modeling individual and networks of
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neurons. NEURON models individual neurons via the use of sections that are
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automatically subdivided into individual compartments, instead of
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requiring the user to manually create compartments. The primary scripting
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language is hoc but a Python interface is also available.
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"""
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homepage = "https://www.neuron.yale.edu/"
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url = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.5/nrn-7.5.tar.gz"
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git = "https://github.com/nrnhines/nrn.git"
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version('develop', branch='master')
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version('7.5', 'fb72c841374dfacbb6c2168ff57bfae9')
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version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf')
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version('7.3', '993e539cb8bf102ca52e9fefd644ab61')
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version('7.2', '5486709b6366add932e3a6d141c4f7ad')
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variant('mpi', default=True, description='Enable MPI parallelism')
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variant('python', default=True, description='Enable python')
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variant('shared', default=False, description='Build shared libraries')
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variant('cross-compile', default=False, description='Build for cross-compile environment')
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variant('multisend', default=True, description="Enable multi-send spike exchange")
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variant('rx3d', default=False, description="Enable cython translated 3-d rxd")
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depends_on('flex', type='build')
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depends_on('bison', type='build')
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depends_on('automake', type='build')
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depends_on('automake', type='build')
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depends_on('autoconf', type='build')
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depends_on('libtool', type='build')
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depends_on('pkgconfig', type='build')
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depends_on('mpi', when='+mpi')
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depends_on('python@2.6:', when='+python')
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depends_on('ncurses', when='~cross-compile')
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conflicts('~shared', when='+python')
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filter_compiler_wrappers('*/bin/nrniv_makefile')
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def get_neuron_archdir(self):
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"""Determine the architecture-specific neuron base directory.
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Instead of recreating the logic of the neuron's configure
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we dynamically find the architecture-specific directory by
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looking for a specific binary.
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"""
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file_list = find(self.prefix, '*/bin/nrniv_makefile')
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# check needed as when initially evaluated the prefix is empty
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if file_list:
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neuron_archdir = os.path.dirname(os.path.dirname(file_list[0]))
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else:
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neuron_archdir = self.prefix
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return neuron_archdir
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def patch(self):
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# aclocal need complete include path (especially on os x)
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pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkgconfig'].prefix)
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libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)
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newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)
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filter_file(r'aclocal -I m4', r'%s' % newpath, "build.sh")
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def get_arch_options(self, spec):
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options = []
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if spec.satisfies('+cross-compile'):
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options.extend(['cross_compiling=yes',
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'--without-memacs',
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'--without-nmodl'])
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# need to enable bg-q arch
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if 'bgq' in self.spec.architecture:
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options.extend(['--enable-bluegeneQ',
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'--host=powerpc64'])
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# on os-x disable building carbon 'click' utility
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if 'darwin' in self.spec.architecture:
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options.append('macdarwin=no')
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return options
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def get_python_options(self, spec):
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options = []
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if spec.satisfies('+python'):
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python_exec = spec['python'].command.path
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py_inc = spec['python'].headers.directories[0]
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py_lib = spec['python'].prefix.lib
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if not os.path.isdir(py_lib):
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py_lib = spec['python'].prefix.lib64
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options.extend(['--with-nrnpython=%s' % python_exec,
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'--disable-pysetup',
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'PYINCDIR=%s' % py_inc,
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'PYLIBDIR=%s' % py_lib])
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if spec.satisfies('~cross-compile'):
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options.append('PYTHON_BLD=%s' % python_exec)
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else:
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options.append('--without-nrnpython')
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return options
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def get_compiler_options(self, spec):
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flags = '-O2 -g'
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if 'bgq' in self.spec.architecture:
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flags = '-O3 -qtune=qp -qarch=qp -q64 -qstrict -qnohot -g'
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if self.spec.satisfies('%pgi'):
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flags += ' ' + self.compiler.pic_flag
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return ['CFLAGS=%s' % flags,
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'CXXFLAGS=%s' % flags]
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def build_nmodl(self, spec, prefix):
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# build components for front-end arch in cross compiling environment
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options = ['--prefix=%s' % prefix,
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'--with-nmodl-only',
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'--without-x']
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if 'bgq' in self.spec.architecture:
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flags = '-qarch=ppc64'
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options.extend(['CFLAGS=%s' % flags,
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'CXXFLAGS=%s' % flags])
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if 'cray' in self.spec.architecture:
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flags = '-target-cpu=x86_64 -target-network=none'
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options.extend(['CFLAGS=%s' % flags,
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'CXXFLAGS=%s' % flags])
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configure = Executable(join_path(self.stage.source_path, 'configure'))
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configure(*options)
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make()
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make('install')
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def install(self, spec, prefix):
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options = ['--prefix=%s' % prefix,
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'--without-iv',
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'--without-x',
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'--without-readline']
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if spec.satisfies('+multisend'):
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options.append('--with-multisend')
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if spec.satisfies('~rx3d'):
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options.append('--disable-rx3d')
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if spec.satisfies('+mpi'):
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options.extend(['MPICC=%s' % spec['mpi'].mpicc,
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'MPICXX=%s' % spec['mpi'].mpicxx,
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'--with-paranrn'])
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else:
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options.append('--without-paranrn')
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if spec.satisfies('~shared'):
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options.extend(['--disable-shared',
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'linux_nrnmech=no'])
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options.extend(self.get_arch_options(spec))
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options.extend(self.get_python_options(spec))
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options.extend(self.get_compiler_options(spec))
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build = Executable('./build.sh')
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build()
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with working_dir('build', create=True):
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if spec.satisfies('+cross-compile'):
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self.build_nmodl(spec, prefix)
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srcpath = self.stage.source_path
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configure = Executable(join_path(srcpath, 'configure'))
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configure(*options)
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make('VERBOSE=1')
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make('install')
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def setup_environment(self, spack_env, run_env):
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neuron_archdir = self.get_neuron_archdir()
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run_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
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run_env.prepend_path(
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'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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neuron_archdir = self.get_neuron_archdir()
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spack_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
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spack_env.prepend_path(
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'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
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