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
This commit is contained in:
Pramod S Kumbhar
Adam J. Stewart
parent
395ee97f3b
commit
d24782c86d
224
var/spack/repos/builtin/packages/neuron/package.py
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224
var/spack/repos/builtin/packages/neuron/package.py
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##############################################################################
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# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/llnl/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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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 modeling individual
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and networks of neurons. NEURON models individual neurons via
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the use of sections that are automatically subdivided into individual
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compartments, instead of requiring the user to manually create
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compartments. The primary scripting language is hoc but a Python
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interface is also available."""
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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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github = "https://github.com/nrnhines/nrn"
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version('7.5', '1641ae7a7cd02728e5ae4c8aa93b3749')
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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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version('develop', git=github)
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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('pkg-config', 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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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['pkg-config'].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_arch_dir(self):
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if 'bgq' in self.spec.architecture:
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arch = 'powerpc64'
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elif 'cray' in self.spec.architecture:
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arch = 'x86_64'
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elif 'ppc64le' in self.spec.architecture:
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arch = 'powerpc64le'
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else:
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arch = self.spec.architecture.target
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return arch
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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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@run_after('install')
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def filter_compilers(self):
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"""run after install to avoid spack compiler wrappers
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getting embded into nrnivmodl script"""
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arch = self.get_arch_dir()
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nrnmakefile = join_path(self.prefix, arch, 'bin/nrniv_makefile')
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kwargs = {
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'backup': False,
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'string': True
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}
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filter_file(env['CC'], self.compiler.cc, nrnmakefile, **kwargs)
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filter_file(env['CXX'], self.compiler.cxx, nrnmakefile, **kwargs)
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def setup_environment(self, spack_env, run_env):
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arch = self.get_arch_dir()
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run_env.prepend_path('PATH', join_path(self.prefix, arch, 'bin'))
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def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
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arch = self.get_arch_dir()
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spack_env.prepend_path('PATH', join_path(self.prefix, arch, 'bin'))
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