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authorPramod S Kumbhar <pramod.r.s.kumbhar@gmail.com>2018-01-04 16:55:30 +0100
committerAdam J. Stewart <ajstewart426@gmail.com>2018-01-04 09:55:30 -0600
commitd24782c86d84d51ac3ef7404c9e4a4eb6b9eab7e (patch)
treee0934030ca985f550fe93d6cd85b54e6bf2adef4
parent395ee97f3b1cdd96ae00bdae6d27d3145c50fc5e (diff)
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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
-rw-r--r--var/spack/repos/builtin/packages/neuron/package.py224
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diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py
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+++ b/var/spack/repos/builtin/packages/neuron/package.py
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+##############################################################################
+# 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'))