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Diffstat (limited to 'var/spack/repos/builtin/packages/neuron/package.py')
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1 files changed, 202 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py new file mode 100644 index 0000000000..ade0552c60 --- /dev/null +++ b/var/spack/repos/builtin/packages/neuron/package.py @@ -0,0 +1,202 @@ +# Copyright 2013-2018 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', 'fb72c841374dfacbb6c2168ff57bfae9') + version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf') + version('7.3', '993e539cb8bf102ca52e9fefd644ab61') + version('7.2', '5486709b6366add932e3a6d141c4f7ad') + + 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')) |