f242e0fd0c
Remove support for `cray` as a separate platform. Any platform previously detected as `cray` is now detected as `linux`. Users who still need platform=cray have to stick to Spack 0.22
189 lines
7.7 KiB
Python
189 lines
7.7 KiB
Python
# Copyright 2013-2024 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)
|
|
|
|
from spack.package import *
|
|
|
|
|
|
class Neuron(CMakePackage):
|
|
"""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.
|
|
"""
|
|
|
|
homepage = "https://www.neuron.yale.edu/"
|
|
url = "https://github.com/neuronsimulator/nrn/releases/download/8.2.3/nrn-full-src-package-8.2.3.tar.gz"
|
|
git = "https://github.com/neuronsimulator/nrn"
|
|
maintainers("pramodk", "nrnhines", "iomaganaris", "ohm314", "matz-e")
|
|
|
|
license("BSD-3-Clause")
|
|
|
|
version("develop", branch="master", submodules="True")
|
|
|
|
version(
|
|
"8.2.3", tag="8.2.3", commit="f0ed3701059aa53ce93387f3d73d13c45de6d87f", submodules="True"
|
|
)
|
|
version(
|
|
"8.1.0", tag="8.1.0", commit="047dd8240c2badadf5ea154b563b29369db1303f", submodules="True"
|
|
)
|
|
version(
|
|
"8.0.0", tag="8.0.0", commit="429d11ef34b1d860b3ddbfffc9f7960acb399b0c", submodules="True"
|
|
)
|
|
version(
|
|
"7.8.2", tag="7.8.2", commit="09b151ecb2b3984335c265932dc6ba3e4fcb318e", submodules="True"
|
|
)
|
|
|
|
variant("backtrace", default=False, description="Enable printing backtraces on failure")
|
|
variant("interviews", default=False, description="Enable GUI with INTERVIEWS")
|
|
variant("legacy-unit", default=False, description="Enable legacy units")
|
|
variant("mpi", default=True, description="Enable MPI parallelism")
|
|
variant("python", default=True, description="Enable python")
|
|
variant("shared", default=True, description="Build shared library (CoreNEURON)")
|
|
variant("tests", default=False, description="Enable building tests")
|
|
variant("rx3d", default=False, description="Enable cython translated 3-d rxd.", when="+python")
|
|
|
|
# variants from coreneuron support
|
|
variant("coreneuron", default=True, description="Enable CoreNEURON support")
|
|
variant(
|
|
"gpu", default=False, description="Enable GPU build (with NVHPC)", when="@9:+coreneuron"
|
|
)
|
|
variant(
|
|
"openmp", default=False, description="Enable CoreNEURON OpenMP support", when="+coreneuron"
|
|
)
|
|
variant(
|
|
"sympy",
|
|
default=False,
|
|
description="Use NMODL with SymPy to solve ODEs",
|
|
when="@9:+coreneuron",
|
|
)
|
|
variant("caliper", default=False, description="Add Caliper support")
|
|
|
|
generator("ninja")
|
|
|
|
depends_on("bison@3:", type="build")
|
|
depends_on("flex@2.6:", type="build")
|
|
depends_on("ninja", type="build")
|
|
|
|
depends_on("gettext")
|
|
depends_on("libdwarf", when="+backtrace")
|
|
depends_on("mpi", when="+mpi")
|
|
depends_on("ncurses")
|
|
depends_on("readline")
|
|
|
|
depends_on("python", when="+python")
|
|
depends_on("py-pytest", when="+python+tests")
|
|
depends_on("py-mpi4py", when="+mpi+python+tests")
|
|
depends_on("py-numpy", when="+python")
|
|
depends_on("py-cython", when="+rx3d", type="build")
|
|
depends_on("py-pytest-cov", when="+tests")
|
|
|
|
# next two needed after neuronsimulator/nrn#2235.
|
|
depends_on("py-pip", type="build")
|
|
depends_on("py-setuptools", type="build")
|
|
depends_on("py-packaging", type="run")
|
|
|
|
depends_on("boost", when="+coreneuron+tests")
|
|
depends_on("cuda", when="+coreneuron+gpu")
|
|
depends_on("py-sympy@1.3:", when="+coreneuron")
|
|
|
|
depends_on("caliper", when="+caliper")
|
|
|
|
gpu_compiler_message = "neuron+gpu needs %nvhpc"
|
|
requires("%nvhpc", when="+gpu", msg=gpu_compiler_message)
|
|
|
|
patch("patch-v782-git-cmake-avx512.patch", when="@7.8.2")
|
|
|
|
def cmake_args(self):
|
|
spec = self.spec
|
|
args = []
|
|
for variant in ["backtrace", "coreneuron", "interviews", "mpi", "python", "rx3d", "tests"]:
|
|
args.append(self.define_from_variant("NRN_ENABLE_" + variant.upper(), variant))
|
|
|
|
args.append(self.define_from_variant("CORENRN_ENABLE_SHARED", "shared"))
|
|
|
|
if spec.satisfies("@:8"):
|
|
args.append(self.define("NRN_ENABLE_BINARY_SPECIAL", "ON"))
|
|
|
|
if "+python" in spec:
|
|
args.append(self.define("PYTHON_EXECUTABLE", spec["python"].command.path))
|
|
|
|
if "+legacy-unit" in spec and spec.satisfies("@:8"):
|
|
args.append(self.define("NRN_DYNAMIC_UNITS_USE_LEGACY", "ON"))
|
|
|
|
if "+caliper" in spec:
|
|
args.append(self.define("NRN_ENABLE_PROFILING", "ON"))
|
|
args.append(self.define("NRN_PROFILER", "caliper"))
|
|
|
|
if spec.satisfies("+coreneuron"):
|
|
options = [
|
|
self.define("CORENRN_ENABLE_SPLAYTREE_QUEUING", "ON"),
|
|
self.define("CORENRN_ENABLE_TIMEOUT", "OFF"),
|
|
self.define_from_variant("CORENRN_ENABLE_OPENMP", "openmp"),
|
|
self.define_from_variant("CORENRN_ENABLE_LEGACY_UNITS", "legacy-unit"),
|
|
self.define_from_variant("CORENRN_ENABLE_UNIT_TESTS", "tests"),
|
|
]
|
|
|
|
nmodl_options = "codegen --force"
|
|
if spec.satisfies("+sympy"):
|
|
nmodl_options += " sympy --analytic"
|
|
options.append(self.define("CORENRN_NMODL_FLAGS", nmodl_options))
|
|
|
|
if spec.satisfies("+gpu"):
|
|
nvcc = spec["cuda"].prefix.bin.nvcc
|
|
options.append(self.define("CMAKE_CUDA_COMPILER", nvcc))
|
|
options.append(self.define("CORENRN_ENABLE_GPU", True))
|
|
|
|
args.extend(options)
|
|
|
|
# Enable math optimisations to enable SIMD/vectorisation in release modes
|
|
if spec.satisfies("build_type=Release") or spec.satisfies("build_type=RelWithDebInfo"):
|
|
args.append(self.define("NRN_ENABLE_MATH_OPT", "ON"))
|
|
|
|
# add cpu arch specific optimisation flags to CMake so that they are passed
|
|
# to embedded Makefile that neuron has for compiling MOD files
|
|
compilation_flags = self.spec.architecture.target.optimization_flags(self.spec.compiler)
|
|
args.append(self.define("CMAKE_CXX_FLAGS", compilation_flags))
|
|
|
|
return args
|
|
|
|
@run_after("install")
|
|
def filter_compilers(self):
|
|
"""run after install to avoid spack compiler wrappers
|
|
getting embded into nrnivmodl script"""
|
|
|
|
spec = self.spec
|
|
|
|
if spec.satisfies("+mpi"):
|
|
cc_compiler = spec["mpi"].mpicc
|
|
cxx_compiler = spec["mpi"].mpicxx
|
|
else:
|
|
cc_compiler = self.compiler.cc
|
|
cxx_compiler = self.compiler.cxx
|
|
|
|
kwargs = {"backup": False, "string": True}
|
|
nrnmech_makefile = join_path(self.prefix, "bin/nrnmech_makefile")
|
|
|
|
# assign_operator is changed to fix wheel support
|
|
assign_operator = "?=" if spec.satisfies("@:7") else "="
|
|
|
|
# replace compilers from makefile
|
|
compilers = [("CC", "cc_compiler"), ("CXX", "cxx_compiler")]
|
|
for compiler_var, compiler_env in compilers:
|
|
pattern = "(?:^|\\s){0}\\s*{1}.+".format(compiler_var, assign_operator)
|
|
replacement = "{0} = {1}".format(compiler_var, locals()[compiler_env])
|
|
filter_file(pattern, replacement, nrnmech_makefile)
|
|
|
|
if spec.satisfies("@8:+coreneuron"):
|
|
nrnmakefile = join_path(self.prefix, "share/coreneuron/nrnivmodl_core_makefile")
|
|
filter_file("(?:^|\\s)CXX\\s*=.+", "CXX = {0}".format(cxx_compiler), nrnmakefile)
|
|
|
|
def setup_run_environment(self, env):
|
|
env.prepend_path("PATH", join_path(self.prefix, "bin"))
|
|
env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "lib"))
|
|
if self.spec.satisfies("+python"):
|
|
env.prepend_path("PYTHONPATH", self.spec.prefix.lib.python)
|