diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/neuron/package.py | 174 |
1 files changed, 108 insertions, 66 deletions
diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py index edad5ec994..c6d33e7030 100644 --- a/var/spack/repos/builtin/packages/neuron/package.py +++ b/var/spack/repos/builtin/packages/neuron/package.py @@ -16,86 +16,137 @@ class Neuron(CMakePackage): """ homepage = "https://www.neuron.yale.edu/" - url = "https://neuron.yale.edu/ftp/neuron/versions/v7.7/nrn-7.7.tar.gz" + 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", "alexsavulescu") + maintainers("pramodk", "nrnhines", "iomaganaris", "ohm314", "matz-e") license("BSD-3-Clause") version("develop", branch="master", submodules="True") + version( - "8.0.0", tag="8.0.0", commit="429d11ef34b1d860b3ddbfffc9f7960acb399b0c", submodules="True" + "8.2.3", tag="8.2.3", commit="f0ed3701059aa53ce93387f3d73d13c45de6d87f", submodules="True" ) version( - "7.8.2", tag="7.8.2", commit="09b151ecb2b3984335c265932dc6ba3e4fcb318e", submodules="True" + "8.1.0", tag="8.1.0", commit="047dd8240c2badadf5ea154b563b29369db1303f", submodules="True" + ) + version( + "8.0.0", tag="8.0.0", commit="429d11ef34b1d860b3ddbfffc9f7960acb399b0c", submodules="True" ) version( - "7.8.1", tag="7.8.1", commit="47cd8c85aa3fde5dbb7319facd6f475438235d7d", submodules="True" + "7.8.2", tag="7.8.2", commit="09b151ecb2b3984335c265932dc6ba3e4fcb318e", submodules="True" ) - variant("coreneuron", default=False, description="Enable CoreNEURON as submodule") - variant("cross-compile", default=False, description="Build for cross-compile environment") + 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("rx3d", default=False, description="Enable cython translated 3-d rxd") - variant("tests", default=False, description="Enable unit tests") - variant("caliper", default=False, description="Add LLNL/Caliper support") + 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") - depends_on("bison", type="build") - depends_on("flex", type="build") - depends_on("py-cython", when="+rx3d", type="build") + 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("python@2.7:", when="+python") + 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("readline") + 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") - depends_on("py-numpy", type="run") - conflicts("+rx3d", when="~python") + 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)) - def cmake_options(spec_options): - value = "TRUE" if spec_options in spec else "FALSE" - cmake_name = spec_options[1:].upper().replace("-", "_") - return "-DNRN_ENABLE_" + cmake_name + ":BOOL=" + value - - args = [ - cmake_options(variant) - for variant in [ - "+coreneuron", - "+interviews", - "+mpi", - "+python", - "+rx3d", - "+coreneuron", - "+tests", - ] - ] - args.append("-DNRN_ENABLE_BINARY_SPECIAL=ON") + args.append(self.define_from_variant("CORENRN_ENABLE_SHARED", "shared")) - if "~mpi" in spec and "+coreneuron" in spec: - args.append("-DCORENRN_ENABLE_MPI=OFF") + if spec.satisfies("@:8"): + args.append(self.define("NRN_ENABLE_BINARY_SPECIAL", "ON")) - if spec.variants["build_type"].value == "Debug": - args.append("-DCMAKE_C_FLAGS=-g -O0") - args.append("-DCMAKE_CXX_FLAGS=-g -O0") - args.append("-DCMAKE_BUILD_TYPE=Custom") + if "+python" in spec: + args.append(self.define("PYTHON_EXECUTABLE", spec["python"].command.path)) - if "+legacy-unit" in spec: - args.append("-DNRN_DYNAMIC_UNITS_USE_LEGACY=ON") + 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("-DCORENRN_CALIPER_PROFILING=ON") + 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 @@ -117,30 +168,21 @@ class Neuron(CMakePackage): cxx_compiler = self.compiler.cxx kwargs = {"backup": False, "string": True} - nrnmech_makefile = join_path(self.prefix, "./bin/nrnmech_makefile") + nrnmech_makefile = join_path(self.prefix, "bin/nrnmech_makefile") # assign_operator is changed to fix wheel support - if self.spec.satisfies("@:7"): - assign_operator = "?=" - else: - assign_operator = "=" - - filter_file( - "CC {0} {1}".format(assign_operator, env["CC"]), - "CC = {0}".format(cc_compiler), - nrnmech_makefile, - **kwargs, - ) - filter_file( - "CXX {0} {1}".format(assign_operator, env["CXX"]), - "CXX = {0}".format(cxx_compiler), - nrnmech_makefile, - **kwargs, - ) - - if spec.satisfies("+coreneuron"): - corenrn_makefile = join_path(self.prefix, "share/coreneuron/nrnivmodl_core_makefile") - filter_file(env["CXX"], cxx_compiler, corenrn_makefile, **kwargs) + 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")) |