NEURON: add v7.8.2, move to CMake and remove all old versions (#20582)

* Update NEURON simulator package
  - update recipe to support autoconf as well as cmake
  - new versions >=7.8 support cmake
  - remove old variants
  - added patch for latest bug fix release 7.8.2

Co-authored-by: Kumbhar Pramod Shivaji <kumbhar@bbpv1.epfl.ch>
Co-authored-by: Kumbhar Pramod Shivaji <kumbhar@bb-c02vf1h0hv2r.epfl.ch>

var/spack/repos/builtin/packages/neuron/package.py

@@ -3,185 +3,123 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
 from spack import *
 
 
-class Neuron(Package):
+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. The primary scripting
+    requiring the user to manually create compartments.
-    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"
+    url      = "https://neuron.yale.edu/ftp/neuron/versions/v7.7/nrn-7.7.tar.gz"
-    git      = "https://github.com/nrnhines/nrn.git"
+    git      = "https://github.com/neuronsimulator/nrn"
+    maintainers = ['pramodk', 'nrnhines', 'iomaganaris', 'alexsavulescu']
 
-    version('develop', branch='master')
+    version('develop', branch='master', submodules='True')
-    version('7.5', sha256='67642216a969fdc844da1bd56643edeed5e9f9ab8c2a3049dcbcbcccba29c336')
+    version("7.8.2", tag="7.8.2", submodules='True')
-    version('7.4', sha256='1403ba16b2b329d2376f4bf007d96e6bf2992fa850f137f1068ad5b22b432de6')
+    version("7.8.1", tag="7.8.1", submodules='True')
-    version('7.3', sha256='71cff5962966c5cd5d685d90569598a17b4b579d342126b31e2d431128cc8832')
-    version('7.2', sha256='c777d73a58ff17a073e8ea25f140cb603b8b5f0df3c361388af7175e44d85b0e')
 
-    variant('mpi',           default=True,  description='Enable MPI parallelism')
+    variant("coreneuron",    default=False, description="Enable CoreNEURON as submodule")
-    variant('python',        default=True,  description='Enable python')
+    variant("cross-compile", default=False, description="Build for cross-compile environment")
-    variant('shared',        default=False, description='Build shared libraries')
+    variant("interviews",    default=False, description="Enable GUI with INTERVIEWS")
-    variant('cross-compile', default=False, description='Build for cross-compile environment')
+    variant("legacy-unit",   default=False, description="Enable legacy units")
-    variant('multisend',     default=True,  description="Enable multi-send spike exchange")
+    variant("mpi",           default=True,  description="Enable MPI parallelism")
-    variant('rx3d',          default=False, description="Enable cython translated 3-d rxd")
+    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")
 
-    depends_on('flex',       type='build')
+    depends_on("bison",     type="build")
-    depends_on('bison',      type='build')
+    depends_on("flex",      type="build")
-    depends_on('automake',   type='build')
+    depends_on("py-cython", when="+rx3d", 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("gettext")
-    depends_on('python@2.6:', when='+python')
+    depends_on("mpi",         when="+mpi")
-    depends_on('ncurses',     when='~cross-compile')
+    depends_on("ncurses")
+    depends_on("python@2.7:", when="+python")
+    depends_on("py-pytest",   when="+python+tests")
+    depends_on("readline")
 
-    conflicts('~shared', when='+python')
+    conflicts("+rx3d",        when="~python")
 
-    filter_compiler_wrappers('*/bin/nrniv_makefile')
+    patch("patch-v782-git-cmake-avx512.patch", when="@7.8.2")
 
-    def get_neuron_archdir(self):
+    def cmake_args(self):
-        """Determine the architecture-specific neuron base directory.
+        spec = self.spec
 
-        Instead of recreating the logic of the neuron's configure
+        def cmake_options(spec_options):
-        we dynamically find the architecture-specific directory by
+            value = "TRUE" if spec_options in spec else "FALSE"
-        looking for a specific binary.
+            cmake_name = spec_options[1:].upper().replace("-", "_")
-        """
+            return "-DNRN_ENABLE_" + cmake_name + ":BOOL=" + value
-        file_list = find(self.prefix, '*/bin/nrniv_makefile')
+
-        # check needed as when initially evaluated the prefix is empty
+        args = [cmake_options(variant) for variant in ["+coreneuron",
-        if file_list:
+                                                       "+interviews",
-            neuron_archdir = os.path.dirname(os.path.dirname(file_list[0]))
+                                                       "+mpi",
+                                                       "+python",
+                                                       "+rx3d",
+                                                       "+coreneuron",
+                                                       "+tests"]]
+        args.append("-DNRN_ENABLE_BINARY_SPECIAL=ON")
+
+        if "~mpi" in spec and '+coreneuron' in spec:
+            args.append("-DCORENRN_ENABLE_MPI=OFF")
+
+        if "+python" in spec:
+            args.append("-DPYTHON_EXECUTABLE:FILEPATH="
+                        + spec["python"].command.path)
+
+        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 "+legacy-unit" in spec:
+            args.append('-DNRN_DYNAMIC_UNITS_USE_LEGACY=ON')
+
+        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 "cray" in spec.architecture:
+            cc_compiler = "cc"
+            cxx_compiler = "CC"
+        elif spec.satisfies("+mpi"):
+            cc_compiler = spec["mpi"].mpicc
+            cxx_compiler = spec["mpi"].mpicxx
         else:
-            neuron_archdir = self.prefix
+            cc_compiler = self.compiler.cc
+            cxx_compiler = self.compiler.cxx
 
-        return neuron_archdir
+        kwargs = {"backup": False, "string": True}
+        nrnmech_makefile = join_path(self.prefix,
+                                     "./bin/nrnmech_makefile")
 
-    def patch(self):
+        assign_operator = "?="
-        # aclocal need complete include path (especially on os x)
+        filter_file("CC {0} {1}".format(assign_operator, env["CC"]),
-        pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkgconfig'].prefix)
+                    "CC = {0}".format(cc_compiler),
-        libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)
+                    nrnmech_makefile,
-        newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)
+                    **kwargs)
-        filter_file(r'aclocal -I m4', r'%s' % newpath, "build.sh")
+        filter_file("CXX {0} {1}".format(assign_operator, env["CXX"]),
+                    "CXX = {0}".format(cxx_compiler),
+                    nrnmech_makefile,
+                    **kwargs)
 
-    def get_arch_options(self, spec):
+        if spec.satisfies("+coreneuron"):
-        options = []
+            corenrn_makefile = join_path(self.prefix,
-
+                                         "share/coreneuron/nrnivmodl_core_makefile")
-        if spec.satisfies('+cross-compile'):
+            filter_file(env["CXX"], cxx_compiler, corenrn_makefile, **kwargs)
-            options.extend(['cross_compiling=yes',
-                            '--without-memacs',
-                            '--without-nmodl'])
-
-        # 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 self.spec.satisfies('%pgi'):
-            flags += ' ' + self.compiler.cc_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 '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_run_environment(self, env):
-        neuron_archdir = self.get_neuron_archdir()
+        env.prepend_path("PATH", join_path(self.prefix, "bin"))
-        env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
+        env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "lib"))
-        env.prepend_path('LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
+        if self.spec.satisfies("+python"):
-
+            env.prepend_path("PYTHONPATH", self.spec.prefix.lib.python)
-    def setup_dependent_build_environment(self, env, dependent_spec):
-        neuron_archdir = self.get_neuron_archdir()
-        env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
-        env.prepend_path('LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))

var/spack/repos/builtin/packages/neuron/patch-v782-git-cmake-avx512.patch

@@ -0,0 +1,139 @@
+diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
+index 391d4daa..20b8b571 100644
+--- a/CONTRIBUTING.md
++++ b/CONTRIBUTING.md
+@@ -98,7 +98,7 @@ Currently we have enabled CMake code formatting using [cmake-format](https://git
+ * Make sure to install cmake-format utility with Python version you are using:
+ 
+ ```
+-pip3.7 install cmake-format==0.6.0 --user
++pip3.7 install cmake-format==0.6.0 pyyaml --user
+ ```
+ Now you should have `cmake-format` command available.
+ 
+diff --git a/cmake/ExternalProjectHelper.cmake b/cmake/ExternalProjectHelper.cmake
+index 57094e7e..eeb6dfc2 100644
+--- a/cmake/ExternalProjectHelper.cmake
++++ b/cmake/ExternalProjectHelper.cmake
+@@ -1,5 +1,15 @@
+ find_package(Git QUIET)
+ 
++if(${GIT_FOUND} AND EXISTS ${CMAKE_SOURCE_DIR}/.git)
++  execute_process(
++    COMMAND ${GIT_EXECUTABLE} --git-dir=.git describe --all
++    RESULT_VARIABLE NOT_A_GIT_REPO
++    ERROR_QUIET
++    WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
++else()
++  set(NOT_A_GIT_REPO "NotAGitRepo")
++endif()
++
+ # initialize submodule with given path
+ function(initialize_submodule path)
+   if(NOT ${GIT_FOUND})
+@@ -9,7 +19,7 @@ function(initialize_submodule path)
+   message(STATUS "Sub-module : missing ${path} : running git submodule update --init --recursive")
+   execute_process(
+     COMMAND
+-      git submodule update --init --recursive -- ${path}
++      ${GIT_EXECUTABLE}  submodule update --init --recursive -- ${path}
+     WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
+ endfunction()
+ 
+@@ -20,6 +30,9 @@ function(add_external_project name)
+     NAMES CMakeLists.txt
+     PATHS "${PROJECT_SOURCE_DIR}/external/${name}")
+   if(NOT EXISTS ${${name}_PATH})
++    if(NOT_A_GIT_REPO)
++      message(FATAL_ERROR "Looks like you are building from source. Git needed for ${name} feature.")
++    endif()
+     initialize_submodule(external/${name})
+   else()
+     message(STATUS "Sub-project : using ${name} from from external/${name}")
+diff --git a/git2nrnversion_h.sh b/git2nrnversion_h.sh
+index d62b7410..4d8e4015 100755
+--- a/git2nrnversion_h.sh
++++ b/git2nrnversion_h.sh
+@@ -20,10 +20,9 @@ if git log > /dev/null && test -d .git ; then
+ elif test -f src/nrnoc/nrnversion.h ; then
+         sed -n '1,$p' src/nrnoc/nrnversion.h
+ else
+-        echo "#define GIT_DATE \"1999-12-31\""
+-        echo "#define GIT_BRANCH \"?\""
+-        echo "#define GIT_CHANGESET \"?\""
+-        echo "#define GIT_DESCRIBE \"?\""
+-        exit 1
++        echo "#define GIT_DATE \"Build Time: $(date "+%Y-%m-%d-%H:%M:%S")\""
++        echo "#define GIT_BRANCH \"unknown branch\""
++        echo "#define GIT_CHANGESET \"unknown commit id\""
++        echo "#define GIT_DESCRIBE \"${PROJECT_VERSION}.dev0\""
+ fi
+ 
+diff --git a/src/ivoc/ivocvect.cpp b/src/ivoc/ivocvect.cpp
+index 4884614a..4da9e17e 100644
+--- a/src/ivoc/ivocvect.cpp
++++ b/src/ivoc/ivocvect.cpp
+@@ -67,7 +67,26 @@ extern "C" {
+ #define FRead(arg1,arg2,arg3,arg4) if (fread(arg1,arg2,arg3,arg4) != arg3) {}
+ #endif
+ 
+-static double dmaxint_;
++/**
++ * As all parameters are passed from hoc as double, we need
++ * to calculate max integer that can fit into double variable.
++ *
++ * With IEEE 64-bit double has 52 bits of mantissa, so it's 2^53.
++ * calculating it with approach `while (dbl + 1 != dbl) dbl++;`
++ * has issues with SSE and other 32 bits platform. So we are using
++ * direct value here.
++ *
++ * The maximum mantissa 0xFFFFFFFFFFFFF which is 52 bits all 1.
++ * In Python it's:
++ *
++ *  >>> (2.**53).hex()
++ *   '0x1.0000000000000p+53'
++ *  >>> (2.**53)
++ *   9007199254740992.0
++ *
++ * See https://stackoverflow.com/questions/1848700/biggest-integer-that-can-be-stored-in-a-double
++ */
++static double dmaxint_ = 9007199254740992;
+ 
+ // Definitions allow machine independent write and read
+ // note that must include BYTEHEADER at head of routine
+@@ -3776,20 +3795,7 @@ static void steer_x(void* v) {
+ }
+ 
+ void Vector_reg() {
+-	dmaxint_ = 1073741824.;
+-	for(;;) {
+-		if (dmaxint_*2. == double(int(dmaxint_*2.))) {
+-			dmaxint_ *= 2.;
+-		}else{
+-			if (dmaxint_*2. - 1. == double(int(dmaxint_*2. - 1.))) {
+-				dmaxint_ = 2.*dmaxint_ - 1.;
+-			}
+-			break;
+-		}
+-	}		
+-	//printf("dmaxint=%30.20g   %d\n", dmaxint_, (long)dmaxint_);
+-        class2oc("Vector", v_cons, v_destruct, v_members, NULL, v_retobj_members,
+-        	v_retstr_members);
++	class2oc("Vector", v_cons, v_destruct, v_members, NULL, v_retobj_members, v_retstr_members);
+ 	svec_ = hoc_lookup("Vector");
+ 	// now make the x variable an actual double
+ 	Symbol* sv = hoc_lookup("Vector");
+diff --git a/src/nrniv/CMakeLists.txt b/src/nrniv/CMakeLists.txt
+index 30024d6e..26f76a98 100644
+--- a/src/nrniv/CMakeLists.txt
++++ b/src/nrniv/CMakeLists.txt
+@@ -139,7 +139,8 @@ set(NRN_INCLUDE_DIRS
+ # is different from the contents of nrnversion.h
+ # ~~~
+ add_custom_target(
+-  nrnversion_h ${PROJECT_SOURCE_DIR}/git2nrnversion_h.sh ${PROJECT_SOURCE_DIR} > nrnversion.h.tmp
++  nrnversion_h
++  COMMAND ${CMAKE_COMMAND} -E env PROJECT_VERSION=${PROJECT_VERSION} $ENV{SHELL} ${PROJECT_SOURCE_DIR}/git2nrnversion_h.sh ${PROJECT_SOURCE_DIR} > nrnversion.h.tmp
+   COMMAND ${CMAKE_COMMAND} -E copy_if_different nrnversion.h.tmp ${NRN_NRNOC_SRC_DIR}/nrnversion.h
+   DEPENDS ${PROJECT_SOURCE_DIR}/git2nrnversion_h.sh)
+