{"action":"created","comment":{"url":"https://api.github.com/repos/LLNL/spack/pulls/comments/133571178","pull_request_review_id":56769326,"id":133571178,"diff_hunk":"@@ -0,0 +1,236 @@\n+##############################################################################\n+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.\n+# Produced at the Lawrence Livermore National Laboratory.\n+#\n+# This file is part of Spack.\n+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.\n+# LLNL-CODE-647188\n+#\n+# For details, see https://github.com/llnl/spack\n+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.\n+#\n+# This program is free software; you can redistribute it and/or modify\n+# it under the terms of the GNU Lesser General Public License (as\n+# published by the Free Software Foundation) version 2.1, February 1999.\n+#\n+# This program is distributed in the hope that it will be useful, but\n+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and\n+# conditions of the GNU Lesser General Public License for more details.\n+#\n+# You should have received a copy of the GNU Lesser General Public\n+# License along with this program; if not, write to the Free Software\n+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA\n+##############################################################################\n+import os\n+import sys\n+from spack import *\n+\n+\n+class Neuron(Package):\n+\n+    \"\"\"NEURON is a simulation environment for modeling individual\n+    and networks of neurons. NEURON models individual neurons via\n+    the use of sections that are automatically subdivided into individual\n+    compartments, instead of requiring the user to manually create\n+    compartments. The primary scripting language is hoc but a Python\n+    interface is also available.\"\"\"\n+\n+    homepage = \"https://www.neuron.yale.edu/\"\n+    url      = \"http://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz\"\n+    github   = \"https://github.com/nrnhines/nrn\"\n+\n+    version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf')\n+    version('7.3', '993e539cb8bf102ca52e9fefd644ab61')\n+    version('7.2', '5486709b6366add932e3a6d141c4f7ad')\n+    version('develop', git=github, preferred=True)\n+\n+    variant('mpi',           default=True,  description='Enable MPI parallelism')\n+    variant('python',        default=True,  description='Enable python')\n+    variant('static',        default=True,  description='Build static libraries')\n+    variant('cross-compile', default=False, description='Build for cross-compile environment')\n+    variant('multisend',     default=True,  description=\"Enable multi-send spike exchange\")\n+    variant('rx3d',          default=False, description=\"Enable cython translated 3-d rxd\")\n+\n+    depends_on('automake',   type='build')\n+    depends_on('autoconf',   type='build')\n+    depends_on('libtool',    type='build')\n+    depends_on('pkg-config', type='build')\n+    depends_on('python@2.6:', when='+python')\n+    depends_on('mpi', when='+mpi')\n+\n+    # on bg-q mpi needs to be enabled : todo test this\n+    conflicts('~mpi', when='platform=bgq')\n+\n+    # pgi compiler can't build static libraries\n+    conflicts('%pgi', when='+static')\n+\n+    def patch(self):\n+        # aclocal need complete include path especially on os x\n+        pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkg-config'].prefix)\n+        libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)\n+        newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)\n+        filter_file(r'aclocal -I m4', r'%s' % newpath, \"build.sh\")\n+\n+    def get_arch_options(self, spec):\n+        options = []\n+\n+        if 'bgq' in self.spec.architecture:\n+            options.extend(['--enable-bluegeneQ',\n+                            '--host=powerpc64',\n+                            '--without-memacs'])\n+\n+        if 'cray' in self.spec.architecture:\n+            options.extend(['--without-memacs',\n+                            '--without-nmodl',\n+                            'cross_compiling=yes'])\n+\n+            # TODO: on cray systems we get an error while linking even if\n+            # we use cc wrapper. Hence add explicitly add mpi library\n+            if spec.satisfies('+mpi'):\n+                options.append('LIBS=%s' % spec['mpi'].libs.link_flags)\n+\n+            # TODO: -pthread is not a valid pthread option for cray compiler.\n+            # for now disable use of pthread with cray compiler.\n+            if spec.satisfies('%cce'):\n+                options.append('use_pthread=no')\n+\n+        return options\n+\n+    def get_opt_flags(self):\n+        if 'bgq' in self.spec.architecture:\n+            return '-O3 -qtune=qp -qarch=qp -q64 -qstrict -qnohot -g'\n+        else:\n+            return '-O2 -g'\n+\n+    def get_arch_dir(self):\n+        if 'bgq' in self.spec.architecture:\n+            arch = 'powerpc64'\n+        elif 'cray' in self.spec.architecture:\n+            arch = 'x86_64'\n+        else:\n+            arch = self.spec.architecture.target\n+\n+        return arch\n+\n+    def get_python_options(self, spec):\n+        options = []\n+\n+        if spec.satisfies('+python'):\n+            py_version = 'python{0}'.format(spec['python'].version.up_to(2))\n+            python_exec = spec['python'].command.path\n+\n+            options.append('--with-nrnpython=%s' % python_exec)\n+            options.append('--disable-pysetup')\n+\n+            if spec.satisfies('+cross-compile'):\n+                # on cross compile builds we have to provide\n+                # PYINCDIR, PYLIB, PYLIBDIR etc\n+\n+                py_lib = spec['python'].prefix.lib\n+                py_inc = spec['python'].headers.directories[0]\n+\n+                if not os.path.isdir(py_lib):\n+                    py_lib = spec['python'].prefix.lib64\n+\n+                options.extend(['PYINCDIR=%s' % (py_inc),\n+                                'PYLIB=-L%s -l%s' % (py_lib, py_version),\n+                                'PYLIBDIR=%s' % py_lib,\n+                                'PYLIBLINK=-L%s -l%s' % (py_lib, py_version)])\n+        else:\n+            options.append('--without-nrnpython')\n+        return options\n+\n+    def get_compiler_options(self, spec):\n+        options = []\n+        flags = self.get_opt_flags()\n+\n+        # TODO: issue with static build and pgi compiler.\n+        # need to add fpic and enabled-shared\n+        if spec.satisfies('%pgi'):\n+            flags += ' ' + self.compiler.pic_flag\n+            options.extend(['CFLAGS=%s' % flags,\n+                            'CXXFLAGS=%s' % flags,\n+                            '--enable-shared'])\n+        else:\n+            options.extend(['CFLAGS=%s' % flags,\n+                            'CXXFLAGS=%s' % flags])\n+\n+        return options\n+\n+    def get_configure_options(self, spec):\n+        options = []\n+\n+        if spec.satisfies('+static'):\n+            options.extend(['--disable-shared',\n+                            'linux_nrnmech=no'])\n+\n+        # on os-x disable building carbon 'click' utility (deprecated)\n+        if (sys.platform == 'darwin'):\n+            options.append('macdarwin=no')\n+\n+        options.extend(self.get_arch_options(spec))\n+        options.extend(self.get_python_options(spec))\n+        options.extend(self.get_compiler_options(spec))\n+        return options\n+\n+    def build_nmodl(self, spec, prefix):\n+        # TODO: NEURON has two stage compilation for systems\n+        # like cray and bg-q. On these platforms it's ok to\n+        # use gcc and g++ as front-end compilers.\n+        options = ['--prefix=%s' % prefix,\n+                   '--with-nmodl-only',\n+                   '--without-x',\n+                   'CC=%s' % which(\"gcc\"),\n+                   'CXX=%s' % which(\"g++\")]\n+\n+        configure = Executable(join_path(self.stage.source_path, 'configure'))\n+        configure(*options)\n+        make()\n+        make('install')\n+\n+    def install(self, spec, prefix):\n+        c_compiler = spack_cc\n+        cxx_compiler = spack_cxx\n+\n+        # for bg-q we can't set XL as CC and CXX compiler\n+        if 'bgq' in self.spec.architecture:\n+            c_compiler = spec['mpi'].mpicc\n+            cxx_compiler = spec['mpi'].mpicxx","path":"var/spack/repos/builtin/packages/neuron/package.py","position":197,"original_position":199,"commit_id":"d260301f8bbcf176d3bd9727a68458dd2f1d0eb7","original_commit_id":"25f7fcdfea5a11a3faca25dda1148f68f700ba9d","user":{"login":"adamjstewart","id":12021217,"avatar_url":"https://avatars2.githubusercontent.com/u/12021217?v=4","gravatar_id":"","url":"https://api.github.com/users/adamjstewart","html_url":"https://github.com/adamjstewart","followers_url":"https://api.github.com/users/adamjstewart/followers","following_url":"https://api.github.com/users/adamjstewart/following{/other_user}","gists_url":"https://api.github.com/users/adamjstewart/gists{/gist_id}","starred_url":"https://api.github.com/users/adamjstewart/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamjstewart/subscriptions","organizations_url":"https://api.github.com/users/adamjstewart/orgs","repos_url":"https://api.github.com/users/adamjstewart/repos","events_url":"https://api.github.com/users/adamjstewart/events{/privacy}","received_events_url":"https://api.github.com/users/adamjstewart/received_events","type":"User","site_admin":false},"body":"It's always a good practice to double check. Someone might remove the conflict someday if they really want to build `~mpi` on `bg-q`. You should also be setting those the same way for `+mpi` on non-BGQ platforms.","created_at":"2017-08-16T21:25:54Z","updated_at":"2017-08-16T21:25:54Z","html_url":"https://github.com/LLNL/spack/pull/5097#discussion_r133571178","pull_request_url":"https://api.github.com/repos/LLNL/spack/pulls/5097","_links":{"self":{"href":"https://api.github.com/repos/LLNL/spack/pulls/comments/133571178"},"html":{"href":"https://github.com/LLNL/spack/pull/5097#discussion_r133571178"},"pull_request":{"href":"https://api.github.com/repos/LLNL/spack/pulls/5097"}}},"pull_request":{"url":"https://api.github.com/repos/LLNL/spack/pulls/5097","id":135660735,"html_url":"https://github.com/LLNL/spack/pull/5097","diff_url":"https://github.com/LLNL/spack/pull/5097.diff","patch_url":"https://github.com/LLNL/spack/pull/5097.patch","issue_url":"https://api.github.com/repos/LLNL/spack/issues/5097","number":5097,"state":"open","locked":false,"title":"Adding NEURON package widely used in computational neuroscience community","user":{"login":"pramodskumbhar","id":27898197,"avatar_url":"https://avatars2.githubusercontent.com/u/27898197?v=4","gravatar_id":"","url":"https://api.github.com/users/pramodskumbhar","html_url":"https://github.com/pramodskumbhar","followers_url":"https://api.github.com/users/pramodskumbhar/followers","following_url":"https://api.github.com/users/pramodskumbhar/following{/other_user}","gists_url":"https://api.github.com/users/pramodskumbhar/gists{/gist_id}","starred_url":"https://api.github.com/users/pramodskumbhar/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pramodskumbhar/subscriptions","organizations_url":"https://api.github.com/users/pramodskumbhar/orgs","repos_url":"https://api.github.com/users/pramodskumbhar/repos","events_url":"https://api.github.com/users/pramodskumbhar/events{/privacy}","received_events_url":"https://api.github.com/users/pramodskumbhar/received_events","type":"User","site_admin":false},"body":"This is still based on `Package` and not on `AutotoolsPackage `. For cross-compiling environment we need to follow two step compilation process and hence it's bit complicated (but still doable). In it's current format it has been tested on all platforms (OS X, Linux, BG-Q, Cray, KNL) and hence submitting this in the current 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