Fixes for Neurodamus and Mac instructions (#841)

Neurodamus link dependency and Mac instructions

Neurodamus, when building in mac suffered always assumed a brew Python
Updated README.md for Mac usage

Co-authored-by: Matthias Wolf <[email protected]>

README.md

@@ -209,6 +209,30 @@ The information for external packages is stored in
   [email protected] +optimize+pic+shared: /gpfs/bbp.cscs.ch/apps/hpc/jenkins/deploy/external-libraries/2019-01-04/linux-rhel7-x86_64/gcc-6.4.0/zlib-1.2.11-w43e56tzqj
 </details>
 
+## Building software on OS X
+
+<details>
+<summary>
+Install software on OS X, using Homebrew for binary packages
+</summary>
+
+On OS X the build process is very similar to Ubuntu. To avoid building
+the whole stack from source we can likewise use another package manager to provide precompiled binaries.
+To that end we have successfully used Homebrew. We also provide a skeleton 
+`packages.yaml` that you should review and adapt to your needs.
+
+Before starting, please install brew and the required packages.
+If you require Python please install a version dowloaded from
+Python.org, as several issues have been found with Homebrew's Python
+
+ $ git clone https://github.com/BlueBrain/spack.git
+ $ mkdir ~/.spack
+ $ cp spack/sysconfig/mac_osx/*.yaml ~/.spack
+ $ . spack/share/spack/setup-env.sh
+ $ spack compiler find
+</details>
+
+
 ## Using Spack for Continuous Integration on BlueBrain5
 
 <details>

etc/spack/defaults/darwin/packages.yaml

@@ -25,7 +25,3 @@ packages:
  # although the version number used here isn't critical
  [email protected]: /usr
  buildable: False
- python:
- paths:
- [email protected]: /usr/local/opt/python3
- version: [3.7.7]

sysconfig/mac_osx/packages.yaml

@@ -0,0 +1,111 @@
+packages:
+ autoconf:
+ paths:
+ [email protected]: /usr/local/opt/autoconf
+ version: [2.69]
+ automake:
+ paths:
+ [email protected]: /usr/local/opt/automake
+ version: [1.16.1]
+ bison:
+ paths:
+ [email protected]: /usr/local/opt/bison
+ version: [3.4]
+ boost:
+ paths:
+ [email protected]: /usr/local/opt/boost
+ buildable: False
+ bzip2:
+ paths:
+ [email protected]: /usr/local/opt/bzip
+ version: [1.0.6]
+ cairo:
+ paths:
+ [email protected]: /usr/local/opt/cairo
+ version: [1.8.10]
+ catch:
+ paths:
+ [email protected]: /usr/local/opt/catch2
+ version: [2.x]
+ cmake:
+ paths:
+ [email protected]: /usr/local/opt/cmake
+ buildable: False
+ curl:
+ paths:
+ [email protected]: /usr/local/opt/curl
+ version: [7.29.0]
+ environment-modules:
+ paths:
+ [email protected]: /usr/local/opt/modules
+ buildable: False
+ flex:
+ paths:
+ [email protected]: /usr/local/opt/flex
+ version: [2.6.4]
+ fontconfig:
+ paths:
+ [email protected]: /usr/local/opt/fontconfig
+ version: [2.10.95]
+ gettext:
+ paths:
+ [email protected]: /usr/local/opt/gettext
+ version: [0.20.1]
+ hdf5:
+ paths:
+ [email protected]+mpi: /usr/local/opt/hdf5-parallel
+ version: [1.12]
+ buildable: False
+ hdf5:
+ paths:
+ [email protected]~mpi: /usr/local/opt/hdf5
+ version: [1.12]
+ hwloc:
+ paths:
+ [email protected]: /usr/local/opt/hwloc
+ version: [1.11.2]
+ openblas:
+ paths:
+ [email protected]: /usr/local/opt/openblas
+ version: [0.3.5]
+ openmpi:
+ paths:
+ [email protected]: /usr/local/opt/openmpi
+ buildable: False
+ openssl:
+ paths:
+ [email protected]: /usr/local/opt/openssl
+ version: [1.0.2k]
+ pcre:
+ paths:
+ [email protected]+jit+utf: /usr/local/opt/pcre
+ version: [8.32]
+ petsc:
+ variants: +patchmpi64
+ pkg-config:
+ paths:
+ [email protected]: /usr/local/opt/pkg-config
+ version: [0.29.2]
+ python:
+ paths:
+ [email protected]+shared: /Library/Frameworks/Python.framework/Versions/3.7
+ version: [3.7.5]
+ tcl:
+ paths:
+ [email protected]: /usr
+ version: [8.5.13]
+ trilinos:
+ variants: +kokkos+teuchos~amesos~hypre~superlu-dist~mumps~metis~suite-sparse
+ version: [xsdk-0.4.0-rc1]
+ tk:
+ paths:
+ [email protected]: /usr
+ version: [8.5.13]
+ xz:
+ paths:
+ [email protected]: /usr/local/opt/xz
+ version: [5.2]
+ zlib:
+ paths:
+ [email protected]: /usr/local/opt/zlib
+ version: [1.2.11]

var/spack/repos/builtin/packages/neurodamus-core/package.py

@@ -72,6 +72,13 @@ class NeurodamusCore(SimModel):
  # Dont apply name for now for compat with neuron+binary
  mech_name = ''
 
+ # We want neurodamus-model to fully depend on core, but no modules
+ # loaded at runtime. 'link' dependency requires libraries which we
+ # dont provide so we override libs to allow an empty LibraryList
+ @property
+ def libs(self):
+ return LibraryList([])
+
  @run_before('build')
  def prepare(self):
  filter_file(r'UNKNOWN_CORE_VERSION', r'%s' % self.spec.version,

var/spack/repos/builtin/packages/neurodamus-model/package.py

@@ -28,8 +28,8 @@ class NeurodamusModel(SimModel):
  # 'run' mode will load the same mpi module
  depends_on("mpi", type=('build', 'run'))
  depends_on('neurodamus-core', type=('build', 'run'))
- depends_on('neurodamus-core@develop', type='build', when='@develop')
- depends_on("hdf5+mpi")
+ depends_on('neurodamus-core@develop', type=('build', 'run'), when='@develop')
+ depends_on('hdf5+mpi')
  depends_on('reportinglib')
  depends_on('libsonata-report')
  depends_on('reportinglib+profile', when='+profile')
@@ -153,7 +153,7 @@ def install(self, spec, prefix):
 
  def setup_run_environment(self, env):
  self._setup_run_environment_common(env)
- for libnrnmech_name in find(self.prefix.lib, 'libnrnmech*.so',
+ for libnrnmech_name in find(self.prefix.lib, 'libnrnmech*',
  recursive=False):
  # We have the two libs and must export them in different vars
  # - NRNMECH_LIB_PATH the combined lib (used by neurodamus-py)