ecearth3/sources/xios-2.5/extern/remap/README.mac

======================== Recipe 2 : using anaconda =========================

# install packages using macports
sudo port install openmpi
# activate what we have just installed (mandatory)
sudo port select mpi openmpi-mp-fortran
# my anaconda is in my $HOME - no need for sudo
pip install mpi4py
conda install netcdf4

compile the remap library
run the remap.py script

==================== Checking which libraries are loaded ======================

Useful to make sure that mpirun, remap and python use the same MPI library.

sudo dtruss -f -t open sudo -u $(whoami) mpirun -np 1 python test.py 2>out
grep mpich out
grep openmpi out

where test.py contains
 from mpi4py import MPI
 import netCDF4
 import ctypes as ct
 import os
 test = ct.cdll.LoadLibrary(os.path.realpath('libmapper.so'))

If grep finds both mpich and openmpi, something is wrong !

====================== Various ways to mess up python/netCDF/MPI on MacOS ====================

Anaconda vs macports python
===========================
I have several pythons installed : 3 from Apple, one from macports and one from the Anaconda distribution, which is the default on my path.

* find whether we use python from MacPorts or anaconda
 which python
the one from macports is in /opt/local/bin

* check active macports python version
 port select python
 (mine : python27)

* if desired, set the path to avoid anaconda
echo $PATH
result :  /Users/dubos/anaconda/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin
export PATH=/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin

Below,  [with macports] assumes that « which python » finds /opt/local/bin/python » while [with anaconda] assumes it finds the anaconda-provided python.

Python-netCDF
=============
[with macports] :
sudo port install py-netcdf4

[with anaconda] :
conda install netcdf4
Notice that this will also compile its own instance of netCDF.

Notice that in principle one could install python-netcdf using pip or easy_install. In my case it fails - there is a version mismatch for the HDF library at runtime

MPI
===
Macports can install openmpi, mpich or both (I have both). If both are installed one is activated by « port select ».

It will install it for a specific compiler.
* checking your active compiler
 port select gcc
* installing openmpi 
 sudo port install openmpi 
* checking for which gcc openmpi has been compiled 
 port installed openmpi-default
* checking your active mpi
 port select mpi
* selecting openmpi (for example)
 sudo port select mpi openmpi-mp-fortran

MPI4py
======
It is important to compile the mapper library with the same MPI as mpi4py !
easy_install fails on my Mac so I must use pip

[with MacPorts] :
  sudo port install py-pip
  sudo port select pip pip27
  sudo pip install mpi4py

[with anaconda]  : pip is already installed,
  which pip
  pip install mpi4py