Introduction

The skeleton codes are available here. At the moment we are only using the 2D MPI-parallelized code ppic2.

Installation

I assume you intend to run the code on OS X and that you're using Homebrew.

1. Make sure that you have Python 2 and 3 as well as Open MPI installed.

   $ brew install python python3 open-mpi
   

2. Install tool for managing virtual Python environments.

   $ pip install virtualenvwrapper
   

3. Create a Python 3 virtual environment.

   $ mkvirtualenv -p python3.5 skeletor
   

4. Go the directory where you've cloned this repository. Then install the required Python packages.

   $ pip install -r requirements.txt
   

5. Now you should have everything to build and run the code.

   $ make
   $ mpirun -np 4 python tests/test_skeletor.py
   

   If you get the error

   ImportError: No module named 'skeletor'
   

   then you need to add the top-level Skeletor directory (i.e. the directory you're in right now) to the PYTHONPATH. To do this in this shell session, run

   $ export PYTHONPATH=${PYTHONPATH}:${PWD}
   

   but you should probably make this permanent by editing your ~/.bashrc.

Running interactively on multiple processors

For details see ipyparallel's documentation.

First time

Make sure ipyparallel and jupyter are installed on your system/in your virtual environment. Then create a parallel iPython profile:

$ ipython profile create --parallel --profile=mpi

Edit the file ~/.ipython/profile_mpi/ipcluster_config.py and add the line

c.IPClusterEngines.engine_launcher_class = 'MPIEngineSetLauncher'

Every time

Start the cluser:

$ ipcluster start -n 4 --profile=mpi

Open another terminal and start the Jupyter notebook:

$ jupyter notebook