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.

Make sure that you have Python 2 and 3 as well as Open MPI installed.
```
$ brew install python python3 open-mpi
```
Install tool for managing virtual Python environments.
```
$ pip install virtualenvwrapper
```
Create a Python 3 virtual environment.
```
$ mkvirtualenv -p python3.5 skeletor
```
Go the directory where you've cloned this repository. Then install the required Python packages.
```
$ pip install -r requirements.txt
```
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.

For details see ipyparallel's documentation.

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'

Start the cluser:

$ ipcluster start -n 4 --profile=mpi

Open another terminal and start the Jupyter notebook:

$ jupyter notebook