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28 August 2017 to 1 September 2017
Europe/Copenhagen timezone

Exercises

Exercises

There are three exercise sessions on Tuesday (ISM), Wednesday (Disks), and Thursday (Feedback).

The aim of the exercise session is to complement the theory presented in the morning lectures, learn how to run simulations, and give hands on knowledge with two important publicly available codes Analysis of the data produced from running the models will be done with Python.

The exercises are made such that they can run on a laptop in a reasonable time, but the resolution of the models can easily be scaled up or down, if participants would like to explore more, and have access to larger computational resources at their home institution.

We expect you to work in groups of two to three persons. This will help in keeping focus, discuss the problems you encounter with your peers, and finish the exercise in a reasonable time.

To run the exercises on a laptop, the following software is required:
  • C and Fortran compilers e.g. gcc and gfortran
  • A Python installation including the matplotlib and numpy packages
  • The YT Python analysis framework
  • The osiris Python analysis framework for analysing RAMSES data
In addition the following tools are useful
  • git for checking out the different codes
  • ipython for interactive python sessions
  • An MPI library (e.g. OpenMPI or MPICH) for speeding up the execution of the codes
  • If you have access to GPUs you can use CUDA to run FARGO3D

Code Clinic

Monday afternoon we will help everybody with installing missing tools, but it is a great help if you try first yourself.


How to install

Simulation Codes and Analysis Tools

  • RAMSES and osiris

(a) Check it out with git with the command:

git clone https://bitbucket.org/rteyssie/ramses.git
git clone https://bitbucket.org/nvaytet/osiris.git


(b) download a zip-file from the page

When osiris has been installed you have to add the folder where you installed it to your pythonpath. This may be done by writing

export PYTHONPATH="path-to-where-osiris-is-installed":$PYHTONPATH

in the terminal window where you will use osiris.

If you use an integrated PYTHON development environment (like Canopy), then check this article for hints about how to do it. 

  • FARGO3D

Download from the hompage:
http://fargo.in2p3.fr/Download

Please have a look at the documentation at http://fargo.in2p3.fr/manuals/FARGO3DUserGuide.pdf

  • YT
First make sure you have Python properly installed (see below). If this is the case, installing YT may be possible using "pip" from a terminal window, by typing

pip install yt

Otherwise, follow instructions on the YT home page: http://yt-project.org


Linux

  • git, gcc, gfortran, OpenMPI / MPICH, and Python: Use your package manager to install


OSX

  • gitgccgfortranOpenMPI / MPICH, and Python: gcc, git and python may already be installed, but maybe not with enough python packages, and gfortran will be missing. We therefore recommend you to install a third party package manager. This could for example be
mac ports: https://www.macports.org
home brew: https://brew.sh

Once you have the package manager installed it is easy to install all the needed software.


WINDOWS

  • To install gcc, gfortran, and python under windows the easiest approach is to install the Cygwin environment. You can read more about it here:

Once you have the package manager installed it is easy to install all the needed software.