Research Programming

This course is ran in the Department of Theoretical Physics and Applied Mathematics in the University of Cambridge. To run and do the exercises, you need access to a desktop/server at either DAMTP or DPMMS or a computer system with petsc4py, ipyparallel, parallel hdf5, matplotlib, an OpenMP compiler and runtime, MPI, and of course git. The DAMTP and DPMMS desktops and servers have all of these: instructions on how to access them can be found in the python nodes in modules directory.

Some familiarity with the unix shell is also necessary.

A training environment is available at slurmcluster01.westeurope.cloudapp.azure.com using the usernames and passwords provided. Further instructions on how to use that during the course as we need them.

Github

You will also need a github account to do some of the exercises: just accessing the material is possible without an account, but as some exercises require modifying a repository, an account is needed. Please surf to https://www.github.com/ if you don’t have an account yet.

Getting the Course Material

• all the course material is available in a git repository — naturally
• the repo to clone is https://github.com/juhaj/damtp-research-programming
• change to the directory where you placed the clone
  • if you used the defaults, do cd damtp-research-programming
• some instructions on using the course repo
  • after cloning, make your own branch: git branch mybranch
  • check it out: git checkout mybranch
  • whatever you do, you do on this branch to avoid complications later
  • when you want the next lecture’s material, do: git checkout master and git pull
  • you now have two options: merge master to mybranch or lose your changes to mybranch
  • merge: git checkout mybranch followed by git merge master, you need to sort your conflicts
  • lose local changes: git checkout -f master, git pull, and git checkout -B mybranch master
  • go back to doing whatever you do
  • note:
    • you do not have write access to the github repo so you cannot push
    • but you cannot screw up anything else than your local copy either so safe to play around if you wish

Licence

These lectures are (c) by Juha Jäykkä <juhaj+github@iki.fi>

All the programs are licensed under a

GNU General Public License version 3

You should have received a copy of the GNU General Public License along with the programs. If not, see http://www.gnu.org/licenses/gpl-3.0.en.html.

The lecture notes are licensed under a

Creative Commons Attribution-ShareAlike 4.0 International License.

You should have received a copy of the license along with this work. If not, see http://creativecommons.org/licenses/by-sa/4.0/.