Docker image for MDToolbox

Ocatve + Jupyter docker image ready for use with MDToolbox. MDToolbox is a MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories.

This image is based on jupyter/datascience-notebook and Octave kernel for Jupyter.

Usage

Jupyter notebook

Starts the Notebook server listening for HTTP connections on port 8888 with a randomly generated authentication token configured.

docker run --rm -p 8888:8888 -v $(pwd):/home/jovyan/work ymatsunaga/octave

Take note of the URL+authentication_token appeared in the notebook startup log messages.

Pase them to your browser's address bar and access to the notebook.

Create a notebook selecting "Octave" from [New] pulldown.

In Mac OSX, you may get black graph when plotting (due to some trouble with png). This problem can be avoided by putting the following before calling plot():

%plot --format svg
y = 1:0.1:10
x = sin(y)
plot(x, y)

Interactive use with terminal (without GUI)

docker run -it --rm -v $(pwd):/home/jovyan/work ymatsunaga/octave octave

Execute an Octave script (batch run)

docker run --rm -v $(pwd):/home/jovyan/work ymatsunaga/octave octave script.m