From time to time I get a very short opportunity to try and do some science, and I find the context switching harder and harder. To that end, I want to make more use of ipython-notebook.

Nowadays my compute environment is a macbook pro running mavericks, and I have two VMS built: a JASMIN analysis platform (JAP) image (based on Centos, for science) and a Linux Mint image (primarily to give me a route to reliable LibreOffice - unlike the version running on the Mac). Both can run ipython notebook, but I couldn’t work out how to get that visible to browsers running in my Mac environment (which is what I wanted this time).

I could probably have worked that out, but I thought, it’s about time I got some hands on experience with docker, since everyone is raving about it, and folks in my team are also starting to use it … so why not try that route?

Herewith a couple of hours on a Saturday afternoon and another hour or so on a Sunday morning:

I got boot2docker working, and then I thought I’d try out the continuumio anaconda image … but I immediately discovered that it didn’t have netcdf4 and basemap by default (and that matplotlib was broken), so herewith my first dockerfile:

# aims to run basemap, and eventually, cf-python
# the anaconder base image is itself based on debian
FROM continuumio/anaconda
MAINTAINER Bryan Lawrence <>

# as of May 10, 2015 the base image needs this to work with matplotlib:
RUN apt-get -y install libglib2.0-0

# now the stuff we want
RUN conda install netcdf4
RUN conda install basemap

I was able to build that using

docker build -t bnlawrence/cfconda .

and run it using:

docker run -it  -v $(pwd):/usr/data -w /usr/data -p 8888:8888 bnlawrence/cfconda

(from within a directory on the mac where I wanted my notebooks to reside.) I then have to run

ipython notebook --ip= --no-browser

inside the container, whereupon, as if by magic, I can access my notebooks on the mac at

(I would have liked to have run the notebook directly on the end of the docker run statement, but when i do that, the notebook kernel seems to be really unstable and repeatedly crash. I don’t know why.)

Now, hopefully I can start using ipython notebook during my working week …