Teaching basic lab skills
for research computing

An Advanced Short Course in Leeds

Helped by Aaron O'Leary, Peter Willetts, Marlene Mengoni and Jo Leng, Martin Callaghan, Devasena Inupakutika and I recently delivered a modified Software Carpentry workshop at the University of Leeds. Aimed at environmental scientists from across the UK and funded by NERC, the course included an extra day where small groups got to develop tools for environmental data analysis.

Training for Graduate Students

The funding landscape for graduate students in science in the UK has changed. Most of our gaggle of research councils now provide funding to universities to train coherent groups of PhD students. These students can be working on related research projects in an area where a particular national training need has been identified (creating doctoral training centres such as the DTC in fluid dynamics in Leeds) or undertaking a broader range of projects where supervision and generic training is provided by a consortium of university departments working with other organisations in the private and public sectors (forming doctoral training partnerships such as the Leeds-York DTP).

Although a late starter in this process, the Natural Environment Research Council (NERC) has embraced the approach and now funds most of its doctoral training via these two routes. NERC now pays closer attention to the training needs of graduate students in the environmental sciences, for example by asking employers about skill gaps and encouraging universities to fill these.

The usual way for research councils to encourage universities to do anything is by providing an opportunity for academics to compete for funding. NERC's Advanced Training Short Course scheme offers funding specifically to address identified skills gaps. These include "scientific computing in environmental sciences" and "data processing in environmental sciences", so Software Carpentry is clearly needed for the UK's environmental scientists. In May this year and working with Neil Chue Hong at the Software Sustainability Institute we applied for for funding under this scheme. The application is available online but, in essence, we asked for funding to:

  • Create modified Software Carpentry lessons targeted at NERC students and including additional material on, for example, handling geospatial data and accessing such data from online repositories.
  • Run two three-day workshops based on the Software Carpentry model to deliver this material to NERC students from around the UK. The third day of these workshops was added to allow small groups of students to work together to practice their skills and begin to develop software that may be useful for their research projects.
  • Offer the modifications back to Software Carpentry, so that they could be used again to train further environmental scientists in the UK and elsewhere.

We have now delivered the first of these workshops and describe some of the successes and difficulties below.

Software Difficulties

As is traditional (and probably inevitable) we discovered a handful challenges with software installation on diverse laptops brought to the workshop. Despite these by 9:30 day 1 everybody had a working installation.

The most notable new problem was a Windows machine where the username contained a non-ascii character. This almost works out of the box. However, accents in the directory name for the homespace propagate into python strings used to to find configuration files (e.g. when matplotlib is imported, or an iPython notebook server is started). This problem will probably go away when we move to python 3, but in the interim the best solution we found was to create a new user account (without accents in the username) and install everything there. It would be good to know if a better solution to this exists.

A second problem with software cropped up unexpectedly over lunch on the first day. Our etherpad, which was being used for collaborative note taking and to ease the distribution of long strings (URLs and the like) failed, getting itself into a state of permanently "loading...". Marlene eventually managed to cajole the old information (in somewhat corrupted form) out of the ether and we moved over to an alternative pad. The lesson for other workshops may be to download text copies of the etherpad fairly frequently to allow a quick recovery.

The third noteable little challenge only emerged when we started looking at environmental data stored in netCDF files. For two people data could not be read despite having the netcdf4 module installed and successfully imported. This turned out to be a problem with the underlying library installed by Anaconda on 32 bit Ubuntu systems. The solution (discovered by Aaron) is to install an alternative version using:

 $ conda remove netcdf4
 $ sudo apt-get build-dep python-netcdf4
 $ sudo apt-get install libhdf5-serial-dev
 $ pip install netcdf4

Programming Success?

Most of day three (apart from a short recap in the morning and wrap up and feedback session at the end of the day) was taken up by a mini data analysis hackathon where small groups worked to create software to solve problems conceived by the participants. This seemed to be remarkably successful with each group producing a working tool written in python that had been developed collaboratively using Git and with at least some documentation and error handling. We ended up with:

  • A tool to download and map historic earthquake data for a region from the USGS data service (GitHub).
  • A flight miles calculator that converts airport codes to locations, calculates the great circle distance between the airports, and plots this on a map (GitHub).
  • An iPython notebook that scrapes a website to determine when a particular satellite will next be overhead (GitHub).
  • Some fairly complex object oriented code to fit a range of equations of state to pressure - volume data for Earth materials (GitHub).
  • An iPython notebook to examine the geographical distribution of the genetics of bacteria using an online database (GitHub).
  • A data gridder for shallow geophysical surveys allowing scattered data sets to be imported into ArcGIS (GitHub).

All the groups managed to demonstrate and talk about their project in a wrap up session at the end of the day. I was amazed. Not only were twenty PhD students exposed to a new programming language, their first version control system, and concepts such as defensive programming and testing in only two days. They were able to demonstrate that they had learned to use their new skills by undertaking collaborative programming project dealing with real data from the environmental sciences and get something working in only five hours.

Going Forward

We will be giving the course again in January and we collected feedback during and after the workshop to help us improve for the next iteration. The biggest trends in feedback across the course were "Git is hard" and "the IPython notebook is great". More detailed feedback from the end of the workshop included:

Good points Places to improve
the helpers needed a general overview for Git, also pictures
practical session on day three lost track of defensive programming
Git was taught and then used it in practice the next day sometimes hard to read text (colours of text difficult)
iPython notebooks! good to type as we are going along difficult to keep up when following along with terminal lessons (esp when writing files)
the hands on approach could do with a Git/GitHub workflow model
working through whole examples end to end (in particular basemap) got lost with Git
the pre course information - install instructions, install tests we weren't introduced to dealing with [general] external files from python until near the end or in the practical part
the number and variety of helpers much more engaged when doing practical examples (problem solving) rather than typing what someone else was typing
forced to do something for a whole day rather than listening and following needed more stuff on shell scripting with regard to automating a process using a pipeline
good number of people. excellent ratio of helpers / students
good to rotate people between tables each day

Overall, I think we probably spent a little too much time on basic shell at the start of day 1 (which most people had seen before) and should have planned to spend more time with Git (perhaps breaking the single two hour slot into two lessons, each with their own exercises). We will try to improve next time, but need to remember that the previous experience of the next group could be significantly different. We should also make sure that when we teach using the terminal, the text is large and clear (what is clear on a projector is different to what is clear on laptop display) and make more reference to some of the useful online help for git. For example, we did not show this or make very much reference to the online tutorial.

NERC have just announced details of next year's ATSC scheme. Scientific computing is still on the list of key skills to be provided and we are starting to discuss a new application for funding. A major objective must be to attempt to embed this kind of training into the training experienced by of most of NERC's PhD students. Key to this would be to work with several of the institutions that host large doctoral training partnerships and seek to leave sufficient instructors and helpers in NERC's research community so that the DTPs will run their own training in the future. This may imply that we need to find and train more instructors.

We are looking forward to our second workshop in January. We will report on the modified material once we have given it another go, when we will need to work out the best way to make this widely available.

BOOTCAMPS · UNIVERSITY OF LEEDS

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