Month: February 2020

Running Jupyter notebooks on Imperial College’s compute cluster

We were really glad to see James Howard (NHLI, Faculty of Medicine) announcing on Twitter that he’d published a Kaggle kernel to accompany his recent publication on MR image analysis for cardiac pacemaker identification using neural networks via PyTorch and torchvision. Sharing code in this way is a great way to promote open research, enable reproducibility and encourage re-use.

Figure 3 from Cardiac Rhythm Device Identification Using Neural Networks

We thought it might be helpful to explain how to run similar notebooks on Imperial’s cluster compute service, given that it can provide some benefits while you’re developing code:

  • Your code and data remain securely on-premise, thanks to the RCS Jupyter Service and Research Data Store
  • You can run parallel interactive and non-interactive jobs that span several days, across multiple GPUs

With James’ permission we’ve lightly modified his notebook and published it in an exemplar repository alongside some instructions to run it on the compute cluster. We hope this can help others to use a combination of Conda, Jupyter and PBS in order to conduct GPU-accelerated machine learning on infrastructure managed by the College’s Research Computing Service – without incurring any cost at the point of use.

Many thanks to James Howard for sharing his notebook and reviewing our instructions

RSLondonSouthEast 2020

RSLondonSouthEast 2020, the annual gathering for Research Software Engineers based in or around London, took place on the 6th February at the Royal Society. The College was strongly represented by contributions from RSEs based at Imperial.

Full talks:

Lightning talks:

Posters:

Jeremy Cohen introduces RSLondonSouthEast 2020 at the Royal Society

Jeremy Cohen (Department of Computing) was the chair of the organising committee. Stefano Galvan (Department of Mechanical Engineering), Alex Hill (Department of Infectious Disease Epidemiology) and Jazz Mack Smith (Department of Metabolism, Digestion and Reproduction) served on the programme committee.

Many thanks to all the committee members and everyone who presented, submitted proposals or attended on the day, and to EPSRC and the Society of Research Software Engineering for their support. For more information from the event check Jeremy’s full report, RESIDE’s blog post or #RSLondonSE2020 on Twitter.