SoHPC meets FFEA at EPCC
Posted: 5 Oct 2015 | 12:24
Since 2013, EPCC has hosted PRACE Summer of HPC (SoHPC) students for eight weeks from early July. I was involved with SoHPC for the first time this year as mentor of two Masters students, Jana Boltersdorf from FH Aachen University of Applied Sciences (Germany) and Ondřej Vysocký from Brno University of Technology (Czech Republic).
Toni Collis, who was also co-mentor, had arranged for Jana and Ondřej to work on the Fluctuating Finite Element Analysis tool (FFEA) with developers Albert Solernou and Ben Hanson as part of a collaboration between EPCC and Sarah Harris' Computational Biophysics group in Leeds. Jana and Ondřej were joined by one other summer student, Anna Chantzoplaki from the University of Macedonia (Greece), who was to work on an exciting supercomputing app with mentors Nick Brown and Amy Krause.
FFEA simulates protein complexes at the meso scale by treating globular proteins as a viscoelastic continuum subject to thermal noise. Parallelised with OpenMP, FFEA simulations output protein trajectories that are viewed and manipulated in FFEA's in-house Python viewer (see above). Jana was tasked with investigating adding MPI parallelisation to improve FFEA's performance and Ondřej's project brief was to develop FFEA's user interace by developing its visualisation tool.
Having arrived in Edinburgh after an intense but fun week of training in Barcelona, the students spent the first few weeks of their placement getting to know FFEA and participating in some ARCHER HPC training courses whilst acclimatising to the bonny Scottish weather. Jana focussed on obtaining scaling results for different protein models using Morar and ARCHER, whilst identifying areas of the code that could be refactored and potentially parallelised with MPI. Ondřej looked into the possibliity of replacing the in-house viewer with Paraview, writing a script to convert FFEA output to VTK format (see some of his results below).
Coming from a computer science background, the students did well to get to grips with the scientific jargon of the project so quickly. Weekly telcons with FFEA developers Albert and Ben helped Jana and Ondřej keep on top of understanding the code and overcoming any stumbling blocks. Aside from their project work, Jana and Ondřej also had to write regular progress reports and blog articles.
The summer seemed to fly by for students and mentors alike. By the start of their final week, the students had made good progress: Jana obtained interesting scaling results and Ondřej did some promising initial work on porting the visualisation part of FFEA to Paraview. The FFEA developers were pleased with Jana and Ondřej's work, which gave them useful avenues to explore for future development.
The students wrapped up their summerships with presentations to EPCC staff, final reports and video summaries (see below). It was a busy last few weeks indeed!
All of us who were involved with SoHPC this year at EPCC enjoyed the programme and I for one am looking forward to being involved next year. SoHPC is a great way to introduce students to the 'real world' of HPC research and development. We wish all our SoHPC students the best of luck in their careers.
Neelofer Banglawala, EPCC