Over the last nine months, Dr. Mark Potse and Dr Alain Vinet, both affiliated with the Research Centre of Sacré-Cœur Hospital and the Biomedical Engineering department at UdM, began running 100 to 120 million-point models as part of their heart disease research on an SGI Altix 4700 system, believed to be the largest shared memory computing system in Canada. They regularly use 60 of the 768 Intel Itanium 2 processors running on the SGI Altix which, as part of the Quebec Network for High-Performance Computing (RQCHP), is shared by many researchers from across Canada.
In late October, Potse and Vinet had the opportunity to run their custom electrocardiography (ECG) code to solve the largest, most detailed heart model ever, using the entire SGI Altix system and1.2TB of shared memory. Originally written by them on an older SGI system and ported to the SGI Altix system's Linux environment in 2003, the ECG code made the leap from 120 million points to 2 billion with ease.
"We have been using the model code for research and not really developing it further, but after the success of the trial I am now thinking about improving the model, making it much larger and much more detailed, and attacking other diseases that we couldn't handle before," said Dr. Potse. "It's a very complicated model and it's much, much easier to write parallel programs on a shared memory machine. The Altix delivers fast processing performance for our application needs; not only because of the shared memory, but also due to the very high bandwidth interconnect. That's good for the kind of mathematical equations I'm solving and saves me a lot of time."
The researchers simulated 5 milliseconds of activation in a tissue block that included some properties of a real heart, such as fibre running in different directions. The simulation solved a system of 2 billion equations a dozen times. The test took two hours, which they describe as short for achieving the desired results. A full heartbeat, Potse outlines, would take two weeks, and they cannot claim use of the entire machine for that length of time right now.
"This was a test to see if the simulation works and to determine that, if we have a much bigger machine, our software will be able to run more efficiently," added Potse. "This capability is really for the future when we can use this size of machine on a regular basis, but with the Altix system we have made the heart model of the future today."