Nvidia supercomputer fights influenza

With the help of a fair few Nvidia Tesla GPUs, a team of Chinese researchers has managed to construct a simulation of the H1N1 influenza virus – down to the atomic level.

A team at the catchy-named Institute of Process Engineering of Chinese Academy of Sciences is taking advantage of molecular dynamic simulations to use as a kind of microscope, letting them look into the atomic structure of H1N1. Over 2,200 Tesla GPUs power the Mole-8.5 supercomputer.

Without the supercomputer they’d be in for a tough job. The problem with studying bacteria and viruses in the lab is that specific reactions happen very quickly, and the detail is so minute they’re often lost forever. Using an accurate simulation means the team can stop-and-start whever they need to.

Even simulating viruses has been difficult in the past, according to Nvidia, because of the complexity of running billions of particles in exactly the right environment.

To get around that, the researchers created a molecular dynamics simulation which uses GPU acceleration, running on 288 server nodes. 

Using the Mole-8.5 supercomputer, they managed to simulate 770 picoseconds perday, with, says the team, an integration time step of one femtosecond for 300 million atoms. A femtosecond is not long at all.

Eventually, the team believes its research could lead to important breakthroughs in anti-viral drugs to control H1N1, and provide the researchers with an insight into controlling epidemics.