SeRC and Intel form the first OneAPI University Center of Excellence

In the opening of this week’s ISC High Performance Conference, the Swedish Center for e-Science Research (SeRC) is excited to announce that it is Intel’s first OneAPI University Center of Excellence (COE). The center will use the OneAPI heterogeneous programming model to accelerate computation for research conducted with GROMACS, advancing solutions for some of the world’s biggest life science challenges. As part of this research, massive HPC simulations will be deployed leveraging CPUs and GPUs from multiple vendors (Intel, Nvidia, AMD) to achieve new levels of efficiency and performance.

GROMACS is molecular dynamics software used by researchers around the world, and one of the flagship codes developed by SeRC. It is used to simulate large biomolecules and allows to study the functioning of molecules such as proteins and lipids at the atomic level, for example when binding other molecules or to design new drugs targeting for example COVID-19. Simulation coupled with full-scale computing gives scientists unprecedented visibility into biological molecular mechanisms and provides a digital microscope that allows them to study simulation scenarios that would be difficult or impossible to test in a traditional laboratory. Many biological processes studied by molecular dynamics (MD) are on the microsecond scale. Molecular dynamics time intervals are about one femtosecond, so it takes about 10^9 simulation intervals. To complete a simulation in about a week, each simulation step must be calculated in less than a millisecond. This is only possible with very efficient communication between CPUs and GPUs working together.

To achieve this, researchers at SeRC, KTH, and SU are working closely with many academic groups and educators around the world, as well as with engineers at Intel on software optimizations for OneAPI.

According to Erik Lindahl, professor of biophysics at KTH & SU, “It is exceptionally important for us that GROMACS is able to efficiently use all of the world’s fastest supercomputers, and the upcoming Exascale machines powered by OneAPI will allow us to simulate processes that we could not even imagine a few years ago, such as how a virus binds to proteins in a cell and infects it.”

As a OneAPI Center of Excellence, SeRC will lead the way in innovation via academia and industry by conducting research, creating compelling applications and solutions based on OneAPI technology, and leading the teaching of key results over multiple years.  “The future of hardware is heterogeneous, making the evolution to open, high-performance portable APIs essential, and we are particularly pleased with the way the ecosystem has been closely involved from the start in developing and driving OneAPI,” says Lindahl.

“Ongoing GROMACS research by Stockholm University/KTH promises new breakthroughs in biomolecular research that will enrich and improve the lives of people around the world. The collaboration with OneAPI in this endeavor will enable developers and researchers to efficiently leverage the performance of diverse computing architectures with a unified, open programming model,” said Jeff McVeigh, Intel vice president for XPU Datacenter Products and Solutions.

Source: e-science.se
Translation: ritme.com