SeRC will use Intel's oneAPI to optimize molecular dynamics workloads...
The Swedish e-Science Research Center (SeRC) has become the first academic center of excellence for Intel’s oneAPI.
OneAPI is Intel’s unified software stack for CPUs, GPUs, FPGAs and other accelerators. As data-centric workloads become more specialized, so do the compute architectures we use to process them, which include FPGAs and ASICs for AI acceleration. OneAPI aims to simplify development across multiple compute architectures and stop developers being locked-in to a single architecture or a single vendor.
Hosted at Stockholm University (SU) and the KTH Royal Institute of Technology, SeRC’s research is concerned with computation of large data sets and the use of high-performance computing.
Specifically, SeRC will use OneAPI’s heterogeneous programming model to accelerate compute for research that uses Gromacs. Gromacs (Groningen machine for chemical simulation) is a software package used for simulation of molecular dynamics in proteins, lipids and nucleic acids, such as in the popular folding@home project. Gromacs is used by researchers worldwide on some of the biggest challenges in life science; its workloads are typically accelerated by CPUs and GPUs.
SeRC will work with Intel engineers on using oneAPI to optimize performance of Gromacs workloads on CPUs and GPUs. Many of the processes being studied in molecular dynamics are on a timescale of microseconds, so the time-steps used in simulation are typically around a femtosecond. To compute all 109 of the required simulation steps with, say, a week, requires computing each step in a millisecond. This requires very efficient communication between CPUs and GPUs at exascale.
“It is exceptionally important to us that Gromacs is able to make efficient use of all the fastest supercomputers in the world, and the upcoming exascale machines powered by oneAPI will make it possible to simulate processes we could not even imagine a few years ago, such as how a virus binds to proteins on a cell and infects it,” said Erik Lindahl, Professor of Biophysics at KTH & SU.
Findings and best practices for software development will be shared across the broad academic community, and via Intel’s academic engagements with top educational institutions worldwide.