UC San Diego oneAPI Center of Excellence to Bring High-performance Simulations to Amber

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The University of California San Diego (UC San Diego) announces the establishment of a new oneAPI Center of Excellence at its San Diego Supercomputer Center (SDSC). The oneAPI Center will focus on enabling high-performance molecular dynamics (MD) simulations in Amber – a biomolecular simulation software package used by thousands of scientists in academia, national laboratories and industry. The channel for this is oneAPI – an open, standards-based, cross-architecture programming model for central processing units (CPUs) and accelerators for faster application performance, more productivity and more innovation.

“MD simulations have greatly accelerated the pace of development from novel medical therapies to new building materials to better batteries,” said Pradeep K. Khosla, Chancellor of UC San Diego. “The San Diego Supercomputer Center at UC San Diego, in partnership with Intel, continues to lead the way in advancing computing and simplifying software development so today’s researchers can work more efficiently to bring life-saving treatments, sustainable building materials and tomorrow’s energy to the world.” to bring efficient technologies to the market.”

According to UC San Diego’s Andreas Goetz, research assistant at SDSC and group leader for Data-Driven and High-Performance Computational Chemistry, MD simulations are crucial to understanding how molecules like proteins and lipids that make up cells or viruses , work at the atomic level and to predict how drugs will interact with therapeutic targets. Goetz explained that MD time steps are on the order of femtoseconds (one quadrillionth of a second), while relevant physical and biomolecular processes often occur on the microsecond time scale or longer, thus requiring billions of time steps.

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“We want to push the frontiers of science to gain insights that are unattainable today, so it is crucial for us to achieve the highest possible computing power on any given hardware and to be able to use all of the world’s fastest supercomputers, including new exascale machines with multi-architecture systems, including the latest CPUs and GPUs,” said Goetz, who leads the oneAPI Center of Excellence and has been an Amber developer for many years. “The oneAPI Center optimizations using oneAPI will modernize Amber’s code for portability, make it multi-architecture ready, and ensure MD simulations can take full advantage of the performance of upcoming graphics processing units (GPUs).”

An additional benefit that oneAPI brings to Amber is the creation of a single source code base that developers can use to gain flexibility in choosing the best hardware for solutions, rather than being limited to a single vendor’s proprietary architecture. This is important because the overhead of maintaining different code bases with vendor-specific programming languages ​​is significant and slows progress. oneAPI’s open and unified programming model provides a solution to support heterogeneous architectures across multiple vendors.

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“We’re really excited about this prospect,” Goetz said, “and the lessons learned and best practices for software development will be shared with the broader molecular simulation and computational science community.”

Frank Würthwein, SDSC director and professor of physics at UC San Diego, said that SDSC has a long history of HPC technology collaborations with Intel, and the company’s engineers will work with SDSC and the oneAPI Center on these efforts. “We are very excited to establish a close working relationship with open standards programming for high performance applications like Amber. Our mission at SDSC is to put innovation into practice and be at the forefront of research efforts in supercomputing. The oneAPI Center will be important in this regard and will be the basis for the adoption of oneAPI for other important high-performance computing applications that our researchers are developing,” he said.

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“This oneAPI Center of Excellence at the San Diego Supercomputer Center at UC San Diego extends Amber with multi-architecture readiness via oneAPI. This achievement will benefit the thousands of scientists using molecular dynamics simulations to achieve the next breakthroughs in drug discovery and related research,” said Scott Apeland, senior director of Intel Developer Ecosystem Programs.

About SDSC

The San Diego Supercomputer Center is a pioneer and leader in high-performance and data-intensive computing, providing cyber infrastructure resources, services and expertise to the national research community, academia and industry. Located on the UC San Diego campus, the SDSC supports hundreds of multidisciplinary programs spanning a variety of fields from astrophysics and earth sciences to disease research and drug discovery.

Via oneAPI

oneAPI is an open, unified, cross-architecture programming model for CPUs and accelerator architectures (GPUs, FPGAs and others). The standards-based programming model simplifies software development and delivers uncompromised performance for accelerated computing without proprietary lock-in, while allowing integration with existing code. With oneAPI, developers can choose the best architecture for the specific problem they are trying to solve without having to rewrite software for the next architecture and platform.

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