GROMACS 2022 advances Open Source Drug Discovery with Intel oneAPI

GROMACS 2022 advances Open Source Drug Discovery with Intel oneAPI

GROMACS, accelerated by Intel oneAPI open programming and multiarchitecture tools, runs on Intel Xe architecture-based GPUs with strong performance. 

Intel is committed to fostering an open ecosystem, including technical contributions to many open source projects that are making direct real-world impacts. One example is GROMACS, a molecular dynamics package designed for simulations of proteins, lipids and nucleic acids used to design new pharmaceuticals. Recently released GROMACS 2022, developed using SYCL and oneAPI, exhibits strong performance running on multiple architectures, including Intel Xe architecture-based GPUs.

“GROMACS is one of the world’s most widely used open source molecular dynamics applications, and it’s easy to see why. The simulations we can conduct with the application grants us better understanding into things as small as the proteins in our bodies to as large as the galaxies in the universe.

Most notably, our work with GROMACS – developed and optimized with oneAPI – allows Intel to have a hand in significant advances in drug discovery and expands GROMACS open development across multiple compute architectures. And this is all while collaborating with the open source community that we so greatly value.”

Roland Schulz, parallel software engineer at Intel

Why It Matters?

GROMACS’ molecular dynamic simulations, which are powered by oneAPI, contribute to the identification of crucial pharmaceutical solutions for conditions like breast cancer, COVID-19, Type 2 diabetes, and others. In modern drug discovery, molecular dynamic simulations are applied widely and successfully. These simulations provide researchers with the structural information on biomacromolecules needed to understand the structure-function relationship that guides the drug discovery and design process. The application of computational tools like GROMACS to drug discovery helps researchers more efficiently design and evaluate new drugs while conserving resources.

The GROMACS research and development team at Stockholm University and KTH Royal Institute of Technology, directed by biophysics professor Erik Lindahl, leads the GROMACS molecular dynamics toolkit development, one of the world’s most widely used HPC applications. Molecular dynamics is among the most time-consuming HPC applications because it is a very iterative, compute-focused problem. With computation happening billions of times, that means there are millions of lines of code involved.

How It Works?

oneAPI, an open and unified programming model for CPUs and accelerators, supports multiple vendors’ architectures, which helped Lindahl and his team expand GROMACS’ support of heterogeneous hardware. This is due to improved productivity using cross-architecture and cross-vendor open standards. Based on these standards, oneAPI programming simplifies software development and delivers performance for accelerated computing without proprietary programming languages or vendor lock-in, while allowing integration of existing code, including OpenMP.

As part of the oneAPI optimization work, Lindahl’s team ported GROMACS’ CUDA code, which only runs on Nvidia hardware, to SYCL using the Intel® DPC++ Compatibility Tool (part of the Intel® oneAPI Base Toolkit), which typically automates 90-95% of the code migration.1,2 This allowed the team to create a new, single portable codebase that is cross-architecture-ready, greatly streamlining development and providing flexibility for deployment in multiarchitecture environments.

GROMACS accelerated compute was made possible through optimizations using Intel oneAPI cross-architecture tools, such as the oneAPI DPC++/C++ Compiler, oneAPI libraries, and HPC analysis and cluster tools. The oneAPI tools are in the Intel® DevCloud, a free environment to develop and test code across a variety of Intel architectures (CPU, GPU, FPGA).

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Source : Intel