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GTC ON-DEMAND

Computational Biology & Chemistry
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Improving NAMD Performance on Volta GPUs
Abstract:
In 2007, NAMD was the first full-featured production molecular dynamics software to use CUDA for accelerating its costliest computations. We'll describe our latest efforts, techniques, and results in our quest to optimize NAMD to make best use of the tremendous computational capabilities of state-of-the-art Volta GPUs, particularly in new dense node configurations such as the NVIDIA DGX and ORNL Summit systems that feature NVLink-connected GPUs. In existence now for over 20 years, NAMD is a sophisticated parallel molecular dynamics program. NAMD development has emphasized parallel scalability to support large-size and long-timescale biomolecular simulations running on petascale supercomputers. As GPU technology has evolved, NAMD has benefited from moving greater amounts of work to the GPU. NVIDIA's release of Volta has now shifted the balance almost entirely to the GPU, with the small remaining CPU calculations often posing bottlenecks to NAMD's performance. Attendees will learn optimization strategies and pitfalls for achieving higher performance as Amdahl's Law poses an ever increasing challenge for mature GPU-accelerated codes like NAMD.
 
Topics:
Computational Biology & Chemistry, HPC and Supercomputing
Type:
Talk
Event:
GTC Silicon Valley
Year:
2018
Session ID:
S8727
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