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A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
Matrix multiplication is a foundational operation in scientific computing and machine learning, yet its computational complexity makes it a significant bottleneck for large-scale applications. The shift to parallel architectures, primarily…
The growing capacity of integration allows to instantiate hundreds of soft-core processors in a single FPGA to create a reconfigurable multiprocessing system. Lately, FPGAs have been proven to give a higher energy efficiency than…
We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…
The non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter…
The pace of improvement in the performance of conventional computer hardware has slowed significantly during the past decade, largely as a consequence of reaching the physical limits of manufacturing processes. To offset this slowdown, new…
Last level cache management and core interconnection network play important roles in performance and power consumption in multicore system. Large scale chip multicore uses mesh interconnect widely due to scalability and simplicity of the…
Molecular dynamics simulations are essential tools in computational biophysics, but their performance depend heavily on hardware choices and configuration. In this work, we presents a comprehensive performance analysis of four NVIDIA GPU…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
The vision of super computer at every desk can be realized by powerful and highly parallel CPUs or GPUs or APUs. Graphics processors once specialized for the graphics applications only, are now used for the highly computational intensive…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
Due to challenging efficiency limits facing conventional and unconventional electronic architectures, information processors based on photonics have attracted renewed interest. Research communities have yet to settle on definitive…
FPMax implements four FPUs optimized for latency or throughput workloads in two precisions, fabricated in 28nm UTBB FDSOI. Each unit's parameters, e.g pipeline stages, booth encoding etc., were optimized to yield 1.42ns latency at…
The exponential growth of floating point power in graphics processing units (GPUs), together with their low cost, has given rise to an attractive platform upon which to deploy lattice QCD calculations. GPUs are essentially many (O(100))…
Quantum Computational Superiority boasts rapid computation and high energy efficiency. Despite recent advances in classical algorithms aimed at refuting the milestone claim of Google's sycamore, challenges remain in generating uncorrelated…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
A high step up dc dc converter based on an isolated dc dc converter with voltage multiplier cells for photovoltaic systems is essentially introduced in this paper. The proposed converter can provide a high step up voltage gain. The switch…
We propose a simulation-based approach for performance modeling of parallel applications on high-performance computing platforms. Our approach enables full-system performance modeling: (1) the hardware platform is represented by an abstract…
High-performance, multi-core processors are the key to accelerating workloads in several application domains. To continue to scale performance at the limit of Moore's Law and Dennard scaling, software and hardware designers have turned to…