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It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
Quantum computing is an emerging technology, promising a paradigm shift in computing, and allowing for speedups in many different problems. However, quantum devices are still in their early stages, most with only a small number qubits. This…
In this tutorial paper, we will firstly review some basic simulation concepts and then introduce the parallel and distributed simulation techniques in view of some new challenges of today and tomorrow. More in particular, in the last years…
This paper presents a comprehensive comparison of three dominant parallel programming models in High Performance Computing (HPC): Message Passing Interface (MPI), Open Multi-Processing (OpenMP), and Compute Unified Device Architecture…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
We introduce synax, a novel library for automatically differentiable simulation of Galactic synchrotron emission. Built on the JAX framework, synax leverages JAX's capabilities, including batch acceleration, just-in-time compilation, and…
Recent progress in artificial intelligence (AI) and high-performance computing (HPC) have brought potentially game-changing opportunities in accelerating reactive flow simulations. In this study, we introduce an open-source computational…
HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008.…
Batched linear solvers play a vital role in computational sciences, especially in the fields of plasma physics and combustion simulations. With the imminent deployment of the Aurora Supercomputer and other upcoming systems equipped with…
Quantum circuit simulators have a long tradition of exploiting massive hardware parallelism. Most of the times, parallelism has been supported by special purpose libraries tailored specifically for the quantum circuits. Quantum circuit…
Recent trends in the HPC field have introduced new CPU architectures with improved vectorization capabilities that require optimization to achieve peak performance and thus pose challenges for performance portability. The deployment of…
Histograms are widely used in medical imaging, network intrusion detection, packet analysis and other stream-based high throughput applications. However, while porting such software stacks to the GPU, the computation of the histogram is a…
High-performance computing has recently seen a surge of interest in heterogeneous systems, with an emphasis on modern Graphics Processing Units (GPUs). These devices offer tremendous potential for performance and efficiency in important…
Parallel computing has turned out to be the enabling technology to solve complex physical systems. However, the transition from shared memory, vector computers to massively parallel, distributed memory systems and, recently, to hybrid…
Modern compute nodes in high-performance computing provide a tremendous level of parallelism and processing power. However, as arithmetic performance has been observed to increase at a faster rate relative to memory and network bandwidths,…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
Finite-difference methods based on high-order stencils are widely used in seismic simulations, weather forecasting, computational fluid dynamics, and other scientific applications. Achieving HPC-level stencil computations on one…
Writing efficient hybrid parallel code is tedious, error-prone, and requires good knowledge of both parallel programming and multithreading such as MPI and OpenMP, resp. Therefore, we present a framework which is based on a job model that…
We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel…