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Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
This paper satisfies the reproducibility challenge of the Student Cluster Competition at Supercomputing 2017. We attempted to reproduce the results of H\"{o}hnerbach et al. (2016) for an implementation of a vectorized code for the Tersoff…
Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
We examine the Xeon Phi, which is based on Intel's Many Integrated Cores architecture, for its suitability to run the FDK algorithm--the most commonly used algorithm to perform the 3D image reconstruction in cone-beam computed tomography.…
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…
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…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
The increasing use of heterogeneous embedded systems with multi-core CPUs and Graphics Processing Units (GPUs) presents important challenges in effectively exploiting pipeline, task and data-level parallelism to meet throughput requirements…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
A current trend in HPC systems is the utilization of architectures with SIMD or vector extensions to exploit data parallelism. There are several ways to take advantage of such modern vector architectures, each with a different impact on the…
The multi-pumping resource sharing technique can overcome the limitations commonly found in single-clocked FPGA designs by allowing hardware components to operate at a higher clock frequency than the surrounding system. However, this…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…
In this paper, we describe our vectorized and parallelized adaptive mesh refinement (AMR) N-body code with shared time steps, and report its performance on a Fujitsu VPP5000 vector-parallel supercomputer. Our AMR N-body code puts…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…