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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 paper addresses the problem of parallelizing computations to study non-linear dynamics in large networks of non-locally coupled oscillators using heterogeneous computing resources. The proposed approach can be applied to a variety of…

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…

Applications to process seismic data employ scalable parallel systems to produce timely results. To fully exploit emerging processor architectures, application will need to employ threaded parallelism within a node and message passing…

We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on…

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…

Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…

Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…

To achieve scalability with today's heterogeneous HPC resources, we need a dramatic shift in our thinking; MPI+X is not enough. Asynchronous Many Task (AMT) runtime systems break down the global barriers imposed by the Bulk Synchronous…

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…

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…

This paper describes how we successfully used the HPX programming model to port the DCA++ application on multiple architectures that include POWER9, x86, ARM v8, and NVIDIA GPUs. We describe the lessons we can learn from this experience as…

We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…

Current HPC systems provide memory resources that are statically configured and tightly coupled with compute nodes. However, workloads on HPC systems are evolving. Diverse workloads lead to a need for configurable memory resources to…

The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…

MPI implementations commonly rely on explicit memory-copy operations, incurring overhead from redundant data movement and buffer management. This overhead notably impacts HPC workloads involving intensive inter-processor communication. In…

The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…

As fusion energy devices advance, plasma simulations are crucial for reactor design. Our work extends BIT1 hybrid parallelization by integrating MPI with OpenMP and OpenACC, focusing on asynchronous multi-GPU programming. Results show…

We present a sparse linear system solver that is based on a multifrontal variant of Gaussian elimination, and exploits low-rank approximation of the resulting dense frontal matrices. We use hierarchically semiseparable (HSS) matrices, which…