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Realistic reservoir simulation is known to be prohibitively expensive in terms of computation time when increasing the accuracy of the simulation or by enlarging the model grid size. One method to address this issue is to parallelize the…
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…
We present magneto-hydrodynamic simulation results for heterogeneous systems. Heterogeneous architectures combine high floating point performance many-core units hosted in conventional server nodes. Examples include Graphics Processing…
Fluid simulations are often performed using the incompressible Navier-Stokes equations (INSE), leading to sparse linear systems which are difficult to solve efficiently in parallel. Recently, kinetic methods based on the…
Numerical investigation of compressible flows faces two main challenges. In order to accurately describe the flow characteristics, high-resolution nonlinear numerical schemes are needed to capture discontinuities and resolve wide…
A high fidelity flow simulation for complex geometries for high Reynolds number ($Re$) flow is still very challenging, which requires more powerful computational capability of HPC system. However, the development of HPC with traditional CPU…
We present an approximate method for solving nonlinear control problems over long time horizons, in which the full nonlinear model is preserved over an initial part of the horizon, while the remainder of the horizon is modeled using a…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
We present a computational method for extreme-scale simulations of incompressible turbulent wall flows at high Reynolds numbers. The numerical algorithm extends a popular method for solving second-order finite differences Poisson/Helmholtz…
Accelerated computing is widely used in high-performance computing. Therefore, it is crucial to experiment and discover how to better utilize GPUGPUs latest generations on relevant applications. In this paper, we present results and share…
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…
A high-performance gas kinetic solver using multi-level parallelization is developed to enable pore-scale simulations of rarefied flows in porous media. The Boltzmann model equation is solved by the discrete velocity method with an…
We present Horizon, a new graphics processing unit (GPU)-accelerated code to solve the equations of general relativistic magnetohydrodynamics in a given spacetime. We evaluate the code in several test cases, including magnetized Riemann…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
We present a new numerical algorithm for the solution of coupled collisional and collisionless systems, based on the block structured adaptive mesh and time refinement strategy (AMR). We describe the issues associated with the…
In this work, we consider the integration of MPI one-sided communication and non-blocking I/O in HPC-centric MapReduce frameworks. Using a decoupled strategy, we aim to overlap the Map and Reduce phases of the algorithm by allowing…
Computational studies that use block-structured adaptive mesh refinement (AMR) approaches suffer from unnecessarily high mesh resolution in regions adjacent to important solution features. This deficiency limits the performance of AMR…
This paper presents a porting of {DG-SWEM}, a first-order discontinuous Galerkin solver for storm surge based on the Advanced Circulation Model (ADCIRC), to NVIDIA GPUs. Time-explicit discontinuous Galerkin methods contain a large number of…