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The special computational challenges of simulating 3-D hydrodynamics in deep stellar interiors are discussed, and numerical algorithmic responses described. Results of recent simulations carried out at scale on the NSF's Blue Waters machine…
In this survey paper, we review recent work on frameworks for the high-level, portable programming of heterogeneous multi-/manycore systems (especially, GPU-based systems) using high-level constructs such as annotated user-level software…
The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and…
Next generation High-Energy Physics (HEP) experiments are presented with significant computational challenges, both in terms of data volume and processing power. Using compute accelerators, such as GPUs, is one of the promising ways to…
This work presents an intermediate resolution model of the hydrodynamics of colloidal particles based on a mixed Eulerian-Lagrangian formulation. The particle is constructed with a small set of overlapping Peskin's Immersed Boundary kernels…
GPUs have become the dominant source of computing power for high performance computing and are increasingly being used across the High Energy Physics computing landscape for a wide variety of tasks. Though NVIDIA is currently the main…
Modern GPU systems are constantly evolving to meet the needs of computing-intensive applications in scientific and machine learning domains. However, there is typically a gap between the hardware capacity and the achievable application…
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…
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 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)…
The future of computing systems is inevitably embracing a disaggregated and composable pattern: from clusters of computers to pools of resources that can be dynamically combined together and tailored around applications requirements.…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
We scrutinize how to accelerate the bottleneck operations of Pythonic coupled cluster implementations performed on a \texttt{NVIDIA} Tesla V100S PCIe 32GB (rev 1a) Graphics Processing Unit (GPU). The \texttt{NVIDIA} Compute Unified Device…
Parallel implementation features of self-gravitating gas dynamics modeling on multiple GPUs are considered applying the GPU-Direct technology. The parallel algorithm for solving of the self-gravitating gas dynamics problem based on hybrid…
Programming efficiently heterogeneous systems is a major challenge, due to the complexity of their architectures. Intel oneAPI, a new and powerful standards-based unified programming model, built on top of SYCL, addresses these issues. In…
Parallel computing can offer an enormous advantage regarding the performance for very large applications in almost any field: scientific computing, computer vision, databases, data mining, and economics. GPUs are high performance many-core…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
We present LBcuda, a GPU accelerated version of LBsoft, our open-source MPI-based software for the simulation of multi-component colloidal flows. We describe the design principles, the optimization and the resulting performance as compared…
GPUs are now used for a wide range of problems within HPC. However, making efficient use of the computational power available with multiple GPUs is challenging. The main challenges in achieving good performance are memory layout, affecting…
Current computational systems are heterogeneous by nature, featuring a combination of CPUs and GPUs. As the latter are becoming an established platform for high-performance computing, the focus is shifting towards the seamless programming…