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MPI applications matter. However, with the advent of many-core processors, traditional MPI applications are challenged to achieve satisfactory performance. This is due to the inability of these applications to respond to load imbalances, to…
In this paper, we present an open-source multi-resolution and multi-physics library: SPHinXsys (pronunciation: s'finksis) which is an acronym for \underline{S}moothed \underline{P}article \underline{H}ydrodynamics (SPH) for…
CFD is a ubiquitous technique central to much of computational simulation such as that required by aircraft design. Solving of the Poisson equation occurs frequently in CFD and there are a number of possible approaches one may leverage. The…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
Gaussian processes are widely used in machine learning domains but remain computationally demanding, limiting their efficient scalability across emerging hardware platforms. The GPRat library addresses these challenges using the HPX…
A stable partitioned algorithm for fluid-structure interaction (FSI) problems that couple viscous incompressible flow with structural shells or beams is described. This added-mass partitioned (AMP) scheme uses Robin (mixed) interface…
Collective communication operations such as MPI_Alltoallv are central to many HPC applications, particularly those with irregular message sizes. We design, implement, and evaluate persistent MPI RMA variants of Alltoallv based on fence and…
Recently, successes have been achieved for the high-order gas-kinetic schemes (HGKS) on unstructured meshes for compressible flows. In this paper, to accelerate the computation, HGKS is implemented with the graphical processing unit (GPU)…
We compare different Poisson solvers within the context of an electrostatic Vlasov-Poisson system. These schemes are implemented as part of the IPPL (Independent Parallel Particle Layer) library (Frey et al., 2024), which provides…
Modular trapped-ion quantum computing hardware, known as QCCDs require shuttling operations in order to maintain effective all-to-all connectivity. Each module or trap can perform only one operation at a time, resulting in low intra-trap…
This paper aims to create a transition path from file-based IO to streaming-based workflows for scientific applications in an HPC environment. By using the openPMP-api, traditional workflows limited by filesystem bottlenecks can be overcome…
The simplex algorithm has been successfully used for many years in solving linear programming (LP) problems. Due to the intensive computations required (especially for the solution of large LP problems), parallel approaches have also…
This paper presents the design, implementation, and performance analysis of a parallel and GPU-accelerated Poisson solver based on the Preconditioned Bi-Conjugate Gradient Stabilized (Bi-CGSTAB) method. The implementation utilizes the MPI…
Fluid-structure interaction (FSI) simulation of biological systems presents significant computational challenges, particularly for applications involving large structural deformations and contact mechanics, such as heart valve dynamics.…
In this paper, we propose LoopLynx, a scalable dataflow architecture for efficient LLM inference that optimizes FPGA usage through a hybrid spatial-temporal design. The design of LoopLynx incorporates a hybrid temporal-spatial architecture,…
We propose two parallel state-space exploration algorithms for hybrid systems with the goal of enhancing performance on multi-core shared memory systems. The first is an adaption of the parallel breadth first search in the SPIN model…
With the stagnation of processor core performance, further reductions in the time-to-solution for geophysical fluid problems are becoming increasingly difficult with standard time integrators. Parallel-in-time exposes and exploits…
As one of open-source codes widely used in computational ocean acoustics, FOR3D can provide a very good estimate for underwater acoustic propagation. In this paper, we propose a performance optimization and parallelization to speed up the…
Dynamic programming (DP) based algorithms are essential yet compute-intensive parts of numerous bioinformatics pipelines, which typically involve populating a 2-D scoring matrix based on a recursive formula, optionally followed by 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…