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Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
We introduce CuPyMag, an open-source, Python-based framework for large-scale micromagnetic simulations with magnetostriction. CuPyMag solves micromagnetics with finite elements in a GPU-resident workflow in which key operations, such as…
The Preconditioned Conjugate Gradient (PCG) method is widely used for solving linear systems of equations with sparse matrices. A recent version of PCG, Pipelined PCG, eliminates the dependencies in the computations of the PCG algorithm so…
Unstructured meshes present challenges in scientific data analysis due to irregular distribution and complex connectivity. Computing and storing connectivity information is a major bottleneck for visualization algorithms, affecting both…
Solving discretized versions of the Dirac equation represents a large share of execution time in lattice Quantum Chromodynamics (QCD) simulations. Many high-performance computing (HPC) clusters use graphics processing units (GPUs) to offer…
High-order gas-kinetic scheme (HGKS) has become a workable tool for the direct numerical simulation (DNS) of turbulence. In this paper, to accelerate the computation, HGKS is implemented with the graphical processing unit (GPU) using the…
Modern GPUs are equipped with tensor cores (TCs) that are commonly used for matrix multiplication in artificial intelligence workloads. However, because they have high computational throughput, they can lead to significant performance gains…
We introduce a CUDA-Accelerated Timestepper for Alpha Particles Using Local Tricubics (CATAPULT) for use in Monte Carlo calculations of alpha particle confinement in stellarators. Our GPU implementation is significantly faster than existing…
The numerical integration of stochastic trajectories to estimate the time to pass a threshold is an interesting physical quantity, for instance in Josephson junctions and atomic force microscopy, where the full trajectory is not accessible.…
Linear Programs (LPs) appear in a large number of applications and offloading them to a GPU is viable to gain performance. Existing work on offloading and solving an LP on a GPU suggests that there is performance gain generally on large…
Block-tridiagonal systems are prevalent in state estimation and optimal control, and solving these systems is often the computational bottleneck. Improving the underlying solvers therefore has a direct impact on the real-time performance of…
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and…
In recent years, the rapidly increasing number of reads produced by next-generation sequencing (NGS) technologies has driven the demand for efficient implementations of sequence alignments in bioinformatics. However, current…
GPUs have been widely used to accelerate computations exhibiting simple patterns of parallelism - such as flat or two-level parallelism - and a degree of parallelism that can be statically determined based on the size of the input dataset.…
Intensive computation is entering data centers with multiple workloads of deep learning. To balance the compute efficiency, performance, and total cost of ownership (TCO), the use of a field-programmable gate array (FPGA) with…
Numerical integration of stochastic differential equations is commonly used in many branches of science. In this paper we present how to accelerate this kind of numerical calculations with popular NVIDIA Graphics Processing Units using the…
This paper introduces cuVegas, a CUDA-based implementation of the Vegas Enhanced Algorithm (VEGAS+), optimized for multi-dimensional integration in GPU environments. The VEGAS+ algorithm is an advanced form of Monte Carlo integration,…
A modern graphics processing unit (GPU) is able to perform massively parallel scientific computations at low cost. We extend our implementation of the checkerboard algorithm for the two dimensional Ising model [T. Preis et al., J. Comp.…
We empirically characterise the cost-efficiency deficit between cloud Tensor Processing Units and GPUs for finite-field cryptography. Against A100 GPU baselines (cuZK), we measure a $[5{,}558\times, 6{,}908\times]$ deficit across v5p and v4…
Modern graphics computing units (GPUs) are designed and optimized to perform highly parallel numerical calculations. This parallelism has enabled (and promises) significant advantages, both in terms of energy performance and calculation. In…