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We present new algorithms for the parallelization of Eulerian-Lagrangian interaction operations in the immersed boundary method. Our algorithms rely on two well-studied parallel primitives: key-value sort and segmented reduce. The use of…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
We propose a new arc consistency enforcement paradigm that transforms arc consistency enforcement into recurrent tensor operations. In each iteration of the recurrence, all involved processes can be fully parallelized with tensor…
We investigate the parallel performance of Parallel Spectral Deferred corrections, a numerical approach that provides small-scale parallelism for the numerical solution of initial value problems. The scheme is applied to the shallow-water…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
The sheer sizes of modern datasets are forcing data-structure designers to consider seriously both parallel construction and compactness. To achieve those goals we need to design a parallel algorithm with good scalability and with low…
Processors with large numbers of cores are becoming commonplace. In order to take advantage of the available resources in these systems, the programming paradigm has to move towards increased parallelism. However, increasing the level of…
The core numbers of vertices in a graph are one of the most well-studied cohesive subgraph models because of the linear running time. In practice, many data graphs are dynamic graphs that are continuously changing by inserting or removing…
Nowadays, parallel computing is ubiquitous in several application fields, both in engineering and science. The computations rely on the floating-point arithmetic specified by the IEEE754 Standard. In this context, an elementary brick of…
Tensor computations, with matrix multiplication being the primary operation, serve as the fundamental basis for data analysis, physics, machine learning, and deep learning. As the scale and complexity of data continue to grow rapidly, the…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
We report on the implementation of an algorithm for computing the set of all regular triangulations of finitely many points in Euclidean space. This algorithm, which we call down-flip reverse search, can be restricted, e.g., to computing…
The use of Model Predictive Control in industry is steadily increasing as more complicated problems can be addressed. Due to that online optimization is usually performed, the main bottleneck with Model Predictive Control is the relatively…
To prepare images for better segmentation, we need preprocessing applications, such as smoothing, to reduce noise. In this paper, we present an enhanced computation method for smoothing 2D object in binary case. Unlike existing approaches,…
Today, very large amounts of data are produced and stored in all branches of society including science. Mining these data meaningfully has become a considerable challenge and is of the broadest possible interest. The size, both in numbers…
The hypercube queueing model was initially developed to address spatial queueing problems and has found wide applications in emergency services, such as ambulance and police systems. While the model was originally designed for homogeneous…
Algebraic matrix multiplication algorithms are designed by bounding the rank of matrix multiplication tensors, and then using a recursive method. However, designing algorithms in this way quickly leads to large constant factors: if one…
In this paper, we describe efficient MapReduce simulations of parallel algorithms specified in the BSP and PRAM models. We also provide some applications of these simulation results to problems in parallel computational geometry for the…
Generalized sparse matrix-matrix multiplication (or SpGEMM) is a key primitive for many high performance graph algorithms as well as for some linear solvers, such as algebraic multigrid. Here we show that SpGEMM also yields efficient…
The interplay of quantum and classical simulation and the delicate divide between them is in the focus of massively parallelized tensor network state (TNS) algorithms designed for high performance computing (HPC). In this contribution, we…