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The strategy of using CUDA-compatible GPUs as a parallel computation solution to improve the performance of programs has been more and more widely approved during the last two years since the CUDA platform was released. Its benefit extends…
Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to…
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…
In this work, we consider the solution of boundary integral equations by means of a scalable hierarchical matrix approach on clusters equipped with graphics hardware, i.e. graphics processing units (GPUs). To this end, we extend our…
Effective intra-node GPU communication is essential for optimizing performance in MPI-based HPC applications, especially when leveraging multiple communication paths. In this study, we propose a novel approach that integrates CUDA Graphs…
Analysis of processing time and similarity of images generated between CPU and GPU architectures and sequential and parallel programming. For image processing a computer with AMD FX-8350 processor and an Nvidia GTX 960 Maxwell GPU was used,…
The main goal in many fields in the empirical sciences is to discover causal relationships among a set of variables from observational data. PC algorithm is one of the promising solutions to learn underlying causal structure by performing a…
Developments in Genome-Wide Association Studies have led to the increasing notion that future healthcare techniques will be personalized to the patient, by relying on genetic tests to determine the risk of developing a disease. To this end,…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
The continued growth of the computational capability of throughput processors has made throughput processors the platform of choice for a wide variety of high performance computing applications. Graphics Processing Units (GPUs) are a prime…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Huffman compression is a statistical, lossless, data compression algorithm that compresses data by assigning variable length codes to symbols, with the more frequently appearing symbols given shorter codes than the less. This work is a…
High-performance computing of array signal processing problems is a critical task as real-time system performance is required for many applications. Noise subspace-based Direction-of-Arrival (DOA) estimation algorithms are popular in the…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Growing heterogeneity and configurability in HPC architectures has made auto-tuning applications and runtime parameters on these systems very complex. Users are presented with a multitude of options to configure parameters. In addition to…
We demonstrate a GPU-accelerated nested sampling framework for efficient high-dimensional Bayesian inference in cosmology. Using JAX-based neural emulators and likelihoods for cosmic microwave background and cosmic shear analyses, our…
Immersed boundary methods (IBMs) facilitate the simulation of flows around stationary, moving, and deforming bodies on Cartesian grids. However, extending these simulations to the large grid sizes required for realistic flow problems…
High-throughput physics experiments require efficient and increasingly complex real-time processing. This paper presents a modular, software-defined platform combining high-bandwidth PCIe digitizers with consumer GPUs to achieve continuous,…
Persistent homology is a crucial invariant that is used in many areas to understand data. The $O(N^4)$ run time is a hindrance to its use on most large datasets. We give a parallelization method to utilize multi-core machines and clusters.…