Related papers: GPU Scheduler for De Novo Genome Assembly with Mul…

Several classic problems in graph processing and computational geometry are solved via incremental algorithms, which split computation into a series of small tasks acting on shared state, which gets updated progressively. While the…

One of the most important and commonly used operations in many linear algebra functions is matrix-matrix multiplication (GEMM), which is also a key component in obtaining high performance of many scientific codes. It is a computationally…

NVIDIA's Multi-Instance GPU (MIG) is a feature that enables system designers to reconfigure one large GPU into multiple smaller GPU slices. This work characterizes this emerging GPU and evaluates its effectiveness in designing…

Efficient implementations of parallel applications on heterogeneous hybrid architectures require a careful balance between computations and communications with accelerator devices. Even if most of the communication time can be overlapped by…

Maximal Biclique Enumeration (MBE) holds critical importance in graph theory with applications extending across fields such as bioinformatics, social networks, and recommendation systems. However, its computational complexity presents…

Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…

This paper presents Nova, a real-time scheduling framework for serving agentic vision-language models (VLMs) on a single GPU with balanced per-request latency and overall request process throughput. Our design begins by enabling effective…

Genetic Algorithms (GAs) are used to solve search and optimization problems in which an optimal solution can be found using an iterative process with probabilistic and non-deterministic transitions. However, depending on the problem's…

In this paper we present an optimized parallel implementation of a flexible MAP decoder for synchronization error correcting codes, supporting a very wide range of code sizes and channel conditions. On mid-range GPUs we demonstrate decoding…

Achieving high performance for GPU codes requires developers to have significant knowledge in parallel programming and GPU architectures, and in-depth understanding of the application. This combination makes it challenging to find…

Pipelining between data loading and computation is a critical tensor program optimization for GPUs. In order to unleash the high performance of latest GPUs, we must perform a synergetic optimization of multi-stage pipelining across the…

Deep learning (DL) shows its prosperity in a wide variety of fields. The development of a DL model is a time-consuming and resource-intensive procedure. Hence, dedicated GPU accelerators have been collectively constructed into a GPU…

In cloud machine learning (ML) inference systems, providing low latency to end-users is of utmost importance. However, maximizing server utilization and system throughput is also crucial for ML service providers as it helps lower the…

This work presents a fully GPU-accelerated algorithm for the polygonal mesh generator known as Polylla. Polylla is a tri-to-polygon mesh generator, which benefits from the half-edge data structure to manage any polygonal shape. The proposed…

Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…

With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…

Genetic Programming (GP) is a computationally intensive technique which is naturally parallel in nature. Consequently, many attempts have been made to improve its run-time from exploiting highly parallel hardware such as GPUs. However, a…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

This paper investigates the parallelization of Dijkstra's algorithm for computing the shortest paths in large-scale graphs using MPI and CUDA. The primary hypothesis is that by leveraging parallel computing, the computation time can be…

In order to satisfy timing constraints, modern real-time applications require massively parallel accelerators such as General Purpose Graphic Processing Units (GPGPUs). Generation after generation, the number of computing clusters made…