10 papers · ranked by Valyu relevance
Zhenyu Li, Yong Ding, Ruwen Zhao, Shuo Wang + 2 more
With the widespread deployment of Industrial Cyber-Physical Systems (ICPS), their inherent vulnerabilities have increasingly exposed them to sophisticated cybersecurity threats. Although existing protective mechanisms can block attacks at runtime, the risk of defense failure remains. To proactively evaluate and harden…
Sangjin Lee, Sunggon Kim, Yongseok Son, Agbotiname Lucky Imoize
We propose ScaleDefrag, a parallel and asynchronous defragmentation tool that reduces defragmentation time by up to 3.8× compared to e4defrag, while improving scalability on multi-core systems. Flash-based solid-state drives (SSDs) have been widely adopted in various large-scale storage systems including cloud and HPC…
Ge Zhang
bcftools is the standard toolkit for handling VCF and BCF variant files, but it processes records on a single core; its --threads option speeds up only compression of the output, not the work done on variant records. Processing large call sets is therefore slow, and users often divide the genome and reassemble the…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Jose L Figueroa, Richard Allen White
We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC)…
Marco Savioli, Paolo Calligari, Ugo Locatelli, Gianfranco Bocchinfuso
We introduce GROMODEX, a novel tool designed to optimise GROMACS molecular dynamics (MD) simulations using a structured Design of Experiments (DoE) approach. GROMACS, though efficient, requires extensive tuning of parameters to perform optimally on different hardware and molecular systems. Manual tuning is tedious and…
Mohammed Alaa Ala’anzy, Nurdaulet Tolendi, Baizhan Baubek, Abdulmohsen Algarni + 1 more
Sorting can be approached in two main ways: sequentially and in parallel. In sequential sorting, data is processed in a single-threaded manner, which can be slow for large datasets. However, parallel sorting divides the task across multiple processing units, enabling faster results by processing data simultaneously.…
G. Kandemir, D. H. Duncan, D. van Moorselaar, J. Theeuwes
For almost half a century, target-distractor similarity has been known to induce different visual search modes. When a target is highly salient, it can pop out, suggesting parallel processing of all items irrespective of set size. By contrast, high similarity among items requires item-by-item comparison with an…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…