Search · four archives
Search · four archives
12 papers · ranked by Valyu relevance
Temitayo Adefemi
—Parallelization has become a cornerstone of modern computing, influencing everything from high-performance supercomputers to everyday mobile devices. This paper presents a comprehensive guide on the fundamentals of parallelization that every computer scientist should know, beginning with a historical perspective that…
Onur Cankur, Aditya Tomar, Daniel Nichols, Connor Scully-Allison + 2 more
'Katherine E. Isaacs' 'Abhinav Bhatelé'] A variety of performance measurement tools exist, including profilers and tracing tools that can generate performance data [1, 7, 17, 28]. However, the data generated can be extremely large, making it challenging to sift through this data to identify performance issues. Several…
Rafael Terra, Diego Carvalho, Denis Jacob Machado, Carla Osthoff + 1 more
Advances in High-Performance Computing (HPC) have enabled increasingly complex genomic analyses, including those in phylogenomics. These analyses contribute to understanding the evolution of viruses and pathogens, improving our knowledge of disease transmission, and supporting targeted public health strategies.…
V. Schwambach, S. Cleyet-Merle, Alain Issard, Stéphane Mancini
—Computer vision applications constitute one of the key drivers for embedded multicore architectures. Although the number of available cores is increasing in new architectures, designing an application to maximize the utilization of the platform is still a challenge. In this sense, parallel performance prediction tools…
Łukasz P. Olech, Jan Kwiatkowski
In the recent years it can be observed increasing popularity of parallel processing using multi-core processors, local clusters, GPU and others. Moreover, currently one of the main requirements the IT users is the reduction of maintaining cost of the computer infrastructure. It causes that the performance evaluation of…
Donald S. Ene, V.I.E Anireh
- Evaluating how well a whole system or set of subsystems performs is one of the primary objectives of performance testing. We can tell via performance assessment if the architecture implementation meets the design objectives. Performance evaluations of several parallel algorithms are compared in this study. Both…
Garip Kusoglu, Bérenger Bramas, Stéphane Genaud
Currently, multi/many-core CPUs are considered standard in most types of computers including, mobile phones, PCs or supercomputers. However, the parallelization of applications as well as refactoring/design of applications for efficient hardware usage remains restricted to experts who have advanced technical knowledge…
Satya N. V. Arjunan, Atsushi Miyauchi, Kazunari Iwamoto, Koichi Takahashi
Studies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although…
Raja Appuswamy, Jacques Fellay, Nimisha Chaturvedi
Rapid advances in sequencing technologies are producing genomic data on an unprecedented scale. The first, and often one of the most time consuming, step of genomic data analysis is sequence alignment, where sequenced reads must be aligned to a reference genome. Several years of research on alignment algorithms has led…
Tong Zhu, Pankaj Vats, Seth Onken, Al Dunstan + 13 more
Next-generation sequencing (NGS) has transformed genomics, enabling breakthroughs in biotechnology, healthcare, and pharmaceuticals. However, exponential data growth-outpacing Moore’s Law-presents critical computational challenges for secondary analysis. We introduce Parabricks, a freely accessible, GPU-accelerated…
Kyle A. O’Connell, Zelaikha B. Yosufzai, Ross A. Campbell, Collin J. Lobb + 7 more
As genome sequencing becomes a more integral part of scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing these vast datasets. Although much work has been done to reduce compute times using various configurations of…
Costanza Pascal, Herzeel Charlotte, Verachtert Wilfried
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other…