23 papers · ranked by Valyu relevance
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes + 5 more
'Leonor Sirotti' 'Paul Paganiban' 'Firmin Martin' 'Michael McManus' 'Philippe Hupé'] Life science has entered the so-called 'big data era' where biologists, clinicians and bioinformaticians are overwhelmed with high-throughput sequencing data. While they offer new insights to decipher the genome structure they also…
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.…
Michael Axtmann, Peter Sanders
—We investigate distributed memory parallel sorting algorithms that scale to the largest available machines and are robust with respect to input size and distribution of the input elements. The main outcome is that four sorting algorithms cover the entire range of possible input sizes. For three algorithms we devise…
Daniel Bascones, Borja Morcillo
—Sorting is one of the fundamental problems in computer science. Playing a role in many processes, it has a lower complexity bound imposed by O(n log n) when executing on a sequential machine. This limit can be brought down to sublinear times thanks to parallelization techniques that increase the number of comparisons…
Vipul Harsh, Laxmikant V. Kalé, Edgar Solomonik
To minimize data movement, state-of-the-art parallel sorting algorithms use techniques based on sampling and histogramming to partition keys prior to redistribution. Sampling enables partitioning to be done using a representative subset of the keys, while histogramming enables evaluation and iterative improvement of a…
Tomoyuki Tokuue, Tomoaki Ishiyama
Sorting is one of the most basic algorithms, and developing highly parallel sorting programs is becoming increasingly important in high-performance computing because the number of CPU cores per node in modern supercomputers tends to increase. In this study, we have implemented two multi-threaded sorting algorithms…
Dmitri I. Arkhipov, Di Wu, Keqin Li, Amelia Regan
—Sorting is a fundamental operation in computer science and is a bottleneck in many important fields. Sorting is critical to database applications, online search and indexing, biomedical computing, and many other applications. The explosive growth in computational power and availability of GPU coprocessors has allowed…
Benjamin G Jackson, Patrick S Schnable, Srinivas Aluru
Background The de novo assembly of genomes and transcriptomes from short sequences is a challenging problem. Because of the high coverage needed to assemble short sequences as well as the overhead of modeling the assembly problem as a graph problem, the methods for short sequence assembly are often validated using data…
Alexandros V Gerbessiotis
We propose new sequential sorting operations by adapting techniques and methods used for designing parallel sorting algorithms. Although the norm is to parallelize a sequential algorithm to improve performance, we adapt a contrarian approach: we employ parallel computing techniques to speed up sequential sorting. Our…
Bérenger Bramas, Muhammad Aleem
The way developers implement their algorithms and how these implementations behave on modern CPUs are governed by the design and organization of these. The vectorization units (SIMD) are among the few CPUs’ parts that can and must be explicitly controlled. In the HPC community, the x86 CPUs and their vectorization…
Alexandros V. Gerbessiotis, Constantinos J. Siniolakis
The Bulk-Synchronous Parallel model of computation has been used for the architecture independent design and analysis of parallel algorithms whose performance is expressed not only in terms of problem size n but also in terms of parallel machine properties. In this paper the performance of implementations of…
Mohammad Fasha
This work presents a comparison for the performance of sequential sorting algorithms under four different modes of execution, the sequential processing mode, a conventional multi-threading implementation, multi-threading with OpenMP Library and finally parallel processing on a super computer. Quick Sort algorithm was…
Alessio P. Buccino, Arjun Sridhar, David Feng, Karel Svoboda + 1 more
The scale of in vivo electrophysiology has expanded in recent years, with simultaneous recordings across thousands of electrodes now becoming routine. These advances have enabled a wide range of discoveries, but they also impose substantial computational demands. Spike sorting, the procedure that extracts spikes from…
Zeinab Mohammadi, Daniel Denman, Achim Klug, Tim C. Lei
Sorting neural voltages measured from a multichannel neural probe to extract the single unit activities of neuronal firing, especially in real-time, remains a significant technical challenge, largely due to the large amount of acquired data and the technical difficulties involved in processing and classifying these…
Stuart Byma, Akash Dhasade, Adrian Altenhoff, Christophe Dessimoz + 1 more
This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find similar pairs in a set of n elements such as protein sequences. Precise…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
Motivated by load balance issues in parallel calculations of the phylogenetic likelihood function, we recently introduced an approximation algorithm for efficiently distributing partitioned alignment data to a given number of CPUs. The goal is to balance the accumulated number of sites per CPU, and, at the same time…
Babu Bassa
In this communication the author describes a software tool named "ChameleonSort". The software program, developed by the present author is useful in the sorting of biological sequence variants like those accumulating mutations while diverging from the common ancestors. Examples include viral protein variants, protein…
Authors not listed
With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
Alexander S. Shved, Blake E. Ocampo, Elena S. Burlova, Casey L. Olen + 2 more
The construction, management and analysis of large in silico molecular libraries is critical in many areas of modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, "molli", which is a Python 3 cheminformatics module that provides a streamlined interface for manipulating large in silico libraries.…
Ido Ben-Shalom, Charles Lin, Brian Radak, Woody Sherman + 1 more
Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging applications spanning chemistry, biophysics, and drug discovery. However, MD can be inefficient at equilibrating water occupancy for buried cavities in proteins that…