12 papers · ranked by Valyu relevance
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…
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…
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…
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…