Related papers: DNA sequence alignment: An assignment for OpenMP, …
The idea of dynamic programming (DP), proposed by Bellman in the 1950s, is one of the most important algorithmic techniques. However, in parallel, many fundamental and sequentially simple problems become more challenging, and open to a…
In this paper, we study various parallelization schemes for the Variable Neighborhood Search (VNS) metaheuristic on a CPU-GPU system via OpenMP and OpenACC. A hybrid parallel VNS method is applied to recent benchmark problem instances for…
Deep Learning (DL) algorithms have become the de facto Machine Learning (ML) algorithm for large scale data analysis. DL algorithms are computationally expensive - even distributed DL implementations which use MPI require days of training…
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…
The massive quantities of genomic data being made available through gene sequencing techniques are enabling breakthroughs in genomic science in many areas such as medical advances in the diagnosis and treatment of diseases. Analyzing this…
In the past decade, high performance compute capabilities exhibited by heterogeneous GPGPU platforms have led to the popularity of data parallel programming languages such as CUDA and OpenCL. Such languages, however, involve a steep…
MDMP is a new parallel programming approach that aims to provide users with an easy way to add parallelism to programs, optimise the message passing costs of traditional scientific simulation algorithms, and enable existing MPI-based…
The aim of parallel computing is to increase an application performance by executing the application on multiple processors. OpenMP is an API that supports multi platform shared memory programming model and shared-memory programs are…
Pseudo-arclength continuation is a well-established method for generating a numerical curve approximating the solution of an underdetermined system of nonlinear equations. It is an inherently sequential predictor-corrector method in which…
A typical enterprise uses a local area network of computers to perform its business. During the off-working hours, the computational capacities of these networked computers are underused or unused. In order to utilize this computational…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
This paper studies the utility of using data analytics and machine learning techniques for identifying, classifying, and characterizing the dynamics of large-scale parallel (MPI) programs. To this end, we run microbenchmarks and realistic…
Dynamic programming is a powerful technique that is, unfortunately, often inherently sequential. That is, there exists no unified method to parallelize algorithms that use dynamic programming. In this paper, we attempt to address this issue…
Exactly solving multi-objective integer programming (MOIP) problems is often a very time consuming process, especially for large and complex problems. Parallel computing has the potential to significantly reduce the time taken to solve such…
Similarity search in high-dimentional spaces is a pivotal operation found a variety of database applications. Recently, there has been an increase interest in similarity search for online content-based multimedia services. Those services,…
Partite, $3$-uniform hypergraphs are $3$-uniform hypergraphs in which each hyperedge contains exactly one point from each of the $3$ disjoint vertex classes. We consider the degree sequence problem of partite, $3$-uniform hypergraphs, that…
We modified a MPI-friendly density functional theory (DFT) source code within hybrid parallelization including CUDA. Our objective is to find out how simple conversions within the hybrid parallelization with mid-range GPUs affect DFT code…
An existing hybrid MPI-OpenMP scheme is augmented with a CUDA-based fine grain parallelization approach for multidimensional distributed Fourier transforms, in a well-characterized pseudospectral fluid turbulence code. Basics of the hybrid…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Given an array $\mathcal{A}$ of $n$ elements and a value $2 \leq k \leq n$, a frequent item or $k$-majority element is an element occurring in $\mathcal{A}$ more than $n/k$ times. The $k$-majority problem requires finding all of the…