Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed wi...

| Overheads due to synchronisation and loop scheduling are an important factor in determining the performance of shared memory parallel programs. We present set of benchmarks to measure these classes of overhead for language constructs in OpenMP. Results are presented for three diierent hardware platforms, each with its own implementation of OpenMP. Signiicant diierences are observed, which sug...

In this work we report on our experiences running OpenMP programs on a commodity cluster of PCs running a software distributed shared memory (DSM) memory system. We compare the performance of message passing implementations of a subset of the NAS Parallel Benchmarks with their OpenMP counterpart and quantify the difference in performance in terms of remote and local memory access and synchroniz...

In this paper, we evaluate the recently available directives in OpenMP 4 to parallelize a computational kernel using both the traditional shared memory approach and the newer accelerator targeting capabilities. In addition, we explore various transformations that attempt to increase application performance portability, and examine the expressiveness and performance implications of using these a...

Writing a parallel shared memory application that scales well on the future multi-core processors is a challenging task. The contention among shared resources increases as the number of threads increases. This may cause a false sharing problem, which can degrade the performance of an application. OpenMP Tools (OMPT) [2]a performance tool APIs for OpenMPenables performance tools to gather useful...

The recent addition of task parallelism to the OpenMP shared memory API allows programmers to express concurrency at a high level of abstraction and places the burden of scheduling parallel execution on the OpenMP run time system. Efficient scheduling of tasks on modern multi-socket multicore shared memory systems requires careful consideration of an increasingly complex memory hierarchy, inclu...

The main goal of this research is to use OpenMP, Posix Threads and Microsoft Parallel Patterns libraries to design an algorithm to compute Matrix Multiplication effectively. By using the libraries of OpenMP, Posix Threads and Microsoft Parallel Patterns Libraries, one can optimize the speedup of the algorithm. First step is to write simple program which calculates a predetermined Matrix and giv...

State-of-the-art multiprocessor systems pose several difficulties: (i) the user has to parallelize the existing serial code; (ii) explicitly threaded programs using a thread library are not portable; (iii) writing efficient multi-threaded programs requires intimate knowledge of machine’s architecture and micro-architecture. Thus, well-tuned parallelizing compilers are in high demand to leverage...

Programming a multicore processor is difficult. It is even more difficult if the processor has software-managed memory hierarchy, e.g. the IBM Cyclops-64 (C64). A widely accepted parallel programming solution for multicore processor is OpenMP. Currently, all OpenMP directives are only used to decompose computation code (such as loop iterations, tasks, code sections, etc.). None of them can be u...