Empirical Evaluation of the Parallel Distribution Sweeping Framework on Multicore Architectures

In this paper, we perform an empirical evaluation of the Parallel External Memory (PEM) model in the context of geometric problems. In particular, we implement the parallel distribution sweeping framework of Ajwani, Sitchinava and Zeh to solve batched 1-dimensional stabbing max problem. While modern processors consist of sophisticated memory systems (multiple levels of caches, set associativity, TLB, prefetching), we empirically show that algorithms designed in simple models, that focus on minimizing the I/O transfers between shared memory and single level cache, can lead to efficient software on current multicore architectures. Our implementation exhibits significantly fewer accesses to slow DRAM and, therefore, outperforms traditional approaches based on plane sweep and two-way divide and conquer.Comment: Longer version of ESA'13 pape

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs

Assessing metric structures on GPGPU environments

Similarity search consists on retrieving objects within a database that are similar or relevant to a particular query. It is a topic of great interest to scientific community because of its many fields of application, such as searching for words and images on the World Wide Web, pattern recognition, detection of plagiarism, multimedia databases, among others. It is modeled through metric spaces, in which objects are represented in a black-box that contains only the distance between objects; calculating the distance function is costly and search systems operate at a high query rate. Metrical structures have been developed to optimize this process; such structures work as indexes and preprocess data to decrease the distance evaluations during the search. Processing large volumes of data makes unfeasible the use of such structures without using parallel processing environments. Technologies based on multi- CPU and GPU architectures are among the most force due to its costs and performance.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Assessing metric structures on GPGPU environments

Similarity search consists on retrieving objects within a database that are similar or relevant to a particular query. It is a topic of great interest to scientific community because of its many fields of application, such as searching for words and images on the World Wide Web, pattern recognition, detection of plagiarism, multimedia databases, among others. It is modeled through metric spaces, in which objects are represented in a black-box that contains only the distance between objects; calculating the distance function is costly and search systems operate at a high query rate. Metrical structures have been developed to optimize this process; such structures work as indexes and preprocess data to decrease the distance evaluations during the search. Processing large volumes of data makes unfeasible the use of such structures without using parallel processing environments. Technologies based on multi- CPU and GPU architectures are among the most force due to its costs and performance.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI