Browsing by Author "Bozkus,Z."

Now showing 1 - 6 of 6

Citation Count: 10
Big data platform development with a domain specific language for telecom industries
(IEEE Computer Society, 2013) Arsan, Taner; Altuntas,S.; Bozkus,Z.; Arsan,T.
This paper introduces a system that offer a special big data analysis platform with Domain Specific Language for telecom industries. This platform has three main parts that suggests a new kind of domain specific system for processing and visualization of large data files for telecom organizations. These parts are Domain Specific Language (DSL), Parallel Processing/Analyzing Platform for Big Data and an Integrated Result Viewer. In addition to these main parts, Distributed File Descriptor (DFD) is designed for passing information between these modules and organizing communication. To find out benefits of this domain specific solution, standard framework of big data concept is examined carefully. Big data concept has special infrastructure and tools to perform for data storing, processing, analyzing operations. This infrastructure can be grouped as four different parts, these are infrastructure, programming models, high performance schema free databases, and processing-analyzing. Although there are lots of advantages of Big Data concept, it is still very difficult to manage these systems for many enterprises. Therefore, this study suggest a new higher level language, called as DSL which helps enterprises to process big data without writing any complex low level traditional parallel processing codes, a new kind of result viewer and this paper also presents a Big Data solution system that is called Petaminer. © 2013 IEEE.
Citation Count: 2
Developing adaptive multi-device applications with the Heterogeneous Programming Library
(Kluwer Academic Publishers, 2015) Viñas,M.; Bozkus,Z.; Fraguela,B.B.; Andrade,D.; Doallo,R.
The usage of heterogeneous devices presents two main problems. One is their complex programming, a problem that grows when multiple devices are used. The second issue is that even if the codes for these devices can be portable on top of OpenCL, they lack performance portability, effectively requiring specialized implementations for each device to get good performance. In this paper we extend the Heterogeneous Programming Library (HPL), which improves the usability of heterogeneous systems on top of OpenCL, to better handle both issues. First, we provide HPL with mechanisms to support the implementation of any multi-device application that requires arbitrary patterns of communication between several devices and a host memory. In a second stage HPL is improved with an adaptive scheme to optimize communications between devices depending on the execution environment. An evaluation using benchmarks with very different nature shows that HPL reduces the SLOCs and programming effort of OpenCL applications by 27 and 43 %, respectively, while improving the performance of applications that exchange data between devices by 28 % on average. © 2015, Springer Science+Business Media New York.
Citation Count: 27
Exploiting heterogeneous parallelism with the Heterogeneous Programming Library
(2013) Viñas,M.; Bozkus,Z.; Fraguela,B.B.
While recognition of the advantages of heterogeneous computing is steadily growing, the issues of programmability and portability hinder its exploitation. The introduction of the OpenCL standard was a major step forward in that it provides code portability, but its interface is even more complex than that of other approaches. In this paper, we present the Heterogeneous Programming Library (HPL), which permits the development of heterogeneous applications addressing both portability and programmability while not sacrificing high performance. This is achieved by means of an embedded language and data types provided by the library with which generic computations to be run in heterogeneous devices can be expressed. A comparison in terms of programmability and performance with OpenCL shows that both approaches offer very similar performance, while outlining the programmability advantages of HPL. © 2013 Elsevier Inc. All rights reserved.
Citation Count: 8
GPU accelerated molecular docking simulation with genetic algorithms
(Springer Verlag, 2016) Altuntaş,S.; Bozkus,Z.; Fraguela,B.B.
Receptor-Ligand Molecular Docking is a very computationally expensive process used to predict possible drug candidates for many diseases. A faster docking technique would help life scientists to discover better therapeutics with less effort and time. The requirement of long execution times may mean using a less accurate evaluation of drug candidates potentially increasing the number of false-positive solutions, which require expensive chemical and biological procedures to be discarded. Thus the development of fast and accurate enough docking algorithms greatly reduces wasted drug development resources, helping life scientists discover better therapeutics with less effort and time. In this article we present the GPU-based acceleration of our recently developed molecular docking code. We focus on offloading the most computationally intensive part of any docking simulation, which is the genetic algorithm, to accelerators, as it is very well suited to them. We show how the main functions of the genetic algorithm can be mapped to the GPU. The GPU-accelerated system achieves a speedup of around ~ 14x with respect to a single CPU core. This makes it very productive to use GPU for small molecule docking cases. © Springer International Publishing Switzerland 2016.
Citation Count: 15
Improving OpenCL programmability with the Heterogeneous Programming Library
(Elsevier B.V., 2015) Viñas,M.; Fraguela,B.B.; Bozkus,Z.; Andrade,D.
The use of heterogeneous devices is becoming increasingly widespread. Their main drawback is their low programmability due to the large amount of details that must be handled. Another important problem is the reduced code portability, as most of the tools to program them are vendor or device-specific. The exception to this observation is OpenCL, which largely suffers from the reduced programmability problem mentioned, particularly in the host side. The Heterogeneous Programming Library (HPL) is a recent proposal to improve this situation, as it couples portability with good programmability. While the HPL kernels must be written in a language embedded in C++, users may prefer to use OpenCL kernels for several reasons such as their growing availability or a faster development from existing codes. In this paper we extend HPL to support the execution of native OpenCL kernels and we evaluate the resulting solution in terms of performance and programmability, achieving very good results. © The Authors. Published by Elsevier B.V.
Citation Count: 4
A portable high-productivity approach to program heterogeneous systems
(2012) Bozkus,Z.; Fraguela,B.B.
The exploitation of heterogeneous resources is becoming increasingly important for general purpose computing. Unfortunately, heterogeneous systems require much more effort to be programmed than the traditional single or even multi-core computers most programmers are familiar with. Not only new concepts, but also new tools with different restrictions must be learned and applied. Additionally, many of these approaches are specific to one vendor or device, resulting in little portability or rapid obsolescence for the applications built on them. Open standards for programming he terogeneous systems such as OpenCL contribute to improve the situation, but the requirement of portability has led to a programming interface more complex than that of other approaches. In this paper we present a novel library-based approach to programming heterogeneous systems that couples portability with ease of use. Our evaluations indicate that while the performance of our library, called Heterogeneous Programming Library (HPL), is on par with that of OpenCL, the current standard for portable heterogeneous computing, the programming effort required by HPL is 3 to 10 times smaller than that of OpenCL based on the authors' implementation of five benchmarks. © 2012 IEEE.