Bilgisayar Mühendisliği Bölümü Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/45

Browse

Now showing 1 - 12 of 12

Citation - WoS: 1
Citation - Scopus: 1
Accelerating Brain Simulations on Graphical Processing Units
(IEEE, 2015) Kayraklıoğlu, Engin; El-Ghazawi, Tarek A.; Bozkuş, Zeki
NEural Simulation Tool(NEST) is a large scale spiking neuronal network simulator of the brain. In this work we present a CUDA(R) implementation of NEST. We were able to gain a speedup of factor 20 for the computational parts of NEST execution using a different data structure than NEST's default. Our partial implementation shows the potential gains and limitations of such possible port. We discuss possible novel approaches to be able to adapt generic spiking neural network simulators such as NEST to run on commodity or high-end GPGPUs.
Citation - WoS: 1
Citation - Scopus: 3
Analytical Expense Management System
(IEEE, 2009) Bozkuş, Zeki; Bisson, Christophe; Arsan, Taner
Although the development of communication technologies (e.g: UMTS ADSL) allowed the elaboration of multiple users' web applications (e.g. information storage) there are still many improvements on many applications to be done and uncovered areas. Expense management systems on web application area are still in their infancy. Expense management software is widely spread in companies and most of time supported by their intranet. These solutions are quite simple as they mainly collect the information related to the expenses and may propose a simple aggregation of these figures. The result is close to what an excel sheet provides.
Citation - WoS: 7
Big Data Platform Development With a Domain Specific Language for Telecom Industries
(IEEE, 2013) Şenbalcı, Cüneyt; Altuntaş, Serkan; Bozkuş, Zeki; Arsan, Taner
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. hi 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.
Citation - WoS: 2
Citation - Scopus: 2
Developing Adaptive Multi-Device Applications With the Heterogeneous Programming Library
(Springer, 2015) Vinas, Moises; Bozkuş, Zeki; Fraguela, Basilio B.; Andrade, Diego; Doallo, Ramon
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.
Citation - WoS: 27
Citation - Scopus: 27
Exploiting Heterogeneous Parallelism With the Heterogeneous Programming Library
(Academic Press Inc Elsevier Science, 2013) Vinas, Moises; Bozkuş, Zeki; Fraguela, Basilio 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. (C) 2013 Elsevier Inc. All rights reserved.
Citation - WoS: 6
Citation - Scopus: 8
Gpu Accelerated Molecular Docking Simulation With Genetic Algorithms
(Springer International Publishing Ag, 2016) Altuntaş, Serkan; Bozkuş, Zeki; Fraguela, Basilio 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 similar to 14x with respect to a single CPU core. This makes it very productive to use GPU for small molecule docking cases.
Citation - WoS: 1
Citation - Scopus: 1
Hybrid Mpi Plus Upc Parallel Programming Paradigm on an Smp Cluster
(TUBITAK Scientific & Technical Research Council Turkey, 2012) Bozkuş, Zeki
The symmetric multiprocessing (SMP) cluster system which consists of shared memory nodes with several multicore central processing units connected to a high-speed network to form a distributed memory system is the most widely available hardware architecture for the high-performance computing community. Today the Message Passing Interface (MPI) is the most widely used parallel programming paradigm for SMP clusters in which the MPI provides programming both for an SMP node and among nodes simultaneously. However Unified Parallel C (UPC) is an emerging alternative that supports the partitioned global address space model that can be again employed within and across the nodes of a cluster. In this paper we describe a hybrid parallel programming paradigm that was designed to combine MPI and UPC programming models. This paradigm's objective is to mix the MPI's data locality control and scalability strengths with UPC's fine-grain parallelism and ease of programming to achieve multiple-level parallelism at the SMP cluster which itself has multilevel parallel architecture. Utilizing a proposed hybrid model and comparing MPI-only to UPC-only implementations this paper presents a detailed description of Cannon's algorithm benchmark application with performance results of a random-access benchmark and the Barnes-Hut N-Body simulation. Experiments indicate that the hybrid MPI+UPC model can significantly provide performance increases of up to double in comparison with UPC-only implementation and up to 20% increases in comparison to MPI-only implementation. Furthermore an optimization was achieved that improved the hybrid performance by an additional 20%.
Citation - WoS: 12
Citation - Scopus: 15
Improving Opencl Programmability With the Heterogeneous Programming Library
(Elsevier Science Bv, 2015) Vinas, Moises; Fraguela, Basilio B.; Bozkuş, Zeki; Andrade, Diego
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.
Citation - WoS: 1
Citation - Scopus: 5
Optimizing Neuron Brain Simulator With Remote Memory Access on Distributed Memory Systems
(Institute of Electrical and Electronics Engineers Inc., 2016) Shehzad, Danish; Bozkuş, Zeki
The Complex neuronal network models require support from simulation environment for efficient network simulations. To compute the models increasing complexity necessitated the efforts to parallelize the NEURON simulation environment. The computational neuroscientists have extended NEURON by dividing the equations for its subnet among multiple processors for increasing the competence of hardware. For spiking neuronal networks inter-processor spikes exchange consume significant portion of overall simulation time on parallel machines. In NEURON Message Passing Interface (MPI) is used for inter processor spikes exchange MPI-Allgather collective operation is used for spikes exchange generated after each interval across distributed memory systems. However as the number of processors become larger and larger MPI-Allgather method become bottleneck and needs efficient exchange method to reduce the spike exchange time. This work has improved MPI-Allgather method to Remote Memory Access (RMA) based on MPI-3.0 for NEURON simulation environment MPI based on RMA provides significant advantages through increased communication concurrency in consequence enhances efficiency of NEURON and scaling the overall run time for the simulation of large network models.1 © 2015 IEEE.
Optimizing Neuron Simulation Environment Using Remote Memory Access With Recursive Doubling on Distributed Memory Systems
(Hindawi Ltd, 2016) Shehzad, Danish; Bozkuş, Zeki
Increase in complexity of neuronal network models escalated the efforts to make NEURON simulation environment efficient. The computational neuroscientists divided the equations into subnets amongst multiple processors for achieving better hardware performance. On parallel machines for neuronal networks interprocessor spikes exchange consumes large section of overall simulation time. In NEURON for communication between processors Message Passing Interface (MPI) is used. MPI Allgather collective is exercised for spikes exchange after each interval across distributed memory systems. The increase in number of processors though results in achieving concurrency and better performance but it inversely affects MPI Allgather which increases communication time between processors. This necessitates improving communication methodology to decrease the spikes exchange time over distributed memory systems. This work has improved MPI Allgather method using Remote Memory Access (RMA) by moving two-sided communication to one-sided communication and use of recursive doubling mechanism facilitates achieving efficient communication between the processors in precise steps. This approach enhanced communication concurrency and has improved overall runtime making NEURON more efficient for simulation of large neuronal network models.
Citation - WoS: 4
Citation - Scopus: 4
A Portable High-Productivity Approach To Program Heterogeneous Systems
(IEEE, 2012) Bozkuş, Zeki; Fraguela, Basilio 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 heterogeneous 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.
Citation - Scopus: 4
A Software Architecture for Inventory Management System
(2013) Arsan, Taner; Başkan, Emrah; Ar, Emrah; Bozkuş, Zeki
Inventory Management is one of the basic problems in almost every company. Before computer age and integration paper tables and paperwork solutions were being used as inventory management tools. These we very far from being a solution took so much time even needed employees just for this section of organization. There was no an efficient solution available in the many companies during these days. Every process was based on paperwork human fault rate was high the process and the tracing the inventory losses were not possible and there was no efficient logging systems. After the computer age every process is started to be integrated into electronic environment. And now we have qualified technology to implement new solutions to these problems. Software based systems bring the advantages of having the most efficient control with less effort and employees. These developments provide new solutions for also inventory management systems in this context. In this paper a new solution for Inventory Management System (IMS) is designed and implemented. Most importantly this system is designed for Kadir Has University and used as Inventory Management System. © 2013 Springer Science+Business Media.

Browse

Browsing Bilgisayar Mühendisliği Bölümü Koleksiyonu by Institution Author "Bozkuş, Zeki"