Putchong Uthayopas

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This practices and experience paper describes the coordination, design, implementation, availability, and performance of the Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) grid testbed. Applications in high-energy physics, genome annotation, quantum computational chemistry, wildfire simulation, and protein sequence alignment have driven the(More)
The use of an efficient multicast tree can substantially speed up many communication-intensive MPI applications. This is even more crucial for Grid environment since MPI runtime has to work on wide area network with very different and unbalanced network bandwidth. This paper proposes a new and efficient algorithm called, GADT (Genetics Algorithm based(More)
The virtual screening approach for docking small molecules into a known protein structure is a powerful tool for drug design. In this work, a combined docking and neural network approach, using a self-organizing map, has been developed and applied to screen anti-HIV-1 inhibitors for two targets, HIV-1 RT and HIV-1 PR, from active compounds available in the(More)
M. Riedel∗,†, E. Laure, Th. Soddemann, L. Field, J. P. Navarro, J. Casey,M. Litmaath, J. Ph. Baud, B. Koblitz, C. Catlett, D. Skow,C. Zheng, P. M. Papadopoulos,M. Katz, N. Sharma, O. Smirnova, B. Kónya, P. Arzberger, F. Würthwein, A. S. Rana, T. Martin,M. Wan,V. Welch, T. Rimovsky, S. Newhouse, A. Vanni, Y. Tanaka, Y. Tanimura, T. Ikegami, D. Abramson, C.(More)
To develop grid scheduling algorithms, a high performance simulator is necessary since grid is an uncontrollable and unrepeatable environment. In this paper, a discrete event simulation library called HyperSim is used as extensible building blocks for grid scheduling simulator. The use of event graph model for the grid simulation are proposed. This model is(More)
As the system size of Beowulf-Class cluster system scale up, system administration becomes challenging due to the increases complexity of the system. The lack of powerful tools for the administrative tasks even make the matter worse. This paper presents a proposed framework for system management of large Beowulf cluster that divided the management task into(More)
In this paper, the challenge of scheduling a parallel application on a cloud environment to achieve both time and energy efficiency is addressed. Two energy-aware task scheduling algorithms called the EHEFT and the ECPOP are proposed to address the challenge. These algorithms have the objective of trying to sustain the makespan and energy consumption at the(More)
Association rule mining is one of the most important techniques in data mining. It extracts significant patterns from transaction databases and generates rules used in many decision support applications. Many organizations such as industrial, commercial, or even scientific sites may produce large amount of transactions and attributes. Mining effective rules(More)
The multicast operation used by MPI under Grid environment can have a substantial impact on performance of parallel applications. Since the finding of an optimal multicast operation is an NP-hard problem, a near-optimal heuristic is crucial for building an efficient MPI runtime. This paper presents a new multicast algorithm called Longest Parallel Branch(More)