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Adapting Reproducible Research Capabilities to Resilient distributed calculations

INTERNATIONAL JOURNAL OF GRID AND HIGH PERFORMANCE COMPUTING 2016年第1期8卷 58-69页

作者： Rodriguez-Pascual, Manuel Kanellopoulos, Christos Juan Rubio-Montero, Antonio Darriba, Diego Prnjat, Ognjen Posada, David Mayo-Garcia, Rafael CIEMAT Madrid Spain GRNET Athens Greece Univ A Coruna La Coruna Spain Univ Vigo Vigo Spain

Nowadays, computing calculations are becoming more and more demanding due to the huge pool of resources available. This demand must be satisfied in terms of computational efficiency and resilience, which is compromised in distributed and heterogeneous platforms. Not only this, data obtained are often either reused by other researchers or recalculated. In this work, a set of tools to overcome the problem of creating and executing fault tolerant distributed applications on dynamic environments is presented. Such a set also ensures the reproducibility of the performed experiments providing a portable, unattended and resilient framework that encapsulates the infrastructure-dependent operations away from the application developers and users, allowing performing experiments based on Open Access data repositories. In this way, users can seamlessly search and lately access datasets that can be automatically retrieved as input data into a code already integrated in the proposed workflow. Such a search is based on metadata standards and relies on Persistent Identifiers (PID) to assign specific repositories. The applications profit from distributed Toolbox, a framework devoted to the creation and execution of distributed applications and includes tools for unattended cluster and grid execution, where a total fault tolerance is provided. By decoupling the definition of the remote tasks from its execution and control, the development, execution and maintenance of distributed applications is significantly simplified with respect to previous solutions, increasing their robustness and allowing running them on different computational platforms with little effort. The integration with Open Access databases and employment of PIDs for long-lasting references ensures that the data related to the experiments will persist, closing a complete research circle of data access/processing/storage/dissemination of results.

关键词： distributed calculations Fault Tolerance Persistent Identifiers Resilience

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Cloud-based Approach on Genetic Data Imputation Parameters' Optimization 7

Cloud-based Approach on Genetic Data Imputation Parameters' ...

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7th International Conference on Informatics and Data-Driven Medicine, IDDM 2024

作者： Horun, Pavlo Strauss, Chirstine Lviv Polytechnic National University Kniazia Romana St. 5 Lviv79000 Ukraine University of Vienna Oskar Morgenstern Platz 1 Vienna1090 Austria

The imputation process for genetic data is cost and time-intensive, primarily due to the high complexity of the methods involved, and the substantial volume of data processed. A thorough performance evaluation of the imputation algorithms such as Beagle, AlphaPlantImpute, LinkImputeR, MACH and others shows that while some algorithms are highly accurate, they are often computationally expensive. Being widely used, they have multiple input parameters which impact the quality and accuracy of the imputation. Traditional machine learning techniques for parameter optimization like grid search and randomized search become inefficient in high-dimensional parameter spaces, leading to prohibitive computational costs, especially in large-scale applications. Our study proposes the cloud-based approach for input parameters optimization by using Bayesian optimization with consecutive Domain Reduction Transformer (DRT). Described algorithm and developed library allow users to find the optimal input parameters for the data imputation in a more flexible way. © 2024 CEUR-WS. All rights reserved.

关键词： Bayesian optimization Beagle bioinformatics 1 cloud technologies data imputation distributed calculations parameters optimization

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Automating the Integration of Services for the Web Processing of Environmental Monitoring Data with distributed Scientific Applications

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OPTOELECTRONICS INSTRUMENTATION AND DATA PROCESSING 2022年第4期58卷 373-380页

作者： Bychkov, I. V. Feoktistov, A. G. Gorsky, S. A. Kostromin, R. O. Fedorov, R. K. Russian Acad Sci Matrosov Inst Syst Dynam & Control Theory Siberian Branch Irkutsk 664033 Russia

The solution of environmental monitoring problems reasonably requires the collection, digitization, storage, and analysis of a large volume of spatiotemporal data. Their processing frequently necessitates the application of distributed calculations. The known geoinformation systems do not usually contain the means, which could support the calculations of this kind to a full extent. An approach to the solution of this problem is proposed on the basis of a geoinformation system integrated with the means of the development and use of distributed scientific applications presented by web data processing services in a heterogeneous computational environment. An advantage of this approach consists in a decrease in the labour efforts in the preparation and implementation of experiments with geodata.

关键词： environmental monitoring web data processing services geoinformation systems distributed calculations scientific working processes

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On a conjugate directions method for solving strictly convex QP problem

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MATHEMATICAL METHODS OF OPERATIONS RESEARCH 2017年第3期86卷 523-548页

作者： Stachurski, Andrzej Warsaw Univ Technol Inst Control & Computat Engn Nowowiejska 15-19 PL-00665 Warsaw Poland

Problem of solving the strictly convex, quadratic programming problem is studied. The idea of conjugate directions is used. First we assume that we know the set of directions conjugate with respect to the hessian of the goal function. We apply n simultaneous directional minimizations along these conjugate directions starting from the same point followed by the addition of the directional corrections. Theorem justifying that the algorithm finds the global minimum of the quadratic goal function is proved. The way of effective construction of the required set of conjugate directions is presented. We start with a vector with zero value entries except the first one. At each step new vector conjugate to the previously generated is constructed whose number of nonzero entries is larger by one than in its predecessor. Conjugate directions obtained by means of the above construction procedure with appropriately selected parameters form an upper triangular matrix which in exact computations is the Cholesky factor of the inverse of the hessian matrix. Computational cost of calculating the inverse factorization is comparable with the cost of the Cholesky factorization of the original second derivative matrix. Calculation of those vectors involves exclusively matrix/vector multiplication and finding an inverse of a diagonal matrix. Some preliminary computational results on some test problems are reported. In the test problems all symmetric, positive definite matrices with dimensions from to from the repository of the Florida University were used as the hessians.

关键词： Conjugate directions Quadratic programming problems distributed calculations

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INTERFERENCE OF WAVES BASED USAGE OF AN OPTIMIZATION ALGORITHM FOR FINDING RULES WHICH CAN COPY THE LEARNED BEHAVIOR FROM LEARNING CLASSIFIER SYSTEMS AND NEURAL NETWORKS

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INTERNATIONAL JOURNAL OF INNOVATIVE COMPUTING INFORMATION AND CONTROL 2016年第3期12卷 1005-1019页

作者： Cadrik, Tomas Mach, Marian Sincak, Peter Tech Univ Kosice Dept Cybernet & Artificial Intelligence Letna 9 Kosice 04200 Slovakia

Cloud computing is getting very popular these days. It is also used with the combination of robotics. This potentially new field of robotics is called cloud robotics. The main goal in cloud robotics is to do the hard calculations on the cloud so we can spare the resources of the robot. When we have some mechanism which can be used as a controller for a robotic system, for instance, algorithms based on neural networks, evolutionary classifier systems, and other similar learning systems, we have a problem to place those controllers to the cloud. It is because they are saving the discovered data in the form of a model characteristic of this algorithm. If we want to use those in the agent domain, we need to have this method in the agent to interpret the data. Or the agent will need to access the cloud service each time step for another action. With the extension of using the cloud with a combination of robotics, it is not very effective to use this approach. So we need to build a method that can extract the data in the form of rules from the algorithms and then we can use only the extracted rules. It is also logical to use a distributed extraction mechanism because we can fully use the power of the cloud. This paper introduces a method that extracts rules from the interaction of the learned model of Zeroth Level Classifier System and neural network with the environment or the problem. The new method uses an interference of waves inspired approach based on a simple evolutionary algorithm.

关键词： Animat problem distributed calculations Evolutionary algorithm Interference of waves k-multiplexer Neural network Rule extractor ZCS

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Decomposition-coordination interior point method and its application to multi-area optimal reactive power flow

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INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS 2011年第1期33卷 55-60页

作者： Yan, Wei Wen, Lili Li, W. Chung, C. Y. Wong, K. P. Chongqing Univ State Key Lab Power Transmiss Equipment & Syst Se Coll Elect Engn Chongqing 400030 Peoples R China Test & Res Inst Chongqing Elect Power Chongqing 401123 Peoples R China British Columbia Transmiss Corp Vancouver BC V7X 1V5 Canada Hong Kong Polytech Univ Dept Elect Engn Kowloon Hong Kong Peoples R China

A decomposition-coordination interior point method (DIPM) is presented and applied to the multi-area optimal reactive power flow (ORPF) problem in this paper. In the method, the area distributed ORPF problem is first formed by introducing duplicated border variables. Then the nonlinear primal dual interior point method (IPM) is directly applied to the distributed ORPF problem in which a Newton system with border-matrix-blocks is formulated. Finally the overall ORPF problem is solved in decomposition iterations with the Newton system being decoupled. The proposed DIPM inherits the good performance of the traditional IPM with a feature appropriate for distributed calculations among multiple areas. It can be easily extended to other distributed optimization problems of power systems. Numeric results of five IEEE Test Systems are demonstrated and comparisons are made with those obtained using the traditional auxiliary problem principle (APP) method. The results show that the DIPM for the multi-area OPRF problem requires less iterations and CPU time, has better stability in convergence, and reaches better optimality compared to the traditional auxiliary problem principle method. (C) 2010 Elsevier Ltd. All rights reserved.

关键词： distributed calculations Interior point method Multi-area problems Optimal reactive power flow Power system decomposition

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Application of Grid technology in computational chemistry

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RUSSIAN CHEMICAL BULLETIN 2011年第7期60卷 1508-1515页

作者： Volokhov, V. M. Varlamov, D. A. Pivushkov, A. V. Volokhov, A. V. Russian Acad Sci Inst Problems Chem Phys Chernogolovka 142432 Moscow Region Russia Russian Acad Sci Inst Expt Mineral Chernogolovka 142432 Moscow Region Russia

The key trends and prospects of development of computational chemistry that formed in the early 2010s are considered. The most advanced methods for solution of various types of challenges in the computational and quantum chemistry by calculations in the distributed environments (Grid) and on high-performance supercomputer installations and the application methods of parallel and distributed computations are demonstrated;the tailor-made technologies developed for these calculations are described.

关键词： computational chemistry quantum chemistry distributed calculations Grid technology supercomputers

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Development of distributed Multi-agent Resource Conversion Processes based Simulation System ***

Development of Distributed Multi-agent Resource Conversion P...

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IEEE International Conference on System, Man, and Cybernetic

作者： Aksyonov, Konstantin A. Bykov, Eugene A. Kolosov, Denis M. Smoliy, Elena F. Khrenov, Alexey A. Ural State Tech Univ UPI Ekaterinburg Russia NPP Business Support Syst Ekaterinburg Russia

ISBN: (纸本)9781424423835

Necessity to mind a huge amount of factors while developing modern enterprises models dictates new requirements for modeling software, which needs to process all data to achieve precise results, make use of all possible means for that, such as distributed calculations and introduce original approaches where possible to avoid extra time waste for multiple simulation experiments. The article focuses on the software apparatus used in distributed multi-agent resource conversion processes based tool ***, pointing out its advantages and describing used technologies.

关键词： resource conversion processes agents distributed calculations

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Implementation of the replica-exchange molecular dynamics method for rigid bodies

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INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2006年第10期106卷 2208-2213页

作者： Moskovsky, A. A. Vanovschi, V. V. Konyukhov, S. S. Nemukhin, A. V. Moscow MV Lomonosov State Univ Dept Chem Moscow 119992 Russia Russian Acad Sci Inst Biochem Phys Moscow 119997 Russia

We describe an implementation of the replica-exchange molecular dynamics (REMD) algorithm for rigid-body molecular dynamics targeting its application in the flexible effective fragment quantum mechanical-molecular mechanical (QM/MM4) method. The main objective of the stage of the project is to obtain an efficient minimization tool for the MM subsystem. The computer program developed allows one to carry out calculations of molecular dynamics trajectories for atomic particles and for rigid bodies at constant temperature, using the chain Nose-Hoover thermostat. For REMD calculations, the OpenTS dynamic parallelization is used, which allows one to run simulations either on single computational clusters or on meta-clusters. A two-level parallelization scheme has been implemented, assuming that both REMD (upper level) and individual molecular dynamics trajectories (lower level) are parallelized. Structures of small and large water clusters as well as protein conformations are considered as first applications. (c) 2006 Wiley Periodicals, Inc.

关键词： geometry optimization QM/MM methods replica-exchange molecular dynamics (REMD) rigid-body molecular dynamics distributed calculations

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distributed genetic algorithm of test generation for digital circuits

Distributed genetic algorithm of test generation for digital...

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10th Biennial Baltic Electronics Conference

作者： Skobtsov, Y. A. El-Khatib, A. I. Ivanov, D. E. Donetsk Natl Tech Univ UA-83000 Donetsk Ukraine NAS Ukraine Inst Appl Math & Mech UA-83114 Donetsk Ukraine

The distributed genetic algorithms are considered for problem of test generation. The different forms of parallelization of genetic algorithms are investigated for test generation.

ISBN: (纸本)9781424404148

The distributed genetic algorithms are considered for problem of test generation. The different forms of parallelization of genetic algorithms are investigated for test generation.

关键词： genenic algorithms distributed calculations test generation fault simulation digital circuits

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