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Special Zeszyt on New Developments in Scalable Computing

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Special issue on Innovations in Intelligent Systems and Applications

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Special Thematic Zeszyt on Optimal Codes and Related Topics

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Tom 17 (2017): Zeszyt 5 (December 2017)
Special Zeszyt With Selected Papers From The Workshop “Two Years Avitohol: Advanced High Performance Computing Applications 2017

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Tom 16 (2016): Zeszyt 6 (December 2016)
Special issue with selection of extended papers from 6th International Conference on Logistic, Informatics and Service Science LISS’2016

Tom 16 (2016): Zeszyt 5 (October 2016)
Zeszyt Title: Special Zeszyt on Application of Advanced Computing and Simulation in Information Systems

Tom 16 (2016): Zeszyt 4 (December 2016)

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Special Zeszyt on Information Fusion

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Special Zeszyt on Logistics, Informatics and Service Science

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Special Zeszyt on Control in Transportation Systems

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Special Zeszyt

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Tom 13 (2013): Zeszyt Special-Zeszyt (December 2013)

Tom 13 (2013): Zeszyt 4 (December 2013)
The publishing of the present issue (Tom 13, No 4, 2013) of the journal “Cybernetics and Information Technologies” is financially supported by FP7 project “Advanced Computing for Innovation” (ACOMIN), grant agreement 316087 of Call FP7 REGPOT-2012-2013-1.

Tom 13 (2013): Zeszyt 3 (September 2013)

Tom 13 (2013): Zeszyt 2 (June 2013)

Tom 13 (2013): Zeszyt 1 (March 2013)

Tom 12 (2012): Zeszyt 4 (December 2012)

Tom 12 (2012): Zeszyt 3 (September 2012)

Tom 12 (2012): Zeszyt 2 (June 2012)

Tom 12 (2012): Zeszyt 1 (March 2012)

Informacje o czasopiśmie
Format
Czasopismo
eISSN
1314-4081
Pierwsze wydanie
13 Mar 2012
Częstotliwość wydawania
4 razy w roku
Języki
Angielski

Wyszukiwanie

Tom 17 (2017): Zeszyt 5 (December 2017)
Special Zeszyt With Selected Papers From The Workshop “Two Years Avitohol: Advanced High Performance Computing Applications 2017

Informacje o czasopiśmie
Format
Czasopismo
eISSN
1314-4081
Pierwsze wydanie
13 Mar 2012
Częstotliwość wydawania
4 razy w roku
Języki
Angielski

Wyszukiwanie

11 Artykułów
Otwarty dostęp

Preface

Data publikacji: 16 Jan 2018
Zakres stron: 3 - 4

Abstrakt

Otwarty dostęp

High Performance Computing Applications

Data publikacji: 16 Jan 2018
Zakres stron: 5 - 16

Abstrakt

Abstract

High Performance Computing (HPC) is required for many important applications in chemistry, computational fluid dynamics, etc., see, e.g., an overview in [1]. In this paper we shortly describe an application (a multiscale material design problem) that requires HPC for several reasons. The problem of interest is analysis of the fiber-reinforced concrete and we focus on modelling of stiffness through numerical homogenization and computing local material properties by inverse analysis. Both problems require a repeated solution of large-scale finite element problems up to 200 million degrees of freedom and therefore the importance of HPC computing is evident.

Słowa kluczowe

  • Analysis of fiber-reinforced concrete
  • homogenization
  • identification of parameters
  • parallelizable solver
  • additive Schwarz method
  • two-level parallelization
Otwarty dostęp

Sensitivity Study of Different RegCM4.4 Model Set-Ups – Recent Results from the TVRegCM Experiment

Data publikacji: 16 Jan 2018
Zakres stron: 17 - 26

Abstrakt

Abstract

The oncoming climate changes will exert influence on the ecosystems, on all branches of the international economy, and on the quality of life. Global Circulation Models (GCMs) are the most widespread and successful tools employed for both numerical weather forecast and climate research since the 1980s. However, growing demands on accurate and reliable information on regional and sub-regional scale are not directly met by relatively coarse resolution global models, mainly due to the excessive costs affiliated with the use of the model in very high resolution. Regional Climate Models (RCMs) are important instruments used for downscaling climate simulations from GCMs. Main aim of the numerical experiment Tuning an Validation of Regional Climate Model (RegCM-TVRegCM) is to quantify the impact of some tunable factors in the RegCM set-up on the model outputs. Thus, on the first stage of the study, the skill of 20 different model configurations in representing the basic spatial and temporal patterns of the Southeast European (SE) climate for the period 1999-2009, is evaluated. Based on these outcomes, the present work is dedicated on more detailed inspection of the model set-ups with recognizable better performance. The Pearson’s correlation coefficient between the time series of the temperature and precipitation of the 6 most promising model set-ups and the E-OBS on monthly basis are calculated. The main conclusion is that this test does not reveal single one model set-up that definitely over performs the other considered ones.

Słowa kluczowe

  • Regional climate simulation
  • RegCM4.4
  • sensitivity study
  • high performance computing
Otwarty dostęp

Scalability Issues for Wind Simulation Using OpenFOAM

Data publikacji: 16 Jan 2018
Zakres stron: 27 - 36

Abstrakt

Abstract

The use of the OpenFOAM software for wind simulation over rugged terrain is studied in the paper. OpenFOAM requirements for runtime, virtual memory and disk space are considered using small and medium resolution Digital Elevation Models (DEM) models for single-process and multi-process cases when running on local workstation and small parallel systems. Based on obtained data, extrapolation of requirements for relatively high resolution models are made and issues concerning the scalability are discussed.

Słowa kluczowe

  • OpenFOAM
  • wind simulation
  • rugged terrain
  • High Performance Computing (HPC) scalability
Otwarty dostęp

High Performance Computing Simulations of the Atmospheric Composition in Bulgaria and the City of Sofia

Data publikacji: 16 Jan 2018
Zakres stron: 37 - 48

Abstrakt

Abstract

Some extensive numerical simulations of the atmospheric composition fields in Bulgaria and Sofia have been recently performed. The US EPA Model-3 system was chosen as а modeling tool. A very extensive database was created from simulations which was used for different studies of the atmospheric composition, including the Air Quality (AQ) climate.

Słowa kluczowe

  • High Performance Computing (HPC)
  • simulations
  • atmospheric composition
  • air pollutants
Otwarty dostęp

On the Monte Carlo Matrix Computations on Intel MIC Architecture

Data publikacji: 16 Jan 2018
Zakres stron: 49 - 59

Abstrakt

Abstract

The tightened energy requirements when designing state-of-the-art high performance computing systems lead to the increased use of computational accelerators. Intel introduced the Many Integrated Core (MIC) architecture for their line of accelerators and successfully competes with NVIDIA on basis of price/performance and ease of development. Although some codes may be ported successfully to Intel MIC architecture without significant modifications, in order to achieve optimal performance one has to make the best use of the vector processing capabilities of the architecture. In this work we present our implementation of Quasi-Monte Carlo methods for matrix computations specifically optimised for the Intel Xeon Phi accelerators. To achieve optimal parallel efficiency we make use of both MPI and OpenMP.

Słowa kluczowe

  • Monte Carlo
  • matrix computations
  • Intel MIC
  • High Performance Computing (HPC) scalability
Otwarty dostęp

Comparison of RNA-Seq Differential Expression Methods

Data publikacji: 16 Jan 2018
Zakres stron: 60 - 67

Abstrakt

Abstract

There are many methods designed to find differentially expressed genes using RNA-seq data. Their outputs differ a lot, some genes are determined to be differentially expressed by most or all methods, and others - by very few or even by just one method. Here we derive a systematic approach to quantifying the proximity of such methods, allowing us also to discover patterns and to determine whether some of them are significantly different than others.

Słowa kluczowe

  • partially ranked lists
  • RNA-seq
  • high-throughput sequencing
  • NGS
  • differential expression
Otwarty dostęp

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Data publikacji: 16 Jan 2018
Zakres stron: 68 - 80

Abstrakt

Abstract

High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. The study aims to understand the scaling behavior of Gromacs (Groningen machine for chemical simulations) on various platforms, and the maximum performance in the prospect of energy consumption that can be accomplished by tuning the hardware and software parameters. Different system sizes (48K, 64K, and 272K) from scientific investigations have been studied show that the GPU (Graphics Processing Unit) scales rather beneficial than other resources, i.e., with GPU support. We track 2-3 times speedup compared to the latest multi-core CPUs. However, the so-called “threading effect” leads to the better results.

Słowa kluczowe

  • Molecular dynamics simulations
  • protein
  • DNA
  • sodium dodecyl sulphate
  • energy consumption
  • Gromacs
  • benchmarking
  • HPC
Otwarty dostęp

Tools and Services for High Performance Computing

Data publikacji: 16 Jan 2018
Zakres stron: 81 - 88

Abstrakt

Abstract

The accounting platform is a web-service based system for collection and analysis of accounting data from different infrastructure resources like High Performance Computing (HPC), Cloud and storage systems. The platform has two major components - backend API services along with different data publishers and a client web UI module for visualization and operations. The backend API is designed to gather information from different job management systems, cloud vendors, and storage providers and use micro-service architecture. The web UI module is written in Python, JavaScript and has integrated SAML login module for user authentication and authorization. It is capable of visualizing the gathered data in dynamic OLAP style and supports standard export formats like CSV and Excel. Through the accounting platform, it is possible to obtain a full view of the usage patterns of an integrated electronic infrastructure and to see from one point all information about the different resources comprising the hybrid computing and data infrastructure.

Słowa kluczowe

  • Distributed systems
  • containers
  • scalable development
  • analytics
Otwarty dostęp

Cloud Service for Numerical Calculations and Visualizations of Photonic Dissipative Systems

Data publikacji: 16 Jan 2018
Zakres stron: 89 - 100

Abstrakt

Abstract

Nowadays quantum physics is crucial for several scientific applications, where it is no longer possible to neglect the environmental interaction, like dissipation and decoherence. In these cases, the quantum systems are usually treated as open systems and their time-evolution is described by a density matrix in frames of the master equation, instead of the Hilbert-space vector and the Schrodinger equation. The visualization of such quantum systems allows users to calculate and study the sensitivity of the parameters, like excitation photon numbers or photonnumber distribution functions or Wigner functions. In this paper, a cloud service for numerical calculations and visualization of photonic dissipative systems is presented, which enables numerical simulations and visualizations of a wide variety of Hamiltonians, including those with arbitrary time-dependences widely used in many physics applications. The service allows creating graphics and charts for interacting complex systems and simulating their time evolution with many available timeevolution drivers.

Słowa kluczowe

  • Quantum optics
  • quantum simulations
  • visualization
  • Big Data
  • cloud service
Otwarty dostęp

On the Use of Large Intel Xeon Phi Clusters for GEANT4-Based Simulations

Data publikacji: 16 Jan 2018
Zakres stron: 101 - 109

Abstrakt

Abstract

GEANT4 is the basic software for fast and precise simulation of particle interactions with matter. Along the way towards enabling the execution of GEANT4 based simulations on hybrid High Performance Computing (HPC) architectures with large clusters of Intel Xeon Phi co-processors, we study the performance of this software suit on the supercomputer system Avitohol@BAS, Some practical scripts are collected in the supplementary material shown in the appendix.

Słowa kluczowe

  • Co-processors
  • multithreading
  • acceleration
  • hybrid architecture
  • particle-matter interactions
  • simulations
11 Artykułów
Otwarty dostęp

Preface

Data publikacji: 16 Jan 2018
Zakres stron: 3 - 4

Abstrakt

Otwarty dostęp

High Performance Computing Applications

Data publikacji: 16 Jan 2018
Zakres stron: 5 - 16

Abstrakt

Abstract

High Performance Computing (HPC) is required for many important applications in chemistry, computational fluid dynamics, etc., see, e.g., an overview in [1]. In this paper we shortly describe an application (a multiscale material design problem) that requires HPC for several reasons. The problem of interest is analysis of the fiber-reinforced concrete and we focus on modelling of stiffness through numerical homogenization and computing local material properties by inverse analysis. Both problems require a repeated solution of large-scale finite element problems up to 200 million degrees of freedom and therefore the importance of HPC computing is evident.

Słowa kluczowe

  • Analysis of fiber-reinforced concrete
  • homogenization
  • identification of parameters
  • parallelizable solver
  • additive Schwarz method
  • two-level parallelization
Otwarty dostęp

Sensitivity Study of Different RegCM4.4 Model Set-Ups – Recent Results from the TVRegCM Experiment

Data publikacji: 16 Jan 2018
Zakres stron: 17 - 26

Abstrakt

Abstract

The oncoming climate changes will exert influence on the ecosystems, on all branches of the international economy, and on the quality of life. Global Circulation Models (GCMs) are the most widespread and successful tools employed for both numerical weather forecast and climate research since the 1980s. However, growing demands on accurate and reliable information on regional and sub-regional scale are not directly met by relatively coarse resolution global models, mainly due to the excessive costs affiliated with the use of the model in very high resolution. Regional Climate Models (RCMs) are important instruments used for downscaling climate simulations from GCMs. Main aim of the numerical experiment Tuning an Validation of Regional Climate Model (RegCM-TVRegCM) is to quantify the impact of some tunable factors in the RegCM set-up on the model outputs. Thus, on the first stage of the study, the skill of 20 different model configurations in representing the basic spatial and temporal patterns of the Southeast European (SE) climate for the period 1999-2009, is evaluated. Based on these outcomes, the present work is dedicated on more detailed inspection of the model set-ups with recognizable better performance. The Pearson’s correlation coefficient between the time series of the temperature and precipitation of the 6 most promising model set-ups and the E-OBS on monthly basis are calculated. The main conclusion is that this test does not reveal single one model set-up that definitely over performs the other considered ones.

Słowa kluczowe

  • Regional climate simulation
  • RegCM4.4
  • sensitivity study
  • high performance computing
Otwarty dostęp

Scalability Issues for Wind Simulation Using OpenFOAM

Data publikacji: 16 Jan 2018
Zakres stron: 27 - 36

Abstrakt

Abstract

The use of the OpenFOAM software for wind simulation over rugged terrain is studied in the paper. OpenFOAM requirements for runtime, virtual memory and disk space are considered using small and medium resolution Digital Elevation Models (DEM) models for single-process and multi-process cases when running on local workstation and small parallel systems. Based on obtained data, extrapolation of requirements for relatively high resolution models are made and issues concerning the scalability are discussed.

Słowa kluczowe

  • OpenFOAM
  • wind simulation
  • rugged terrain
  • High Performance Computing (HPC) scalability
Otwarty dostęp

High Performance Computing Simulations of the Atmospheric Composition in Bulgaria and the City of Sofia

Data publikacji: 16 Jan 2018
Zakres stron: 37 - 48

Abstrakt

Abstract

Some extensive numerical simulations of the atmospheric composition fields in Bulgaria and Sofia have been recently performed. The US EPA Model-3 system was chosen as а modeling tool. A very extensive database was created from simulations which was used for different studies of the atmospheric composition, including the Air Quality (AQ) climate.

Słowa kluczowe

  • High Performance Computing (HPC)
  • simulations
  • atmospheric composition
  • air pollutants
Otwarty dostęp

On the Monte Carlo Matrix Computations on Intel MIC Architecture

Data publikacji: 16 Jan 2018
Zakres stron: 49 - 59

Abstrakt

Abstract

The tightened energy requirements when designing state-of-the-art high performance computing systems lead to the increased use of computational accelerators. Intel introduced the Many Integrated Core (MIC) architecture for their line of accelerators and successfully competes with NVIDIA on basis of price/performance and ease of development. Although some codes may be ported successfully to Intel MIC architecture without significant modifications, in order to achieve optimal performance one has to make the best use of the vector processing capabilities of the architecture. In this work we present our implementation of Quasi-Monte Carlo methods for matrix computations specifically optimised for the Intel Xeon Phi accelerators. To achieve optimal parallel efficiency we make use of both MPI and OpenMP.

Słowa kluczowe

  • Monte Carlo
  • matrix computations
  • Intel MIC
  • High Performance Computing (HPC) scalability
Otwarty dostęp

Comparison of RNA-Seq Differential Expression Methods

Data publikacji: 16 Jan 2018
Zakres stron: 60 - 67

Abstrakt

Abstract

There are many methods designed to find differentially expressed genes using RNA-seq data. Their outputs differ a lot, some genes are determined to be differentially expressed by most or all methods, and others - by very few or even by just one method. Here we derive a systematic approach to quantifying the proximity of such methods, allowing us also to discover patterns and to determine whether some of them are significantly different than others.

Słowa kluczowe

  • partially ranked lists
  • RNA-seq
  • high-throughput sequencing
  • NGS
  • differential expression
Otwarty dostęp

On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

Data publikacji: 16 Jan 2018
Zakres stron: 68 - 80

Abstrakt

Abstract

High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. The study aims to understand the scaling behavior of Gromacs (Groningen machine for chemical simulations) on various platforms, and the maximum performance in the prospect of energy consumption that can be accomplished by tuning the hardware and software parameters. Different system sizes (48K, 64K, and 272K) from scientific investigations have been studied show that the GPU (Graphics Processing Unit) scales rather beneficial than other resources, i.e., with GPU support. We track 2-3 times speedup compared to the latest multi-core CPUs. However, the so-called “threading effect” leads to the better results.

Słowa kluczowe

  • Molecular dynamics simulations
  • protein
  • DNA
  • sodium dodecyl sulphate
  • energy consumption
  • Gromacs
  • benchmarking
  • HPC
Otwarty dostęp

Tools and Services for High Performance Computing

Data publikacji: 16 Jan 2018
Zakres stron: 81 - 88

Abstrakt

Abstract

The accounting platform is a web-service based system for collection and analysis of accounting data from different infrastructure resources like High Performance Computing (HPC), Cloud and storage systems. The platform has two major components - backend API services along with different data publishers and a client web UI module for visualization and operations. The backend API is designed to gather information from different job management systems, cloud vendors, and storage providers and use micro-service architecture. The web UI module is written in Python, JavaScript and has integrated SAML login module for user authentication and authorization. It is capable of visualizing the gathered data in dynamic OLAP style and supports standard export formats like CSV and Excel. Through the accounting platform, it is possible to obtain a full view of the usage patterns of an integrated electronic infrastructure and to see from one point all information about the different resources comprising the hybrid computing and data infrastructure.

Słowa kluczowe

  • Distributed systems
  • containers
  • scalable development
  • analytics
Otwarty dostęp

Cloud Service for Numerical Calculations and Visualizations of Photonic Dissipative Systems

Data publikacji: 16 Jan 2018
Zakres stron: 89 - 100

Abstrakt

Abstract

Nowadays quantum physics is crucial for several scientific applications, where it is no longer possible to neglect the environmental interaction, like dissipation and decoherence. In these cases, the quantum systems are usually treated as open systems and their time-evolution is described by a density matrix in frames of the master equation, instead of the Hilbert-space vector and the Schrodinger equation. The visualization of such quantum systems allows users to calculate and study the sensitivity of the parameters, like excitation photon numbers or photonnumber distribution functions or Wigner functions. In this paper, a cloud service for numerical calculations and visualization of photonic dissipative systems is presented, which enables numerical simulations and visualizations of a wide variety of Hamiltonians, including those with arbitrary time-dependences widely used in many physics applications. The service allows creating graphics and charts for interacting complex systems and simulating their time evolution with many available timeevolution drivers.

Słowa kluczowe

  • Quantum optics
  • quantum simulations
  • visualization
  • Big Data
  • cloud service
Otwarty dostęp

On the Use of Large Intel Xeon Phi Clusters for GEANT4-Based Simulations

Data publikacji: 16 Jan 2018
Zakres stron: 101 - 109

Abstrakt

Abstract

GEANT4 is the basic software for fast and precise simulation of particle interactions with matter. Along the way towards enabling the execution of GEANT4 based simulations on hybrid High Performance Computing (HPC) architectures with large clusters of Intel Xeon Phi co-processors, we study the performance of this software suit on the supercomputer system Avitohol@BAS, Some practical scripts are collected in the supplementary material shown in the appendix.

Słowa kluczowe

  • Co-processors
  • multithreading
  • acceleration
  • hybrid architecture
  • particle-matter interactions
  • simulations

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