Peter Sloot | University of Amsterdam (original) (raw)

Papers by Peter Sloot

Research paper thumbnail of Using HLA and Grid for Distributed Multiscale Simulations

Lecture Notes in Computer Science

Research paper thumbnail of A Grid-based Virtual Reactor: Parallel performance and adaptive load balancing

Journal of Parallel and Distributed Computing, 2008

Research paper thumbnail of Pulsatile flow in model cerebral aneurysms

Procedia Computer Science, 2011

Research paper thumbnail of Simulation of City Evacuation Coupled to Flood Dynamics

Pedestrian and Evacuation Dynamics 2012, 2013

Research paper thumbnail of A 3D Virtual Reactor for Simulation of Silicon-Based Film Production

Computational Technologies for Fluid/Thermal/Structural/Chemical Systems With Industrial Applications, Volume 2, 2004

In this paper we introduce a Grid-based Virtual Reactor, a problem-solving environment that suppo... more In this paper we introduce a Grid-based Virtual Reactor, a problem-solving environment that supports detailed numerical study of industrial thin film production in Plasma Enhanced Chemical Vapor Deposition (PECVD) reactors. We describe the physics and chemistry underpinning the deposition process, the numerical approach to simulate these processes on advanced computer architectures as well as the associated software environment supporting computational experiments. In the developed 3D model we took into account ...

Research paper thumbnail of Signal analysis and anomaly detection for flood early warning systems

Journal of Hydroinformatics, 2014

Research paper thumbnail of Experimental Grid Access for Dynamic Discovery and Data Transfer in Distributed Interactive Simulation Systems

Lecture Notes in Computer Science, 2003

Research paper thumbnail of Controlling flow-induced vibrations of flood barrier gates with data-driven and finite-element modelling

Research for Policy and Practice, 2012

Research paper thumbnail of Portable Library of Migratable Sockets

Scientific Programming, 2001

Efficient load balancing is essential for parallel distributed computing. Many parallel computing... more Efficient load balancing is essential for parallel distributed computing. Many parallel computing environments use TCP or UDP through the socket interface as a communication mechanism. This paper presents the design and development of a prototype implementation of a network interface that can preserve communication between processes during process migration. This new communication library is a substitution for the well-known socket interface. It is implemented in user — space; it is portable, and no modifications of user applications are required. TCP/IP is applied for internal communication, which guarantees relatively high performance and portability.

Research paper thumbnail of Modeling of Plasma Chemical Deposition and Degradation of Silicon Thin Films

Fracture of Nano and Engineering Materials and Structures, 2006

Research paper thumbnail of Computational engineering on the grid: Crafting a distributed virtual reactor

e-Science 2006 - Second IEEE International Conference on e-Science and Grid Computing, 2006

Abstract This paper reports on our research into supporting collaborative distributed application... more Abstract This paper reports on our research into supporting collaborative distributed applications on the Grid. Our case study application, a Virtual Reactor problem solving environment, was built for simulation of industrially important technology of plasma chemical deposition. It incorporates a number of components distributed among different organizations and requires both high-performance and high-throughput computing, as well as interactivity and advanced visualization. The application has been ported to the Grid ...

Research paper thumbnail of Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes

Research paper thumbnail of Grid-Based Interactive Decision Support in Biomedicine

Grid Computing for Bioinformatics and Computational Biology, 2007

Research paper thumbnail of Grid-Based Simulation of Industrial Thin-Film Production

SIMULATION, 2005

In this article, the authors introduce a Grid-based virtual reactor, a High Level Architecture (H... more In this article, the authors introduce a Grid-based virtual reactor, a High Level Architecture (HLA)- supported problem-solving environment that allows for detailed numerical study of industrial thin-film production in plasma-enhanced chemical vapor deposition (PECVD) reactors. They briefly describe the physics and chemistry underpinning the deposition process, the numerical approach to simulate these processes on advanced computer architectures, and the associated software environment supporting computational experiments. The authors built an efficient problem-solving environment for scientists studying PECVD processes and end users working in the chemical industry and validated the resulting virtual reactor against real experiments.

Research paper thumbnail of Distributed Simulation of City Inundation by Coupled Surface and Subsurface Porous Flow for Urban Flood Decision Support System

Procedia Computer Science, 2013

Research paper thumbnail of Modeling earthen dikes using real-time sensor data

Journal of Hydrology, 2013

Research paper thumbnail of Free-surface flow simulations for discharge-based operation of hydraulic structure gates

Journal of Hydroinformatics, 2014

We combine non-hydrostatic flow simulations of the free surface with a discharge model based on e... more We combine non-hydrostatic flow simulations of the free surface with a discharge model based on elementary gate flow equations for decision support in the operation of hydraulic structure gates. A water level-based gate control used in most of today's general practice does not take into account the fact that gate operation scenarios producing similar total discharged volumes and similar water levels may have different local flow characteristics. Accurate and timely prediction of local flow conditions around hydraulic gates is important for several aspects of structure management: ecology, scour, flow-induced gate vibrations and waterway navigation. The modelling approach is described and tested for a multi-gate sluice structure regulating discharge from a river to the sea. The number of opened gates is varied and the discharge is stabilized with automated control by varying gate openings. The free-surface model was validated for discharge showing a correlation coefficient of 0.9...

Research paper thumbnail of High-performance computer management based on Java

Future Generation Computer Systems, 1999

Research paper thumbnail of HIV decision support: from molecule to man

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2009

Human immunodeficiency virus (HIV) is recognized to be one of the most destructive pandemics in r... more Human immunodeficiency virus (HIV) is recognized to be one of the most destructive pandemics in recorded history. Effective highly active antiretroviral therapy and the availability of genetic screening of patient virus data have led to sustained viral suppression and higher life expectancy in patients who have been infected with HIV. The sheer complexity of the disease stems from the multiscale and highly dynamic nature of the system under study. The complete cascade from genome, proteome, metabolome and physiome to health forms a multidimensional system that crosses many orders of magnitude in temporal and spatial scales. Understanding, quantifying and handling this complexity is one of the biggest challenges of our time, which requires a highly multidisciplinary approach. In order to supply researchers with an interactive framework and to provide the medical professional with appropriate tools and information for making a balanced and reliable clinical decision, we have developed...

Research paper thumbnail of Comparing the Parix and PVM parallel programming environments

Genericity of parallel programming environments, enabling development of portable parallel progra... more Genericity of parallel programming environments, enabling development of portable parallel programs, is expected to result in performance penalties. Furthermore, programmability and tool support of programming environments are important issues if a choice between programming environments has to be made. We propose a methodology to compare native and generic parallel programming environments, taking into account such competing issues as portability and performance. As a case study, this paper compares the Parix and PVM parallel programming environments on a 512 node Parsytec GCel. Furthermore, we apply our methodology to compare Parix and PVM on a new architecture, a 32 node Parsytec PowerXplorer, which is based on the PowerPC chip. In our approach we start with a representative application and isolate the basic (environment) dependent building blocks. These basic building blocks, which depend on floating point performance and communication capabilities of the environments, are analy...

Research paper thumbnail of Using HLA and Grid for Distributed Multiscale Simulations

Lecture Notes in Computer Science

Research paper thumbnail of A Grid-based Virtual Reactor: Parallel performance and adaptive load balancing

Journal of Parallel and Distributed Computing, 2008

Research paper thumbnail of Pulsatile flow in model cerebral aneurysms

Procedia Computer Science, 2011

Research paper thumbnail of Simulation of City Evacuation Coupled to Flood Dynamics

Pedestrian and Evacuation Dynamics 2012, 2013

Research paper thumbnail of A 3D Virtual Reactor for Simulation of Silicon-Based Film Production

Computational Technologies for Fluid/Thermal/Structural/Chemical Systems With Industrial Applications, Volume 2, 2004

In this paper we introduce a Grid-based Virtual Reactor, a problem-solving environment that suppo... more In this paper we introduce a Grid-based Virtual Reactor, a problem-solving environment that supports detailed numerical study of industrial thin film production in Plasma Enhanced Chemical Vapor Deposition (PECVD) reactors. We describe the physics and chemistry underpinning the deposition process, the numerical approach to simulate these processes on advanced computer architectures as well as the associated software environment supporting computational experiments. In the developed 3D model we took into account ...

Research paper thumbnail of Signal analysis and anomaly detection for flood early warning systems

Journal of Hydroinformatics, 2014

Research paper thumbnail of Experimental Grid Access for Dynamic Discovery and Data Transfer in Distributed Interactive Simulation Systems

Lecture Notes in Computer Science, 2003

Research paper thumbnail of Controlling flow-induced vibrations of flood barrier gates with data-driven and finite-element modelling

Research for Policy and Practice, 2012

Research paper thumbnail of Portable Library of Migratable Sockets

Scientific Programming, 2001

Efficient load balancing is essential for parallel distributed computing. Many parallel computing... more Efficient load balancing is essential for parallel distributed computing. Many parallel computing environments use TCP or UDP through the socket interface as a communication mechanism. This paper presents the design and development of a prototype implementation of a network interface that can preserve communication between processes during process migration. This new communication library is a substitution for the well-known socket interface. It is implemented in user — space; it is portable, and no modifications of user applications are required. TCP/IP is applied for internal communication, which guarantees relatively high performance and portability.

Research paper thumbnail of Modeling of Plasma Chemical Deposition and Degradation of Silicon Thin Films

Fracture of Nano and Engineering Materials and Structures, 2006

Research paper thumbnail of Computational engineering on the grid: Crafting a distributed virtual reactor

e-Science 2006 - Second IEEE International Conference on e-Science and Grid Computing, 2006

Abstract This paper reports on our research into supporting collaborative distributed application... more Abstract This paper reports on our research into supporting collaborative distributed applications on the Grid. Our case study application, a Virtual Reactor problem solving environment, was built for simulation of industrially important technology of plasma chemical deposition. It incorporates a number of components distributed among different organizations and requires both high-performance and high-throughput computing, as well as interactivity and advanced visualization. The application has been ported to the Grid ...

Research paper thumbnail of Short-Term Forecasting of Taiwanese Earthquakes Using a Universal Model of Fusion-Fission Processes

Research paper thumbnail of Grid-Based Interactive Decision Support in Biomedicine

Grid Computing for Bioinformatics and Computational Biology, 2007

Research paper thumbnail of Grid-Based Simulation of Industrial Thin-Film Production

SIMULATION, 2005

In this article, the authors introduce a Grid-based virtual reactor, a High Level Architecture (H... more In this article, the authors introduce a Grid-based virtual reactor, a High Level Architecture (HLA)- supported problem-solving environment that allows for detailed numerical study of industrial thin-film production in plasma-enhanced chemical vapor deposition (PECVD) reactors. They briefly describe the physics and chemistry underpinning the deposition process, the numerical approach to simulate these processes on advanced computer architectures, and the associated software environment supporting computational experiments. The authors built an efficient problem-solving environment for scientists studying PECVD processes and end users working in the chemical industry and validated the resulting virtual reactor against real experiments.

Research paper thumbnail of Distributed Simulation of City Inundation by Coupled Surface and Subsurface Porous Flow for Urban Flood Decision Support System

Procedia Computer Science, 2013

Research paper thumbnail of Modeling earthen dikes using real-time sensor data

Journal of Hydrology, 2013

Research paper thumbnail of Free-surface flow simulations for discharge-based operation of hydraulic structure gates

Journal of Hydroinformatics, 2014

We combine non-hydrostatic flow simulations of the free surface with a discharge model based on e... more We combine non-hydrostatic flow simulations of the free surface with a discharge model based on elementary gate flow equations for decision support in the operation of hydraulic structure gates. A water level-based gate control used in most of today's general practice does not take into account the fact that gate operation scenarios producing similar total discharged volumes and similar water levels may have different local flow characteristics. Accurate and timely prediction of local flow conditions around hydraulic gates is important for several aspects of structure management: ecology, scour, flow-induced gate vibrations and waterway navigation. The modelling approach is described and tested for a multi-gate sluice structure regulating discharge from a river to the sea. The number of opened gates is varied and the discharge is stabilized with automated control by varying gate openings. The free-surface model was validated for discharge showing a correlation coefficient of 0.9...

Research paper thumbnail of High-performance computer management based on Java

Future Generation Computer Systems, 1999

Research paper thumbnail of HIV decision support: from molecule to man

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2009

Human immunodeficiency virus (HIV) is recognized to be one of the most destructive pandemics in r... more Human immunodeficiency virus (HIV) is recognized to be one of the most destructive pandemics in recorded history. Effective highly active antiretroviral therapy and the availability of genetic screening of patient virus data have led to sustained viral suppression and higher life expectancy in patients who have been infected with HIV. The sheer complexity of the disease stems from the multiscale and highly dynamic nature of the system under study. The complete cascade from genome, proteome, metabolome and physiome to health forms a multidimensional system that crosses many orders of magnitude in temporal and spatial scales. Understanding, quantifying and handling this complexity is one of the biggest challenges of our time, which requires a highly multidisciplinary approach. In order to supply researchers with an interactive framework and to provide the medical professional with appropriate tools and information for making a balanced and reliable clinical decision, we have developed...

Research paper thumbnail of Comparing the Parix and PVM parallel programming environments

Genericity of parallel programming environments, enabling development of portable parallel progra... more Genericity of parallel programming environments, enabling development of portable parallel programs, is expected to result in performance penalties. Furthermore, programmability and tool support of programming environments are important issues if a choice between programming environments has to be made. We propose a methodology to compare native and generic parallel programming environments, taking into account such competing issues as portability and performance. As a case study, this paper compares the Parix and PVM parallel programming environments on a 512 node Parsytec GCel. Furthermore, we apply our methodology to compare Parix and PVM on a new architecture, a 32 node Parsytec PowerXplorer, which is based on the PowerPC chip. In our approach we start with a representative application and isolate the basic (environment) dependent building blocks. These basic building blocks, which depend on floating point performance and communication capabilities of the environments, are analy...