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2011 Advances in Complex Systems  
In the case study, we illustrated the internal data flow between the ecological models and the performance enhancement of the integrated simulation via the coupling component.  ...  In this paper, authors first present the considerations in the course of design and implementation of a coupling component to support integrated parallel multimodeling.  ...  implementation and performance of PALFISH.  ... 
doi:10.1142/s1793962311000554 fatcat:yddrofh3vfezzcwkgq3tznmbuu

ECOSIMNET: A Framework For Ecological Simulations

Antonio Pereira, Luis Paulo Reis, Pedro Duarte
2009 ECMS 2009 Proceedings edited by J. Otamendi, A. Bargiela, J. L. Montes, L. M. Doncel Pedrera  
This paper presents a framework for ecological simulations that intends to increase system performance through the ability to do parallel simulations, allowing the joint analysis of different scenarios  ...  Simulating ecological models is always a difficult task, not only because of its complexity but also due to the slowness associated with each simulation run as more variables and processes are incorporated  ...  ACKNOWLEDGEMENTS This work was started during the ABSES project -"Agent-Based Simulation of Ecological Systems" (FCT/POSC/EIA/57671/2004) and António Pereira was supported by the FCT scholarship SFRH/BD  ... 
doi:10.7148/2009-0219-0225 dblp:conf/ecms/PereiraRD09 fatcat:ifn5xg5a3zbwjfxecio7xpa4tm

4P: fast computing of population genetics statistics from large DNA polymorphism panels

Andrea Benazzo, Alex Panziera, Giorgio Bertorelle
2014 Ecology and Evolution  
Massive DNA sequencing has significantly increased the amount of data available for population genetics and molecular ecology studies.  ...  However, the parallel computation of simple statistics within and between populations from large panels of polymorphic sites is not yet available, making the exploratory analyses of a set or subset of  ...  This work was supported by the Italian Ministry for Research and Education, the University of Ferrara and the Fondazione Edmund Mach.  ... 
doi:10.1002/ece3.1261 pmid:25628874 pmcid:PMC4298444 fatcat:hpz5vvs3vrc3zolycirxtcwbh4

Parallel k-Means Clustering for Quantitative Ecoregion Delineation Using Large Data Sets

Jitendra Kumar, Richard T. Mills, Forrest M. Hoffman, William W. Hargrove
2011 Procedia Computer Science  
This paper focuses on the development of a massively parallel multivariate geographical spatio-temporal clustering code for analysis of very large datasets using tens of thousands processors on one of  ...  Identification of geographic ecoregions has long been of interest to environmental scientists and ecologists for identifying regions of similar ecological and environmental conditions.  ...  Application Study Datasets Performance of the parallel k-means algorithm and implementation was evaluated using three real-world example datasets.  ... 
doi:10.1016/j.procs.2011.04.173 fatcat:vhqh3citivh2bhu26i32vjtfby

Accelerating a Virtual Ecology Model with FPGAs

Julien Lamoureux, Tony Field, Wayne Luk
2009 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors  
Using FPGAs, hardware implementations can be customized to the specific requirements of the ecological system under study and provide significant speed-ups compared to software implementations.  ...  This paper describes a framework for maximizing the speedup of VEW generated models implemented on FPGA-based acceleration platforms and then describes the implementation of a typical VEW generated model  ...  CONCLUSIONS AND FUTURE WORK Agent-based modelling involves updating the state of each agent in each time step of a simulation and this yields significant amounts of parallelism.  ... 
doi:10.1109/asap.2009.27 dblp:conf/asap/LamoureuxFL09 fatcat:zyaa5ueg6ngfjioqqoejrrdpu4

A Parallel Structured Ecological Model for High End Shared Memory Computers [chapter]

Dali Wang, Michael W. Berry, Louis J. Gross
2008 Lecture Notes in Computer Science  
Identical simulation results, validated by a comparison with a sequential implementation, and impressive parallel model performance demonstrate that layer-wised partitioning offers advantages in parallelizing  ...  As an example, we use a parallel spatially-explicit structured fish model (ALFISH) for regional ecosystem restoration to demonstrate the parallelization procedure and associated model performance evaluation  ...  Geological Survey, through Cooperative Agreement No. 1445-CA09-95-0094 with the University of Tennessee, and the Department of Interior's Critical Ecosystem Studies Initiative.  ... 
doi:10.1007/978-3-540-68555-5_9 fatcat:5ukncwm3qffbpdhze32aonrb7i

SPUX: Scalable Particle Markov Chain Monte Carlo for uncertainty quantification in stochastic ecological models [article]

Jonas Šukys, Mira Kattwinkel
2017 arXiv   pre-print
Calibration of individual based models (IBMs), successful in modeling complex ecological dynamical systems, is often performed only ad-hoc.  ...  We present SPUX, a Python implementation of parallel Particle Markov Chain Monte Carlo (PMCMC) algorithm, which mitigates high computational costs by distributing particles over multiple computational  ...  Depending on the available resources, accelerated parallel PMCMC code is capable of reducing the required simulation time for the entire Bayesian inference of predator-prey IBM from almost one month to  ... 
arXiv:1711.01410v1 fatcat:faivqnrkzjhgtf33j4raefxcgi

An Application of Graphics Processing Units to Geosimulation of Collective Crowd Behaviour

Jānis Cjoskāns, Arnis Lektauers
2017 Information Technology and Management Science  
The goal of the paper is to assess the ways for computational performance and efficiency improvement of collective crowd behaviour simulation by using parallel computing methods implemented on graphics  ...  To perform an experimental evaluation of benefits of parallel computing, a new GPU-based simulator prototype is proposed and the runtime performance is analysed.  ...  The goal of the paper is to assess the ways for computational performance and efficiency improvement of collective crowd behaviour simulation by using parallel computing methods implemented on graphics  ... 
doi:10.1515/itms-2017-0017 fatcat:dtbzm6snbvcbhjs4sbivemfbgu

OpenABL: A Domain-Specific Language for Parallel and Distributed Agent-Based Simulations [chapter]

Biagio Cosenza, Nikita Popov, Ben Juurlink, Paul Richmond, Mozhgan Kabiri Chimeh, Carmine Spagnuolo, Gennaro Cordasco, Vittorio Scarano
2018 Lecture Notes in Computer Science  
To cope with the growing computational complexity, parallel and distributed implementations have been developed for a wide range of platforms.  ...  The generated code scales to large clusters and performs similarly to hand-written target-specific code, while requiring significantly fewer lines of codes.  ...  This research has been partially funded by the DFG project CELERITY (CO 1544/1-1) and by the EPSRC fellowship Accelerating Scientific Discovery with Accelerated Computing (EP/N018869/1).  ... 
doi:10.1007/978-3-319-96983-1_36 fatcat:t3vqrgb5uvaclgprpwo6lovx3y


Z. S. Mustafin, Yu. G. Matushkin, S. A. Lashin
2015 Vavilovskij Žurnal Genetiki i Selekcii  
The software was designed for simulating the functioning and evolution of microbial communities.  ...  On GPU systems, the simulation time was reduced to several minutes (dozens of hours on CPU).  ...  ACKNOWLEDGMENTS The study was supported by the following grants: RFBR 12-07-00671-а, project VI.61.1.2, and interdisciplinary SB RAS project 47.  ... 
doaj:37e279cb3a934c66bfb3c6627f5f2320 fatcat:qfvz3kjpdvhqxofgwhckzvqnsy

Программный комплекс HEC 2.0 для моделирования эволюции прокариотических сообществ
HEC 2.0: Improved Simulation of the Evolution of Prokaryotic Communities

С.А. Лашин, S.A. Lashin
2014 Математическая биология и биоинформатика  
High-performance versions of our software have been implemented using OpenMP and MPI technologies, and can be run at both desktops and MPI clusters.  ...  Modeling and simulation of prokaryotes and prokaryotic communities are important for the development of modern fundamental, medical and biotechnological researches.  ...  The computational core is implemented in the C++ programming language with the use of Boost [17] and OpenMP [18] libraries (for the high performance version).  ... 
doi:10.17537/2014.9.585 fatcat:36mrvh4l4zb7vp6y4wzq4ybliy

An Open Geographic Modeling Environment

Thomas Maxwell, Robert Costanza
1997 Simulation (San Diego, Calif.)  
Automatic code generators construct spatial simulations and enable distributed processing over a network of parallel and serial computers, allowing transparent access to state-of-the-art computing facilities  ...  It is hoped that this type of infrastructure will open the simulation arena to a much wider set of participants, and facilitate the application of computer modeling to the study of complex multi-scale  ...  In this step the user configures input to the simulation from the biological/ecological databases and GIS.  ... 
doi:10.1177/003754979706800304 fatcat:tjik4tyxffdiph66doewfo7p2m

Scaling-up spatially-explicit ecological models using graphics processors

Johan van de Koppel, Rohit Gupta, Cornelis Vuik
2011 Ecological Modelling  
Hence, the study of scaling laws in ecology may benefit significantly from implementation of ecological models on graphics processors.  ...  We explain this technique by implementing three classical models of spatial self-organization in ecology: a spiral-wave forming predator-prey model, a model of pattern formation in arid vegetation, and  ...  Acknowledgement We would like to thank Fred Guichard for comments on a draft of the manuscript.  ... 
doi:10.1016/j.ecolmodel.2011.06.004 fatcat:fq64assiq5aw5e66iuxksrroqq

Parallel agent-based modeling of spatial opinion diffusion accelerated using graphics processing units

Wenwu Tang, David A. Bennett
2011 Ecological Modelling  
-Collaborative Research: AOC Social Complexity and the Management of the Commons‖, and NSF TeraGrid Supercomputing Resource Award (TG-SES090019 and TG-SES070004), -Extending and Sustaining GISolve as a  ...  We implement an opinion formation model (see Weisbuch et al. 2002) to simulate this process and tie the results of this model to a land-use change sub-model.  ...  Conclusion In this paper, we described the implementation of a parallel agent-based model of landuse opinion dynamics using the emerging GPU technology.  ... 
doi:10.1016/j.ecolmodel.2011.08.016 fatcat:hx773mtxvbdutfpktvci7ufx44

Parallel Ecology for Intelligent and Smart Cyber–Physical–Social Systems

Fei-Yue Wang, Yanfen Wang
2020 IEEE Transactions on Computational Social Systems  
with the goal of implementing and achieving federated ecological intelligence and learning from artificial ecological systems, through federated data and service.  ...  In my last editorial and final note on parallel science and technology, I would like to discuss the topic of parallel intelligence for ecological systems, not only natural ecological systems but also social-ecological  ...  Wang has served as the Vice Chairman of the China Ecological Society and the China Natural Resources Society since 2018 and 2019, respectively.  ... 
doi:10.1109/tcss.2020.3044129 fatcat:jnipqypk75aqhafnfs2e5z4hvu
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