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ON DESIGN OF A COUPLING COMPONENT FOR PARALLEL MULTIMODELING
2011
Advances in Complex Systems
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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
2009
ECMS 2009 Proceedings edited by J. Otamendi, A. Bargiela, J. L. Montes, L. M. Doncel Pedrera
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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
2014
Ecology and Evolution
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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
2011
Procedia Computer Science
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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
2009
2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors
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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]
2008
Lecture Notes in Computer Science
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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]
2017
arXiv
pre-print
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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
2017
Information Technology and Management Science
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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]
2018
Lecture Notes in Computer Science
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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
HIGH-PERFORMANCE SIMULATIONS OF POPULATION-GENETIC PROCESSES IN BACTERIAL COMMUNITIES USING THE HAPLOID EVOLUTIONARY CONSTRUCTOR SOFTWARE
2015
Vavilovskij Žurnal Genetiki i Selekcii
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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
2014
Математическая биология и биоинформатика
HEC 2.0: Improved Simulation of the Evolution of Prokaryotic Communities
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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
1997
Simulation (San Diego, Calif.)
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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
2011
Ecological Modelling
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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
2011
Ecological Modelling
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-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
2020
IEEE Transactions on Computational Social Systems
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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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