Complex System Simulations with QosCosGrid

Kurowski, Krzystof; Back, Walter de; Dubitzky, Werner; Gulyás, László; Kampis, George; Mamonski, Mariusz; Szemes, Gabor; Swain, Martin

doi:10.1007/978-3-642-01970-8_38

Cited by 25 publications

(9 citation statements)

References 15 publications

(12 reference statements)

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“…The variety of environments might lead to different design solutions, from the distribution of space across processors in the simplest scenario (see for example, Parry and Bithell (2012)) to more sophisticated variations. Although there have been some initiatives to automatize the parallelisation of agent-based simulations (Coakley et al, 2012;Kurowski et al, 2009), overall, the nature of the problem and the properties of the computer platform will often guide the method to split the simulation execution.…”

Section: Challenges Of Parallel Social Simulationmentioning

confidence: 99%

Approaching parallel computing to simulating population dynamics in demography

et al. 2016

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Agent-based modelling and simulation is a promising methodology that can be applied in the study of population dynamics. The main advantage of this technique is that it allows representing the particularities of the individuals that are modeled along with the interactions that take place among them and their environment. Hence, classical numerical simulation approaches are less adequate for reproducing complex dynamics. Nowadays, there is a rise of interest on using distributed computing to perform large-scale simulation of social systems. However, the inherent complexity of this type of applications is challenging and requires the study of possible solutions from the parallel computing perspective (e.g., how to deal with fine grain or irregular workload). In this paper, we discuss the particularities of simulating populating dynamics by using parallel discrete event simulation methodologies. To illustrate our approach, we present a possible solution to make transparent the use of parallel simulation for modeling demographic systems: Yades tool. In Yades, modelers can easily define models that describe different demographic processes with a web user interface and transparently run them on any computer architecture environment thanks to its demographic simulation library and code generator. Therefore, transparency is provided by by two means: the provision of a web user interface where modelers and policy makers can specify their agent-based models with the tools they are familiar with, and the automatic generation of the simulation code that can be executed in any platform (cluster or supercomputer). A study is conducted to evaluate the performance of our solution in a High Performance Computing environment. The main benefit of this outline is that our findings can be generalized to problems with similar characteristics to our demographic simulation model.

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Section: Challenges Of Parallel Social Simulationmentioning

confidence: 99%

Approaching parallel computing to simulating population dynamics in demography

et al. 2016

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“…All major production systems such as PBS Pro [14], LSF [36], Sun Grid Engine (SGE) [11], Condor [32], Maui and Moab [3] as well as higher level metascheduling systems such as GridWay [13], gLite WMS [7], QCG-Broker [23], etc., are so called queueing systems. It means that these systems typically follow the queuebased scheduling approach, using one or more incoming queues where jobs are stored until they are scheduled for execution.…”

Section: Queue-based Systemsmentioning

confidence: 99%

The Extension of Torque Scheduler Allowing the Use of Planning and Optimization in Grids

Chlumský

Klusáček

Ruda³

2012

csci

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In this work we present a major extension of the open source TORQUE Resource Manager system. We have replaced a naive scheduler provided in the TORQUE distribution with complex scheduling system that allows to plan job execution ahead and predict the behavior of the system. It is based on the application of job schedule, which represents the jobs' execution plan. Such a functionality is very useful as the plan can be used by the users to see when and where their jobs will be executed. Moreover, created plans can be easily evaluated in order to identify possible inefficiencies. Then, repair actions can be taken immediately and the inefficiencies can be fixed, producing better schedules with respect to considered criteria.

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“…The BIRN portal [10] that is a biology portal was created based on GridPort. The Vine Toolkit was applied to create the QosCosGrid [11] testbed portal. The G-FLUXO portal [12] specialized in Computational Biochemistry was developed on top of P-GRADE.…”

Section: Application-specific Grid Portalsmentioning

confidence: 99%

Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

Gesing

Hemert

Kacsuk

et al. 2010

Concurrency and Computation

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SUMMARYThe topic 'Portals for life sciences' includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user's interaction with computational resources that are concerted to a supported application domain. Copyright ᭧ 2010 John Wiley & Sons, Ltd. IWPLS'09It is our great pleasure to introduce this special issue on the First International Workshop on Portals for Life Sciences held at the e-Science Institute in Edinburgh, U.K., on 14-15 September 2009. The workshop was focused on research contributions for portals and tools in the field of life sciences and brought together scientists from the fields of life science, bioinformatics, and computer science. It formed an international platform to exchange experience, formulate ideas, and catch up on technological advances in molecular and systems biology in the context of portals. The variety of nationalities covered by the delegates reflects the international interest in a platform on scientific portals. Delegates from Austria, Brazil, Germany, Hungary, Italy, The Netherlands, Norway, Spain, The United Kingdom and The United States of America contributed to and attended the workshop. We especially highlight the mix of technology-related and domain-related talks, which mirrors the diverse scientific background of the delegates.Papers and abstracts for the workshop were accepted through a blind peer-reviewing process. Accepted papers resulted in 30-min presentations and were published in an open-access workshop proceedings. Accepted abstracts resulted in a 10-min 'lightning talk'. The speakers gave excellent and thought-provoking presentations. The highlights were presentations from two invited keynote speakers. In addition to the presentations, lively and promising discussions took place after talks, in coffee breaks and even during the social event. The workshop was highly successful and turned out to be the starting point of an international workshop series with the subject extended to science gateways for e-Science: The International Workshop on Science Gateways.We faced the challenge to invite several authors for extended versions of their papers and abstracts for this special issue. Some of the papers in this special edition are combinations of papers * Correspondence to: Sandra Gesing,

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Complex System Simulations with QosCosGrid

Cited by 25 publications

References 15 publications

Approaching parallel computing to simulating population dynamics in demography

Approaching parallel computing to simulating population dynamics in demography

The Extension of Torque Scheduler Allowing the Use of Planning and Optimization in Grids

Special Issue: Portals for life sciences—Providing intuitive access to bioinformatic tools

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