Going Stupid with EcoLab

In 2005, Railsback et al. proposed a very simple model ({\em Stupid Model}) that could be implemented within a couple of hours, and later extended to demonstrate the use of common ABM platform functionality. They provided implementations of the model in several agent based modelling platforms, and compared the platforms for ease of implementation of this simple model, and performance. In this paper, I implement Railsback et al's Stupid Model in the EcoLab simulation platform, a C++ based modelling platform, demonstrating that it is a feasible platform for these sorts of models, and compare the performance of the implementation with Repast, Mason and Swarm versions

Teadusarvutuse algoritmide taandamine hajusarvutuse raamistikele

Teadusarvutuses kasutatakse arvuteid ja algoritme selleks, et lahendada probleeme erinevates reaalteadustes nagu geneetika, bioloogia ja keemia. Tihti on eesmärgiks selliste loodusnähtuste modelleerimine ja simuleerimine, mida päris keskkonnas oleks väga raske uurida. Näiteks on võimalik luua päikesetormi või meteoriiditabamuse mudel ning arvutisimulatsioonide abil hinnata katastroofi mõju keskkonnale. Mida keerulisemad ja täpsemad on sellised simulatsioonid, seda rohkem arvutusvõimsust on vaja. Tihti kasutatakse selleks suurt hulka arvuteid, mis kõik samaaegselt töötavad ühe probleemi kallal. Selliseid arvutusi nimetatakse paralleel- või hajusarvutusteks. Hajusarvutuse programmide loomine on aga keeruline ning nõuab palju rohkem aega ja ressursse, kuna vaja on sünkroniseerida erinevates arvutites samaaegselt tehtavat tööd. On loodud mitmeid tarkvararaamistikke, mis lihtsustavad seda tööd automatiseerides osa hajusprogrammeerimisest. Selle teadustöö eesmärk oli uurida selliste hajusarvutusraamistike sobivust keerulisemate teadusarvutuse algoritmide jaoks. Tulemused näitasid, et olemasolevad raamistikud on üksteisest väga erinevad ning neist ükski ei ole sobiv kõigi erinevat tüüpi algoritmide jaoks. Mõni raamistik on sobiv ainult lihtsamate algoritmide jaoks; mõni ei sobi olukorras, kus andmed ei mahu arvutite mällu. Algoritmi jaoks kõige sobivama hajusarvutisraamistiku valimine võib olla väga keeruline ülesanne, kuna see nõuab olemasolevate raamistike uurimist ja rakendamist. Sellele probleemile lahendust otsides otsustati luua dünaamiline algoritmide modelleerimise rakendus (DAMR), mis oskab simuleerida algoritmi implementatsioone erinevates hajusarvutusraamistikes. DAMR aitab hinnata milline hajusraamistik on kõige sobivam ette antud algoritmi jaoks, ilma algoritmi reaalselt ühegi hajusraamistiku peale implementeerimata. Selle uurimustöö peamine panus on hajusarvutusraamistike kasutuselevõtu lihtsamaks tegemine teadlastele, kes ei ole varem nende kasutamisega kokku puutunud. See peaks märkimisväärselt aega ja ressursse kokku hoidma, kuna ei pea ükshaaval kõiki olemasolevaid hajusraamistikke tundma õppima ja rakendama.Scientific computing uses computers and algorithms to solve problems in various sciences such as genetics, biology and chemistry. Often the goal is to model and simulate different natural phenomena which would otherwise be very difficult to study in real environments. For example, it is possible to create a model of a solar storm or a meteor hit and run computer simulations to assess the impact of the disaster on the environment. The more sophisticated and accurate the simulations are the more computing power is required. It is often necessary to use a large number of computers, all working simultaneously on a single problem. These kind of computations are called parallel or distributed computing. However, creating distributed computing programs is complicated and requires a lot more time and resources, because it is necessary to synchronize different computers working at the same time. A number of software frameworks have been created to simplify this process by automating part of a distributed programming. The goal of this research was to assess the suitability of such distributed computing frameworks for complex scientific computing algorithms. The results showed that existing frameworks are very different from each other and none of them are suitable for all different types of algorithms. Some frameworks are only suitable for simple algorithms; others are not suitable when data does not fit into the computer memory. Choosing the most appropriate distributed computing framework for an algorithm can be a very complex task, because it requires studying and applying the existing frameworks. While searching for a solution to this problem, it was decided to create a Dynamic Algorithms Modelling Application (DAMA), which is able to simulate the implementation of the algorithm in different distributed computing frameworks. DAMA helps to estimate which distributed framework is the most appropriate for a given algorithm, without actually implementing it in any of the available frameworks. This main contribution of this study is simplifying the adoption of distributed computing frameworks for researchers who are not yet familiar with using them. It should save significant time and resources as it is not necessary to study each of the available distributed computing frameworks in detail

Vcluster: A Portable Virtual Computing Library For Cluster Computing

Message passing has been the dominant parallel programming model in cluster computing, and libraries like Message Passing Interface (MPI) and Portable Virtual Machine (PVM) have proven their novelty and efficiency through numerous applications in diverse areas. However, as clusters of Symmetric Multi-Processor (SMP) and heterogeneous machines become popular, conventional message passing models must be adapted accordingly to support this new kind of clusters efficiently. In addition, Java programming language, with its features like object oriented architecture, platform independent bytecode, and native support for multithreading, makes it an alternative language for cluster computing. This research presents a new parallel programming model and a library called VCluster that implements this model on top of a Java Virtual Machine (JVM). The programming model is based on virtual migrating threads to support clusters of heterogeneous SMP machines efficiently. VCluster is implemented in 100% Java, utilizing the portability of Java to address the problems of heterogeneous machines. VCluster virtualizes computational and communication resources such as threads, computation states, and communication channels across multiple separate JVMs, which makes a mobile thread possible. Equipped with virtual migrating thread, it is feasible to balance the load of computing resources dynamically. Several large scale parallel applications have been developed using VCluster to compare the performance and usage of VCluster with other libraries. The results of the experiments show that VCluster makes it easier to develop multithreading parallel applications compared to conventional libraries like MPI. At the same time, the performance of VCluster is comparable to MPICH, a widely used MPI library, combined with popular threading libraries like POSIX Thread and OpenMP. In the next phase of our work, we implemented thread group and thread migration to demonstrate the feasibility of dynamic load balancing in VCluster. We carried out experiments to show that the load can be dynamically balanced in VCluster, resulting in a better performance. Thread group also makes it possible to implement collective communication functions between threads, which have been proved to be useful in process based libraries

Mixing multi-core CPUs and GPUs for scientific simulation software

Recent technological and economic developments have led to widespread availability of multi-core CPUs and specialist accelerator processors such as graphical processing units (GPUs). The accelerated computational performance possible from these devices can be very high for some applications paradigms. Software languages and systems such as NVIDIA's CUDA and Khronos consortium's open compute language (OpenCL) support a number of individual parallel application programming paradigms. To scale up the performance of some complex systems simulations, a hybrid of multi-core CPUs for coarse-grained parallelism and very many core GPUs for data parallelism is necessary. We describe our use of hybrid applica- tions using threading approaches and multi-core CPUs to control independent GPU devices. We present speed-up data and discuss multi-threading software issues for the applications level programmer and o er some suggested areas for language development and integration between coarse-grained and ne-grained multi-thread systems. We discuss results from three common simulation algorithmic areas including: partial di erential equations; graph cluster metric calculations and random number generation. We report on programming experiences and selected performance for these algorithms on: single and multiple GPUs; multi-core CPUs; a CellBE; and using OpenCL. We discuss programmer usability issues and the outlook and trends in multi-core programming for scienti c applications developers

Supercharging the APGAS Programming Model with Relocatable Distributed Collections

In this article we present our relocatable distributed collections library. Building on top of the AGPAS for Java library, we provide a number of useful intra-node parallel patterns as well as the features necessary to support the distributed nature of the computation through clearly identified methods. In particular, the transfer of distributed collections' entries between processes is supported via an integrated relocation system. This enables dynamic load-balancing capabilities, making it possible for programs to adapt to uneven or evolving cluster performance. The system we developed makes it possible to dynamically control the distribution and the data-flow of distributed programs through high-level abstractions. Programmers using our library can therefore write complex distributed programs combining computation and communication phases through a consistent API. We evaluate the performance of our library against two programs taken from well-known Java benchmark suites, demonstrating superior programmability, and obtaining better performance on one benchmark and reasonable overhead on the second. Finally, we demonstrate the ease and benefits of load-balancing and on a more complex application which uses the various features of our library extensively.Comment: 23 pages 8 figures Consult the source code in the GitHub repository at https://github.com/handist/collection

Distributed simulation optimization and parameter exploration framework for the cloud

Simulation models are becoming an increasingly popular tool for the analysis and optimization of complex real systems in different fields. Finding an optimal system design requires performing a large sweep over the parameter space in an organized way. Hence, the model optimization process is extremely demanding from a computational point of view, as it requires careful, time-consuming, complex orchestration of coordinated executions. In this paper, we present the design of SOF (Simulation Optimization and exploration Framework in the cloud), a framework which exploits the computing power of a cloud computational environment in order to carry out effective and efficient simulation optimization strategies. SOF offers several attractive features. Firstly, SOF requires “zero configuration” as it does not require any additional software installed on the remote node; only standard Apache Hadoop and SSH access are sufficient. Secondly, SOF is transparent to the user, since the user is totally unaware that the system operates on a distributed environment. Finally, SOF is highly customizable and programmable, since it enables the running of different simulation optimization scenarios using diverse programming languages – provided that the hosting platform supports them – and different simulation toolkits, as developed by the modeler. The tool has been fully developed and is available on a public repository1 under the terms of the open source Apache License. It has been tested and validated on several private platforms, such as a dedicated cluster of workstations, as well as on public platforms, including the Hortonworks Data Platform and Amazon Web Services Elastic MapReduce solution

Guppie: A Coordination Framework for Parallel Processing Using Shared Memory Featuring A Master-Worker Relationship

Most programs can be parallelized to some extent. The processing power available in computers today makes parallel computing more desirable and attainable than ever before. Many machines today have multiple processors or multiple processing cores making parallel computing more available locally, as well as over a network. In order for parallel applications to be written, they require a computing language, such as C++, and a coordination language (or library), such as Linda. This research involves the creation and implementation of a coordination framework, Guppie, which is easy to use, similar to Linda, but provides more efficiency when dealing with large amounts of messages and data. Greater efficiency can be achieved in coarse-grained parallel computing through the use of shared memory managed through a master-worker relationship

ALOJA: A benchmarking and predictive platform for big data performance analysis

The main goals of the ALOJA research project from BSC-MSR, are to explore and automate the characterization of cost-effectivenessof Big Data deployments. The development of the project over its first year, has resulted in a open source benchmarking platform, an online public repository of results with over 42,000 Hadoop job runs, and web-based analytic tools to gather insights about system's cost-performance1. This article describes the evolution of the project's focus and research lines from over a year of continuously benchmarking Hadoop under dif- ferent configuration and deployments options, presents results, and dis cusses the motivation both technical and market-based of such changes. During this time, ALOJA's target has evolved from a previous low-level profiling of Hadoop runtime, passing through extensive benchmarking and evaluation of a large body of results via aggregation, to currently leveraging Predictive Analytics (PA) techniques. Modeling benchmark executions allow us to estimate the results of new or untested configu- rations or hardware set-ups automatically, by learning techniques from past observations saving in benchmarking time and costs.This work is partially supported the BSC-Microsoft Research Centre, the Span- ish Ministry of Education (TIN2012-34557), the MINECO Severo Ochoa Research program (SEV-2011-0067) and the Generalitat de Catalunya (2014-SGR-1051).Peer ReviewedPostprint (author's final draft