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2008 22nd International Symposium on High Performance Computing Systems and Applications最新文献

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High-Performance Chemodynamical Simulations of Galaxy Formation 星系形成的高性能化学动力学模拟
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.40
H. Martel
{"title":"High-Performance Chemodynamical Simulations of Galaxy Formation","authors":"H. Martel","doi":"10.1109/HPCS.2008.40","DOIUrl":"https://doi.org/10.1109/HPCS.2008.40","url":null,"abstract":"I will present results of chemo-hydrodynamical simulations of galaxy formation using the algorithm GCD+. This algorithm includes the effects of gravitation, gasdynamics, and radiative cooling, plus a subgrid treatment of star formation, supernovae feedback, and chemical enrichment. The results will focus on the structural, kinematic, and chemical properties of galaxies, their time-evolution, and how they compare with observations.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"49 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134258001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Performance Measurements of a Contact Searching Algorithm for Solving Large Deformation Problems 求解大变形问题的一种接触搜索算法的性能测量
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.42
E. Chamberland, C. Robitaille, A. Fortin
{"title":"Performance Measurements of a Contact Searching Algorithm for Solving Large Deformation Problems","authors":"E. Chamberland, C. Robitaille, A. Fortin","doi":"10.1109/HPCS.2008.42","DOIUrl":"https://doi.org/10.1109/HPCS.2008.42","url":null,"abstract":"Solving contact problems including friction effects in a parallel environment is still a challenge. In this kind of problems, a number of deformable objects interact with each other undergoing large deformations. A typical example is a tire on a road. The interacting objects can be totally distinct objects or parts of a given object interacting with itself. Contact searching, that is identifying potential contact points on other objects (or on itself), is an expensive task in terms of computational costs. In this presentation, an algorithm for solving contact problems including searching contact points in a parallel environment will be described and analysed. The algorithm presented is original and has no constraint on how the domain decomposition is done. The complexity of the resulting algorithm is higher but allows the use of automatic domain decomposition. We will study its performances as a function of the number of degrees of freedom and processors.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131738908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the High Pressure Phase Diagrams of Light Elements Using Large Scale Ab-initio Molecular Dynamics Simulations 利用大规模从头算分子动力学模拟探索轻元素的高压相图
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.26
Isaac Tamblyn, S. Bonev
{"title":"Exploring the High Pressure Phase Diagrams of Light Elements Using Large Scale Ab-initio Molecular Dynamics Simulations","authors":"Isaac Tamblyn, S. Bonev","doi":"10.1109/HPCS.2008.26","DOIUrl":"https://doi.org/10.1109/HPCS.2008.26","url":null,"abstract":"First principles molecular dynamics simulations allow us to model the highly complex and non-intuitive properties that matter exhibits when it is subject to extreme pressure and temperature conditions.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"122 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129134693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Group-Based Optimizaton for Parallel Job Scheduling with Scojo-PECT-O 基于Scojo-PECT-O的并行作业调度组优化
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.19
A. Sodan, Arun Kanavallil, Bryan Esbaugh
{"title":"Group-Based Optimizaton for Parallel Job Scheduling with Scojo-PECT-O","authors":"A. Sodan, Arun Kanavallil, Bryan Esbaugh","doi":"10.1109/HPCS.2008.19","DOIUrl":"https://doi.org/10.1109/HPCS.2008.19","url":null,"abstract":"Typical job scheduling for parallel machines is done on a one-by-one basis because of the dynamic arrival of jobs and the different priorities of the jobs. In the general case, this does not provide the optimum solution from a global point of view. Thus, we propose an approach which selects a group of jobs from the waiting queue and hierarchically optimizes a longer-term scheduling plan. This becomes feasible because the approach is embedded in our Scojo-PECT coarse-grain time sharing scheduler which separates jobs by priority. We demonstrate that we can obtain up to a 30% improvement in relative response times.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"105 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125187209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Simuler la Dynamique des Protéines: Simulation Protein Dynamics 模拟蛋白质动力学
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.30
Normand Mousseau
{"title":"Simuler la Dynamique des Protéines: Simulation Protein Dynamics","authors":"Normand Mousseau","doi":"10.1109/HPCS.2008.30","DOIUrl":"https://doi.org/10.1109/HPCS.2008.30","url":null,"abstract":"The study of protein dynamics has expanded considerably in the last ten years, in large part because of the wider availability of parallel supercomputers. But the growth in computing power is not sufficient: new numerical approaches must also be developed that allow for a more efficient sampling of configuration space. In this presentation, I will present some recent progress on the methodological side - including the replica method and the activation/relaxation technique - and on the description of potentials - internal coordinates representation and coarse-grained force fields. I will also present some applications of these methods to the folding of the A protein, a chain of 60 amino acids used as a toy model, and to amyloid aggregation. As we shall see, despite the recent progress, many challenges remain. The results presented were obtained in collaboration with Philippe Derreumaux, Wei Chen, Xiao Dong, Lilianne Dupuis, Rozita Laghaei, Jean-Francois St-Pierre et Guanghong Wei.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"23 3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130994428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Scalable Tools Communications Infrastructure 可伸缩的工具通信基础设施
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.24
Darius Buntinas, G. Bosilca, R. Graham, Geoffroy R. Vallée, G. R. Watson
{"title":"A Scalable Tools Communications Infrastructure","authors":"Darius Buntinas, G. Bosilca, R. Graham, Geoffroy R. Vallée, G. R. Watson","doi":"10.1109/HPCS.2008.24","DOIUrl":"https://doi.org/10.1109/HPCS.2008.24","url":null,"abstract":"The Scalable Tools Communication Infrastructure (STCI) is an open source collaborative effort intended to provide high-performance, scalable, resilient, and portable communications and process control services for a wide variety of user and system tools. STCI is aimed specifically at tools for ultrascale computing and uses a component architecture to simplify tailoring the infrastructure to a wide range of scenarios. This paper describes STCI's design philosophy, the various components that will be used to provide an STCI implementation for a range of ultrascale platforms, and a range of tool types. These include tools supporting parallel run-time environments, such as MPI, parallel application correctness tools and performance analysis tools, as well as system monitoring and management tools.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129738423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 16
A Framework for Executing Long Running Jobs in Grid Environments 在网格环境中执行长时间运行作业的框架
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.7
Nayden Markatchev, C. Kiddle, R. Simmonds
{"title":"A Framework for Executing Long Running Jobs in Grid Environments","authors":"Nayden Markatchev, C. Kiddle, R. Simmonds","doi":"10.1109/HPCS.2008.7","DOIUrl":"https://doi.org/10.1109/HPCS.2008.7","url":null,"abstract":"Computational jobs that take days, weeks or months to run usually cannot be executed as a single job due to system failures and scheduling constraints. Instead the job must be split into a series of shorter jobs. Solutions for managing the execution of such jobs in grid environments must address many issues. Participating systems and their properties can change over time and therefore it is important to have dynamic resource discovery mechanisms. Data management tools are needed to manage and keep track of data that can be distributed across multiple sites. Fault tolerance is required to handle the many different errors and failures that can occur in such environments. Furthermore, support for job reconfiguration, in terms of the number of processors, run length, and memory required, is necessary to allow jobs to adapt to the heterogeneous resources they are submitted to. This paper presents a framework for executing long running jobs in grid environments that addresses the above issues. The framework automates checkpointing, migration and reconfiguration of jobs. It has been successfully tested with the GROMACS molecular dynamics simulation application in a GT4-based grid environment comprised of resources distributed across Canada.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124856212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
Exploiting Data Locality in FFT Using Indirect Swap Network on Cell/B.E. 利用Cell/B.E.上的间接交换网络开发FFT中的数据局部性
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.11
Meilian Xu, P. Thulasiraman, R. Thulasiram
{"title":"Exploiting Data Locality in FFT Using Indirect Swap Network on Cell/B.E.","authors":"Meilian Xu, P. Thulasiraman, R. Thulasiram","doi":"10.1109/HPCS.2008.11","DOIUrl":"https://doi.org/10.1109/HPCS.2008.11","url":null,"abstract":"Communication and synchronization are two main latency issues in computing FFT on parallel architectures. Both latencies have to be either hidden or tolerated to achieve high performance. One approach to achieve this is by multithreading. Another approach to tolerate latency is to map data efficiently onto the processors' local memory and exploiting data locality. Indirect swap networks, an idea proposed in VLSI circuits can be efficiently used to compute the butterfly computations in FFT. Data mapping in the swap network topology reduces the communication overhead by half at each iteration. Cell broadband engine (Cell/B.E.)processor is a heterogeneous multicoreprocessor for stream data applications and high performance computing. Its eight SIMD processing elements, synergistic processor elements (SPEs), provide multi-folded parallelism. In this paper, we investigate the improved Cooley-Tukey FFT algorithm based on indirect swap network, and design the parallel algorithm taking into consideration all the features of the Cell/B.E. architecture. The performance results show that the new algorithm on Cell/B.E. is 3.7 faster than the cluster for 4K input data size and 6.4 faster than the cluster for 16K input data size at the processor level.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130926153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
MATDCAL: A First Principles Package for Nanoelectronics Modeling MATDCAL:纳米电子学建模的第一原理包
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.35
Z. Ning, Hong Guo
{"title":"MATDCAL: A First Principles Package for Nanoelectronics Modeling","authors":"Z. Ning, Hong Guo","doi":"10.1109/HPCS.2008.35","DOIUrl":"https://doi.org/10.1109/HPCS.2008.35","url":null,"abstract":"We report an ab initio software package MATDCAL for investigating electronic transport properties in nano electronic devices. MATDCAL is based on carrying out real space density functional theory (DFT) within the Keldysh nonequilibrium Green function (NEGF) framework. The code is mainly written in MATLAB, combining with numerically intensive part in Java for efficiency. In order to realize parallelization in MATLAB, we have implemented a C-interface in MATLAB to link to MPI. MATDCAL is the first MATLAB-based electronic package for nanoelectronics research that is based on atomistic first principles. We report some implementation issues using MATLAB for large scale physics computation. Several examples will be given on quantum transport analysis of nano-scale devices.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130776987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Combined Functional and Geometrical Decompositions for Multiphysics Problems with Application to Fluid-Structure Interaction 多物理场问题的组合函数和几何分解及其在流固耦合中的应用
2008 22nd International Symposium on High Performance Computing Systems and Applications Pub Date : 2008-06-09 DOI: 10.1109/HPCS.2008.25
Amine Ben El Haj Ali, A. Soulaïmani
{"title":"Combined Functional and Geometrical Decompositions for Multiphysics Problems with Application to Fluid-Structure Interaction","authors":"Amine Ben El Haj Ali, A. Soulaïmani","doi":"10.1109/HPCS.2008.25","DOIUrl":"https://doi.org/10.1109/HPCS.2008.25","url":null,"abstract":"This paper presents an efficient parallel-distributed methodology for solving multiphysics problems. A functional decomposition of the global problem is used first followed by the classical geometrical decomposition . Several technical details are presented for more clarity and for easing its implementation. All the techniques discussed in this paper are illustrated for a CFD-based aero elasticity simulation. A thorough performance study is shown with simulation results for the aeroelastic AGARD 445.6 and the turbulent flow over the ONERA M6 wing.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2008-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123609984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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