{"title":"The Variational Cluster Approximation for Hubbard Models: Practical Implementation","authors":"D. Sénéchal","doi":"10.1109/HPCS.2008.18","DOIUrl":"https://doi.org/10.1109/HPCS.2008.18","url":null,"abstract":"The Variational cluster approximation (VCA) is an approximate method for finding properties the Hubbard model, the basic model used in the study of strongly correlated electron systems. Such systems include, for instance, high-temperature and organic superconductors. The method involves solving exactly the Hubbard model on a small cluster of lattice sites, after adding fields that represent the effect of the cluster's environment. We present an outline of the method and describe its implementation. In particular, we show how to efficiently carry frequency- wavevector integrals that are central to the method.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"8 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":"123634509","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}
D. Deatrich, Simon Y. Liu, Chris Payne, Réda Tafirout, R. Walker, A. Wong, M. Vetterli
{"title":"Managing Petabyte-Scale Storage for the ATLAS Tier-1 Centre at TRIUMF","authors":"D. Deatrich, Simon Y. Liu, Chris Payne, Réda Tafirout, R. Walker, A. Wong, M. Vetterli","doi":"10.1109/HPCS.2008.27","DOIUrl":"https://doi.org/10.1109/HPCS.2008.27","url":null,"abstract":"The ATLAS experiment at the Large Hadron Collider (LHC), located in Geneva, will collect 3 to 4 petabytes or PB (1015 bytes) of data for each year of its operation, when fully commissioned. Secondary data sets resulting from event reconstruction, reprocessing and calibration will result in an additional 2.5 PB for each year of data taking. Simulated data sets require also significant resources as well nearing 1 PB per year. The data will be distributed worldwide to ten Tier-1 computing centres within the Worldwide LHC computing grid (WLCG) that will operate around the clock. One of these centres is hosted at TRIUMF, Canada's National Laboratory for Particle and Nuclear Physics, located in Vancouver, BC. By the year 2010, the storage capacity at TRIUMF will consist of about 3 Petabyte of disk storage, and 2 PB of tape storage. At present, the disk capacity installed is 750 terabytes or TB (1012 bytes) while the tape capacity is 560 TB, both using state of the art technology. dCache from www.dcache.org is used to manage the entire storage in order to provide a common file namespace. It is a highly scalable solution and highly configurable. In this paper we will describe and review the storage infrastructure and configuration currently in place at the Tier-1 centre at TRIUMF for both disk and tape as well as the management software and tools that have been developed.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"27 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":"126524455","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}
{"title":"Computing Intensive Simulations in Biofilm Modeling","authors":"H. Eberl, Nasim Muhammad, R. Sudarsan","doi":"10.1109/HPCS.2008.20","DOIUrl":"https://doi.org/10.1109/HPCS.2008.20","url":null,"abstract":"We present a brief overview of past and future applications of high performance computing in biofilm modeling. In particular we show that even relative simple two-dimensional models lead to computing expensive simulation experiments, due to data uncertainties inherent in all biofilm models.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"9 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":"127086905","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}
{"title":"Improving Communication Progress and Overlap in MPI Rendezvous Protocol over RDMA-enabled Interconnects","authors":"Mohammad J. Rashti, A. Afsahi","doi":"10.1109/HPCS.2008.10","DOIUrl":"https://doi.org/10.1109/HPCS.2008.10","url":null,"abstract":"Overlapping computation with communication is a key technique to conceal the effect of communication latency on the performance of parallel applications. MPI is a widely used message passing standard for high performance computing. One of the most important factors in achieving a good level of overlap is the MPI ability to make progress on outstanding communication operations. In this paper, we address some of the communication progress shortcomings in the current polling and RDMA Read based Rendezvous protocol used for transferring large messages in MPI. We then propose a novel speculative Rendezvous protocol that uses RDMA Read and RDMA Write to effectively improve communication progress and consequently the overlap ability. Performance results based on a modified MPICH2 over 10-Gigabit iWARP Ethernet reveal a significant (80-100%) improvement in receiver side overlap and progress ability.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"7 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":"121959529","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}
{"title":"Parallel Three-Dimensional Simulation of Ultrasound Imaging","authors":"M. Daoud, J. Lacefield","doi":"10.1109/HPCS.2008.28","DOIUrl":"https://doi.org/10.1109/HPCS.2008.28","url":null,"abstract":"Ultrasound imaging simulations provide an important tool in imaging research. However, realistic imaging simulations involve long execution times and require enormous computational resources that exceed the capabilities of serial computers. In this paper, we present a parallel three-dimensional ultrasound simulator that runs on computer clusters and uses a k-space method to compute acoustic propagation. The simulator achieved a mean error value of 0.57%, which demonstrates its numerical accuracy. Parallel computing enhanced the simulator efficiency by enabling imaging simulations with short execution times. For instance, the parallel execution time of a simulated ultrasound image using 20 cluster nodes was 18.61 hours compared to a serial execution time of 357.50 hours.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"127 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":"124221934","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}
{"title":"Models for Grid Applications and Jobs","authors":"T. Elahi, C. Kiddle, R. Simmonds","doi":"10.1109/HPCS.2008.9","DOIUrl":"https://doi.org/10.1109/HPCS.2008.9","url":null,"abstract":"Grid computing technologies have made it possible for researchers to get access to more computational resources than ever before. However, heterogeneity of resources, scheduling policy and applications makes it difficult to manage the execution of jobs in such environments. The manner in which a job is configured to run on one resource may not be appropriate for another resource. Long running jobs need to be split into a series of shorter jobs with the aid of checkpointing to increase fault tolerance and to meet scheduling policy constraints of different resources. To take full advantage of grid environments, execution management systems need to be able to configure, reconfigure, checkpoint and migrate jobs as necessary. Information models that describe resources, policy and applications help automate execution management and allow for interoperability between tools. This paper presents application and job models that describe the processes required to configure and execute jobs on different resources. Example instances of the application and job models for the GROMACS molecular dynamics simulation example are also presented, illustrating how the models aid in automation.","PeriodicalId":290167,"journal":{"name":"2008 22nd International Symposium on High Performance Computing Systems and Applications","volume":"46 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":"116942597","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}
D. Deatrich, Simon Y. Liu, Chris Payne, Réda Tafirout, R. Walker, A. Wong, M. Vetterli
{"title":"Grid Infrastructure and Large Scale Production for ATLAS","authors":"D. Deatrich, Simon Y. Liu, Chris Payne, Réda Tafirout, R. Walker, A. Wong, M. Vetterli","doi":"10.1109/HPCS.2008.41","DOIUrl":"https://doi.org/10.1109/HPCS.2008.41","url":null,"abstract":"In preparation for the startup of the LHC at CERN, the ATLAS collaboration is performing computing challenges of increasing complexity and scale. Monte Carlo production is ongoing with some 10,000 concurrent jobs worldwide, including at Canadian collaborating institutes. TRIUMF hosts one of the 10 ATLAS 'Tier-1' data and computing centres, where 270 TB of data per year will be transferred, by high performance dedicated networks, processed and redistributed for analysis. We discuss recent large scale tests of all aspects of middleware, hardware infrastructure and procedures to support the 24 times 7 operation of the Tier-1 centre, required for LHC running.","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":"128473540","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}