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Early Experience with Scientific Applications on the Blue Gene/L Supercomputer [chapter]

George Almasi, Gyan Bhanot, Dong Chen, Maria Eleftheriou, Blake Fitch, Alan Gara, Robert Germain, John Gunnels, Manish Gupta, Philip Heidelberg, Mike Pitman, Aleksandr Rayshubskiy (+14 others)
2005 Lecture Notes in Computer Science  
Blue Gene/L uses a large number of low power processors, together with multiple integrated interconnection networks, to build a supercomputer with low cost, space and power consumption.  ...  The results reported in this study represent the highest performance ever demonstrated for most of these applications, and in fact, show effective scaling for the first time ever on thousands of processors  ...  The IBM Blue Gene/L (BG/L) [4] represents a different way of building supercomputers.  ... 
doi:10.1007/11549468_63 fatcat:cnwvrk33j5gzrdrazjkusfq7ri

High Performance File I/O for The Blue Gene/L Supercomputer

H. Yu, R.K. Sahoo, C. Howson, G. Almasi, J.G. Castanos, M. Gupta, J.E. Moreira, J.J. Parker, T.E. Engelsiepen, R.B. Ross, R. Thakur, R. Latham (+1 others)
The Twelfth International Symposium on High-Performance Computer Architecture, 2006.  
We demonstrate the impact of our high performance I/O solution for Blue Gene/L with a comprehensive evaluation that consists of a number of widely used parallel I/O benchmarks and I/O intensive applications  ...  We designed and implemented a highly scalable parallel file I/O architecture for Blue Gene/L, which leverages the benefit of the hierarchical and functional partitioning design of the system software with  ...  By leveraging the benefit of functional partitioning and hierarchical structure of Blue Gene/L system software, our parallel file I/O design, is able to provide scalable file I/O bandwidth far beyond the  ... 
doi:10.1109/hpca.2006.1598125 dblp:conf/hpca/YuSHACGMPERTLG06 fatcat:egmx4tl5z5hwpmz7qe4qxzxu6m

Astronomical real-time streaming signal processing on a Blue Gene/L supercomputer

John W. Romein, P. Chris Broekema, Ellen van Meijeren, Kjeld van der Schaaf, Walther H. Zwart
2006 Proceedings of the eighteenth annual ACM symposium on Parallelism in algorithms and architectures - SPAA '06  
We also discuss how we handle external I/O performance limitations into and out of the Blue Gene/L, to obtain sufficient bandwidth for LOFAR.  ...  CEP consists of a 12,288core IBM Blue Gene/L supercomputer, embedded in several conventional clusters.  ...  Acknowledgments LOFAR is being funded by the Dutch government in the BSIK programme for interdisciplinary research for improvements of the knowledge infrastructure.  ... 
doi:10.1145/1148109.1148118 dblp:conf/spaa/RomeinBMSZ06 fatcat:3x3sqxxr2fdjzmkexujmtrycam

I/O threads to reduce checkpoint blocking for an electromagnetics solver on Blue Gene/P and Cray XK6

Jing Fu, Robert Latham, Misun Min, Christopher D. Carothers
2012 Proceedings of the 2nd International Workshop on Runtime and Operating Systems for Supercomputers - ROSS '12  
Our study shows that threaded rbIO can overlap the I/O latency with computation and achieve near-asynchronous checkpoint with an application-perceived I/O performance of over 70 GB/s (raw of 15 GB/s) and  ...  In this paper, we examine a new thread-based application-level checkpointing for a massively parallel electromagnetic solver system on the IBM Blue Gene/P at Argonne National Laboratory and the Cray XK6  ...  RELATED WORK Our previous work showed performance analysis for rbIO and coIO on Blue Gene/L and Blue Gene/P and parameter tuning practices [13, 14] .  ... 
doi:10.1145/2318916.2318919 fatcat:bdm47bhdrvaghfwyqpbtnox4jq

Application-specific I/O Optimizations on Petascale Supercomputers

Efecan Poyraz, Heming Xu, Yifeng Cui
2014 Procedia Computer Science  
Large-scale simu lations demand significant I/ O workload, and as a result the I/O performance often becomes a bottleneck preventing high performance in scientific applications.  ...  The techniques introduced in this paper are applicab le to other scientific applications facing similar petascale I/O challenges.  ...  Acknowledgements We thank Jun Zhou for his contribution to the development of the fast -t method discussed in this paper, and Kwangyoon Lee for his optimizat ion to collective M PI-IO method for seismic  ... 
doi:10.1016/j.procs.2014.05.082 fatcat:k4kzmje24je67invuvn6o4uxbu

Scalable RF propagation modeling on the IBM Blue Gene/L and Cray XT5 supercomputers

David W. Bauer, Christopher D. Carothers
2009 Proceedings of the 2009 Winter Simulation Conference (WSC)  
We present a performance analysis for a highly accurate, large-scale electromagnetic wave propagation model on two modern supercomputing platforms: the Cray XT5 and the IBM Blue Gene/L.  ...  The model is based on the numerical technique called Transmission Line Matrix, and is implemented in a Time Warp simulation package that employs reverse computation for the rollback mechanism.  ...  Each Blue Gene rack is composed into 1024 nodes consisting of 32 drawers with 32 nodes in each drawer. Additionally, there are specialized I/O nodes that perform all file I/O.  ... 
doi:10.1109/wsc.2009.5429676 dblp:conf/wsc/BauerC09 fatcat:4yzwdq4yuzgyjchvnhuzc7z2iq

Overview of the Blue Gene/L system architecture

A. Gara, M. A. Blumrich, D. Chen, G. L.-T. Chiu, P. Coteus, M. E. Giampapa, R. A. Haring, P. Heidelberger, D. Hoenicke, G. V. Kopcsay, T. A. Liebsch, M. Ohmacht (+3 others)
2005 IBM Journal of Research and Development  
The key architectural features of Blue Gene/L are introduced in this paper: the link chip component and five Blue Gene/L networks, the PowerPCt 440 core and floatingpoint enhancements, the on-chip and  ...  The Blue Genet/L computer is a massively parallel supercomputer based on IBM system-on-a-chip technology.  ...  Acknowledgment The Blue Gene/L project has been supported and partially funded by the Lawrence Livermore National Laboratory on behalf of the United States Department of Energy under Lawrence Livermore  ... 
doi:10.1147/rd.492.0195 fatcat:fod4gj7pbfgdxnd7nsxgfy4ini

Collective I/O Performance on the Santos Dumont Supercomputer

Andre Ramos Carneiro, Jean Luca Bez, Francieli Zanon Boito, Bruno Alves Fagundes, Carla Osthoff, Philippe Olivier Alexandre Navaux
2018 2018 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing (PDP)  
From the point of view of a large-scale, expensive, supercomputer, it is important to ensure applications achieve the best I/O performance to promote an efficient usage of the machine.  ...  In this paper, we evaluate the I/O infrastructure of the Santos Dumont supercomputer, the largest one from Latin America.  ...  The authors acknowledge the National Laboratory for Scientific Computing (LNCC/MCTI, Brazil) for providing HPC resources of the SDumont supercomputer, which have contributed to the research results reported  ... 
doi:10.1109/pdp2018.2018.00015 dblp:conf/pdp/CarneiroBBFON18 fatcat:kjjtb3khhrh4bcbc5wtn7k7gvm

Poster reception---High resolution, high throughput protein structure prediction using IBM Blue Gene supercomputers

Ross C Walker, Srivatsan Raman, David Baker
2006 Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06  
With genome-wide sequencing completed for a number of organisms including humans, the next challenges are to functionally characterize the proteins encoded by these genes and to understand their roles  ...  The Rosetta software suite has been under development in Prof Baker's research group for the last 15 years and currently there are over 80 developers across 6 university campuses actively improving and  ...  Acknowledgements The authors would like to thank IBM for graciously providing access to their Blue Gene Watson machine and San Diego Supercomputer Center and Argonne National Lab for providing computational  ... 
doi:10.1145/1188455.1188626 dblp:conf/sc/WalkerRB06 fatcat:3ht4unhubvc3laqe46utyfpo3i

IBM Blue Gene Supercomputer [chapter]

Alan Gara, José E. Moreira, Tejas S. Karkhanis, José E. Moreira, José E. Moreira, Michael Flynn, Yoichi Muraoka, Matthias Bollhöfer, José I. Aliaga, Alberto F. Martı́n, Enrique S. Quintana-Ortí, Dhabaleswar K. Panda (+11 others)
2011 Encyclopedia of Parallel Computing  
For details on the Blue Gene system software, the reader is referred to [ 9 10, 10]. Finally, examples of the impact of Blue Gene on science can be found in [ 1, 2, 3, 4, 5, 7, 12, 13, 14] .  ...  Other success stories for Blue Gene in science include: (1) Astrophysical simulations in Argonne National Laboratory (ANL) using the FLASH code; (2) Global climate simulations in the National Center for  ...  Various network file systems have been ported to the Blue Gene/L I/O node, including GPFS, Lustre, NFS, and PVFS2. Blue Gene/L I/O nodes never run application processes.  ... 
doi:10.1007/978-0-387-09766-4_409 fatcat:j74ptxyr4ngppiatv25675z5sa

A Flexible Resource Management Architecture for the Blue Gene/P Supercomputer

Sam Miller, Mark Megerian, Paul Allen, Tom Budnik
2007 2007 IEEE International Parallel and Distributed Processing Symposium  
Blue Gene R /P is a massively parallel supercomputer intended as the successor to Blue Gene/L.  ...  This paper describes how the Blue Gene/P resource management architecture is extremely flexible by providing multiple methodologies for obtaining resource usage information to make scheduling decisions  ...  Introduction Blue Gene/P (BG/P) is a petaflop scale system, and the successor to Blue Gene/L (BG/L), which is described in detail in [6] .  ... 
doi:10.1109/ipdps.2007.370628 dblp:conf/ipps/MillerMAB07 fatcat:5iutrrxq3bc4boa6enzy5224au

Simulation of High-Resolution Magnetic Resonance Images on the IBM Blue Gene/L Supercomputer Using SIMRI

K. G. Baum, G. Menezes, M. Helguera
2011 International Journal of Biomedical Imaging  
We have modified SIMRI, a Bloch equation-based magnetic resonance image simulator, in order to successfully generate high-resolution 3D MR images of the Montreal brain phantom using Blue Gene/L systems  ...  Results show that redistribution of the workload allows an anatomically accurate 2563voxel spin-echo simulation in less than 5 hours when executed on an 8192-node partition of a Blue Gene/L system.  ...  Acknowledgments This research utilized resources at the New York Center for Computational Sciences at Stony Brook University/Brookhaven National Laboratory which is supported by the U.S.  ... 
doi:10.1155/2011/305968 pmid:21747818 pmcid:PMC3124258 fatcat:aprqtou5gbfntdvobq5cbm6oxu

Gordon Bell finalists I---Large scale drop impact analysis of mobile phone using ADVC on Blue Gene/L

Hiroshi Akiba, Manish Gupta, John A Gunnels, Vernon Austel, Yogish Sabharwal, Rahul Garg, Shoji Kato, Takashi Kawakami, Satoru Todokoro, Junko Ikeda, Tomonobu Ohyama, Yoshinoir Shibata (+6 others)
2006 Proceedings of the 2006 ACM/IEEE conference on Supercomputing - SC '06  
In this paper, we demonstrate the performance characteristics of a commercial parallel structural analysis code, ADVC, on Blue Gene/L (BG/L).  ...  Existing commercial finite element analysis (FEA) codes do not exhibit the performance necessary for large scale analysis on parallel computer systems.  ...  Jung-kook Hong at IBM Japan for their continuous and careful attention to our project.  ... 
doi:10.1145/1188455.1188503 dblp:conf/sc/AkibaOSYKTHYNGGASGKKTI06 fatcat:lh7teknbubgythumc3v3e26yey

Scaling physics and material science applications on a massively parallel Blue Gene/L system

George Almasi, James N. Glosli, Jeffrey A. Greenough, Francois Gygi, Alison Kubota, Steve Louis, Thomas E. Spelce, Frederick H. Streitz, Peter L. Williams, Robert K. Yates, Charles Archer, Gyan Bhanot (+9 others)
2005 Proceedings of the 19th annual international conference on Supercomputing - ICS '05  
They also validate the scalability of the hardware and software architecture of Blue Gene/L.  ...  Blue Gene/L represents a new way to build supercomputers, using a large number of low power processors, together with multiple integrated interconnection networks.  ...  INTRODUCTION The Blue Gene/L (BG/L) project at IBM, in partnership with Lawrence Livermore National Laboratory (LLNL), has pursued a new approach to building supercomputers [1] .  ... 
doi:10.1145/1088149.1088182 dblp:conf/ics/AlmasiBGGSWBCSGGGKLSSWYAMR05 fatcat:q4ho3aaszjbjnpfy672e7njdzm

Parallel I/O Performance for Application-Level Checkpointing on the Blue Gene/P System

Jing Fu, Misun Min, Robert Latham, Christopher D. Carothers
2011 2011 IEEE International Conference on Cluster Computing  
Our study also demonstrates a 25× production performance improvement for NekCEM. We show how to optimize parameter settings for those parallel I/O approaches and to verify results by I/O profilings.  ...  We discuss an application-level, two-phase I/O approach, called "reduced-blocking I/O" (rbIO), and a tuned MPI-IO collective approach (coIO), and we demonstrate their performance advantage over the "1  ...  [31] investigated file I/O performance for the MAD-bench2 benchmark on different systems, such as Lustre on Cray and GPFS on Blue Gene/L.  ... 
doi:10.1109/cluster.2011.81 dblp:conf/cluster/FuMLC11 fatcat:bqzs6wovobgejeo7e5ybtpm2qq
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