Filters








354 Hits in 3.9 sec

Demonstrating the scalability of a molecular dynamics application on a Petaflop computer

George S. Almasi, José E. Moreira, Dennis Newns, Marc Snir, Henry S. Warren, Cǎlin Caşcaval, José G. Castaños, Monty Denneau, Wilm Donath, Maria Eleftheriou, Mark Giampapa, Howard Ho (+1 others)
2001 Proceedings of the 15th international conference on Supercomputing - ICS '01  
Starting from the sequential version of a well known molecular dynamics code, we developed a new application that exploits the multiple levels of parallelism in the Blue Gene cellular architecture.  ...  As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.  ...  In this paper, we report on the results of analytical-and simulationbased studies on the behavior of a computational molecular dynamics application.  ... 
doi:10.1145/377792.377896 dblp:conf/ics/AlmasiCCDDEGHLMNSW01 fatcat:5nqwixum3bfczgi33t6apubnnu

Multi-scale HPC system for multi-scale discrete simulation—Development and application of a supercomputer with 1 Petaflops peak performance in single precision

Feiguo Chen, Wei Ge, Li Guo, Xianfeng He, Bo Li, Jinghai Li, Xipeng Li, Xiaowei Wang, Xiaolong Yuan
2009 Particuology  
The preliminary applications of this machine in areas of multi-phase flow, molecular dynamics and so on are reported, demonstrating the supercomputer as a paradigm of green computation in new architecture  ...  of Process Engineering (IPE) and implemented in a graphic processing unit (GPU)-based hybrid computing mode.  ...  For industrial applications, Mole-8.7 is now capable of simulating, in 2D, meter-scale fluidized beds on sub-millimeter particle scales in nearly real-time, that is, on the order of one minute computing  ... 
doi:10.1016/j.partic.2009.06.002 fatcat:azyjgvr5qvastdvynrjsonhlym

PROSPECTS FOR CFD ON PETAFLOPS SYSTEMS [chapter]

David E. KEYES, Dinesh K. KAUSHIK, Barry F. SMITH
1998 Computational Fluid Dynamics Review 1998  
After a general outline of the problems and prospects of petaflops computing, we examine the issue of algorithms for PDE computations in particular.  ...  Given that cost-effective one-thousand-fold concurrency is challenging in practical computational fluid dynamics simulations today, algorithms are among the many possible bottlenecks to CFD on petaflops  ...  Acknowledgements The authors owe a large debt of gratitude to W. Kyle Anderson  ... 
doi:10.1142/9789812812957_0060 fatcat:qwy6thxuzvgrto4jge2zsht66u

GRAPE-6: A Petaflops Prototype [article]

Piet Hut, Jeffrey M. Arnold, Junichiro Makino, Stephen L.W. McMillan,, Thomas L. Sterling
1997 arXiv   pre-print
The combination of a hardwired petaflops-class computational engine and a front end with sustained speed on the order of 10 gigaflops can produce extremely high performance, but only for the limited class  ...  We present the outline of a research project aimed at designing and constructing a hybrid computing system that can be easily scaled up to petaflops speeds.  ...  The optimal mix of these two paradigms depends on both the computational mix of the application and on the relative costs.  ... 
arXiv:astro-ph/9704183v1 fatcat:23pxshuc3nc2fotn7zmwtervgu

Prospects for CFD on Petaflops Systems [chapter]

David E. Keyes, Dinesh K. Kaushik, Barry F. Smith
2000 IMA Volumes in Mathematics and its Applications  
After a general outline of the problems and prospects of petaflops computing, we examine the issue of algorithms for PDE computations in particular.  ...  Given that cost-effective one-thousand-fold concurrency is challenging in practical computational fluid dynamics simulations today, algorithms are among the many possible bottlenecks to CFD on petaflops  ...  Acknowledgements The authors owe a large debt of gratitude to W. Kyle Anderson  ... 
doi:10.1007/978-1-4612-1176-1_11 fatcat:ibsclde5x5g6pefdmkoumgr7ou

Massively parallel first-principles simulation of electron dynamics in materials

Erik W. Draeger, Xavier Andrade, John A. Gunnels, Abhinav Bhatele, André Schleife, Alfredo A. Correa
2017 Journal of Parallel and Distributed Computing  
We present a highly scalable, parallel implementation of first-principles electron dynamics coupled with molecular dynamics (MD).  ...  We obtained up to 59% of the theoretical sustained peak performance on 16,384 nodes and performance of 8.75 Petaflop/s (43% of theoretical peak) on the full 98,304 node machine (1,572,864 cores).  ...  ACKNOWLEDGMENTS The authors wish to thank the Livermore Computing team for their tireless dedication and support, the NNSA Advanced Scientific Computing program for their support of this work and William  ... 
doi:10.1016/j.jpdc.2017.02.005 fatcat:dqgosdd3dndubahqvah6eejy5u

Massively Parallel First-Principles Simulation of Electron Dynamics in Materials

Erik W. Draeger, Xavier Andrade, John A. Gunnels, Abhinav Bhatele, Andre Schleife, Alfredo A. Correa
2016 2016 IEEE International Parallel and Distributed Processing Symposium (IPDPS)  
We present a highly scalable, parallel implementation of first-principles electron dynamics coupled with molecular dynamics (MD).  ...  We obtained up to 59% of the theoretical sustained peak performance on 16,384 nodes and performance of 8.75 Petaflop/s (43% of theoretical peak) on the full 98,304 node machine (1,572,864 cores).  ...  ACKNOWLEDGMENTS The authors wish to thank the Livermore Computing team for their tireless dedication and support, the NNSA Advanced Scientific Computing program for their support of this work and William  ... 
doi:10.1109/ipdps.2016.46 dblp:conf/ipps/DraegerAGBSC16 fatcat:hexmouptzrd3dniep5dvzrpjoy

Simulation-Based Performance Prediction for Large Parallel Machines

Gengbin Zheng, Terry Wilmarth, Praveen Jagadishprasad, Laxmikant V. Kalé
2005 International journal of parallel programming  
We present a performance prediction environment for large scale computers such as the Blue Gene machine.  ...  We illustrate the utility of our simulators using validation and prediction studies of several applications using smaller numbers of processors for simulations.  ...  The Molecular Dynamics simulation of biomolecules is one of the important applications for Blue Gene/L and other large parallel machines.  ... 
doi:10.1007/s10766-005-3582-6 fatcat:szbb7zxwuba3fk2p672dk7luoq

D7.5.2: Technical requirement for the second Petaflop/s system(s)

Jonathan Evans
2009 Zenodo  
The PRACE project has the overall objective of preparing for the creation of a persistent pan-European HPC service.  ...  The key objective of this deliverable is to provide a toolbox of technical elements that can be used flexibly in the procurement of systems for the PRACE research infrastructure.  ...  Typically Molecular Dynamics applications have seen speedups of up to 30 when run on GPUs.  ... 
doi:10.5281/zenodo.6546123 fatcat:2x5n7oobpnh4hdin2wvywgnpsu

De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, Ashish Sharma, Priya Vashishta, Fuyuki Shimojo, Adri C. T. van Duin, William A. Goddard, Rupak Biswas, Deepak Srivastava, Lin H. Yang
2008 The international journal of high performance computing applications  
A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto petaflops computers, while achieving performance tunability through a hierarchy of parameterized  ...  Furthermore, performance portability has been demonstrated on a wide range of platforms such as BlueGene/L, Altix 3000, and AMD Opteron-based Linux clusters.  ...  Programs have been developed using the 2048-processor (4 Tflops) Opteron/Xeon/Apple G5 cluster at the Collaboratory for Advanced Computing and Simulations of USC.  ... 
doi:10.1177/1094342007085015 fatcat:tr2nbpzurjesje4jkoatsuecam

Scalability study of molecular dynamics simulation on Godson-T many-core architecture

Liu Peng, Guangming Tan, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta, Dongrui Fan, Hao Zhang, Fenglong Song
2013 Journal of Parallel and Distributed Computing  
Molecular dynamics (MD) simulation has broad applications, and an increasing amount of computing power is needed to satisfy the large scale of the real world simulation.  ...  To address this challenge, this paper presents a joint application/architecture study to enhance the scalability of MD on Godson-T -like manycore architecture.  ...  Related work Molecular dynamics simulation is one of the most prominent applications driving the development of new computer architectures and supercomputing systems.  ... 
doi:10.1016/j.jpdc.2012.07.007 fatcat:hfoousphcfcsnmxm2jjirllbpa

Scalability of DL_POLY on High Performance Computing Platform

Mabule Samuel Mabakane, Daniel Mojalefa Moeketsi, Anton Lopis
2017 South African Computer Journal  
This paper presents a case study on the scalability of several versions of the molecular dynamics code (DL_POLY) performed on South Africa's Centre for High Performance Computing e1350 IBM Linux cluster  ...  Within this study different problem sizes were designed and the same chosen systems were employed in order to test the performance of DL_POLY using weak and strong scalability.  ...  ACKNOWLEDGEMENTS This research study is funded by the Centre for High Performance Computing (CHPC); an initiative of the Department of Science and Technology, South Africa in cooperation with the Council  ... 
doi:10.18489/sacj.v29i3.405 fatcat:gvlsdfm26neobhr44cqixan6p4

Scalable Atomistic Simulation Algorithms for Materials Research

Aiichiro Nakano, Rajiv K. Kalia, Priya Vashishta, Timothy J. Campbell, Shuji Ogata, Fuyuki Shimojo, Subhash Saini
2002 Scientific Programming  
Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations based on the density functional theory.  ...  A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms.  ...  Acknowledgements This work was partially supported by AFOSR, ARL, DOE, NASA, NSF, and Louisiana Board of Regents. Benchmark tests were performed using the 1,088-node Cray  ... 
doi:10.1155/2002/203525 fatcat:5ixjijxbzjgqhi67i5c5k3lmdm

Blue Gene: A vision for protein science using a petaflop supercomputer

F. Allen, G. Almasi, W. Andreoni, D. Beece, B. J. Berne, A. Bright, J. Brunheroto, C. Cascaval, J. Castanos, P. Coteus, P. Crumley, A. Curioni (+40 others)
2001 IBM Systems Journal  
Molecular dynamics is one example of such an application.  ...  The behavior shown here is typical of a parallel molecular dynamics code; scalability is better for systems with large numbers of particles. into communications problems and problems with the machine's  ... 
doi:10.1147/sj.402.0310 fatcat:4swzupm74bgpdbx65jawa4qkfa

Some essential techniques for developing efficient petascale applications

L V Kalé
2008 Journal of Physics, Conference Series  
It will be a substantial challenge to make existing parallel CSE applications run efficiently on them, and even more challenging to design new applications that can effectively leverage the large computational  ...  Multiple PetaFLOPS class machines will appear during the coming year, and many multi-PetaFLOPS machines are on the anvil.  ...  dynamics) so as to prefer placing them on the same node.  ... 
doi:10.1088/1742-6596/125/1/012036 fatcat:i57rn27hjnf7vontusg47p74km
« Previous Showing results 1 — 15 out of 354 results