Exploiting 162-Nanosecond End-to-End Communication Latency on Anton

Authors:
Ron O. Dror;J. P. Grossman;Kenneth M. Mackenzie;Brian Towles;Edmond Chow;John K. Salmon;Cliff Young;Joseph A. Bank;Brannon Batson;Martin M. Deneroff;Jeffrey S. Kuskin;Richard H. Larson;Mark A. Moraes;David E. Shaw
Affiliations:
-;-;-;-;-;-;-;-;-;-;-;-;-;-
Venue:
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
Year:
2010

Citing 32
Cited 1

The J-machine multicomputer: an architectural evaluation

ISCA '93 Proceedings of the 20th annual international symposium on computer architecture
Fast parallel algorithms for short-range molecular dynamics

Journal of Computational Physics
The M-Machine multicomputer

Proceedings of the 28th annual international symposium on Microarchitecture
Synchronization and communication in the T3E multiprocessor

Proceedings of the seventh international conference on Architectural support for programming languages and operating systems
An implementation of the Hamlyn sender-managed interface architecture

OSDI '96 Proceedings of the second USENIX symposium on Operating systems design and implementation
Design and implementation of FMPL, a fast message-passing library for remote memory operations

Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Performance Evaluation of the Quadrics Interconnection Network

Cluster Computing
Ultra-high performance communication with MPI and the Sun fire™ link interconnect

Proceedings of the 2002 ACM/IEEE conference on Supercomputing
An overview of the BlueGene/L Supercomputer

Proceedings of the 2002 ACM/IEEE conference on Supercomputing
Blue Gene: a vision for protein science using a petaflop supercomputer

IBM Systems Journal - Deep computing for the life sciences
QCDOC: A 10 Teraflops Computer for Tightly-Coupled Calculations

Proceedings of the 2004 ACM/IEEE conference on Supercomputing
Scalable Hardware-Based Multicast Trees

Proceedings of the 2003 ACM/IEEE conference on Supercomputing
QsNetII: Defining High-Performance Network Design

IEEE Micro
Optimization of MPI collective communication on BlueGene/L systems

Proceedings of the 19th annual international conference on Supercomputing
An Application-Based Performance Characterization of the Columbia Supercluster

SC '05 Proceedings of the 2005 ACM/IEEE conference on Supercomputing
A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
A performance comparison through benchmarking and modeling of three leading supercomputers: blue Gene/L, Red Storm, and Purple

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Scalable algorithms for molecular dynamics simulations on commodity clusters

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Blue matter: approaching the limits of concurrency for classical molecular dynamics

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Software routing and aggregation of messages to optimize the performance of HPCC randomaccess benchmark

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Design and implementation of a one-sided communication interface for the IBM eServer Blue Gene® supercomputer

Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Anton, a special-purpose machine for molecular dynamics simulation

Proceedings of the 34th annual international symposium on Computer architecture
General purpose molecular dynamics simulations fully implemented on graphics processing units

Journal of Computational Physics
High-performance ethernet-based communications for future multi-core processors

Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Cray XT4: an early evaluation for petascale scientific simulation

Proceedings of the 2007 ACM/IEEE conference on Supercomputing
Entering the petaflop era: the architecture and performance of Roadrunner

Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Adapting a message-driven parallel application to GPU-accelerated clusters

Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Early evaluation of IBM BlueGene/P

Proceedings of the 2008 ACM/IEEE conference on Supercomputing
Designing Next Generation Clusters: Evaluation of InfiniBand DDR/QDR on Intel Computing Platforms

HOTI '09 Proceedings of the 2009 17th IEEE Symposium on High Performance Interconnects
A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Millisecond-scale molecular dynamics simulations on Anton

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis
Interconnect performance evaluation of SGI altix 3700 BX2, cray X1, cray opteron cluster, and dell PowerEdge

IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing

Hardware support for fine-grained event-driven computation in Anton 2

Proceedings of the eighteenth international conference on Architectural support for programming languages and operating systems

Quantified Score

Hi-index	0.00

Visualization

Abstract

Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This paper describes the techniques used to mitigate latency in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art. Achieving this speedup required a combination of hardware mechanisms and software constructs to reduce network latency, sender and receiver overhead, and synchronization costs. Key elements of Anton's approach, in addition to tightly integrated communication hardware, include formulating data transfer in terms of counted remote writes, leveraging fine-grained communication, and establishing fixed, optimized communication patterns. Anton delivers software-to-software inter-node latency significantly lower than any other large-scale parallel machine, and the total critical-path communication time for an Anton MD simulation is less than 4% that of the next fastest MD platform.