A fast algorithm for particle simulations
Journal of Computational Physics
Computer simulation using particles
Computer simulation using particles
Computer simulation of liquids
Computer simulation of liquids
Fast parallel algorithms for short-range molecular dynamics
Journal of Computational Physics
Parallel molecular dynamics: implications for massively parallel machines
Journal of Parallel and Distributed Computing
Scalable molecular dynamics for large biomolecular systems
Proceedings of the 2000 ACM/IEEE conference on Supercomputing
Understanding Molecular Simulation: From Algorithms to Applications
Understanding Molecular Simulation: From Algorithms to Applications
IBM Journal of Research and Development
A lightweight idempotent messaging protocol for faulty networks
Proceedings of the fourteenth annual ACM symposium on Parallel algorithms and architectures
Demonstrating the Scalability of a Molecular Dynamics Application on a Petaflops Computer
International Journal of Parallel Programming
A survey of processors with explicit multithreading
ACM Computing Surveys (CSUR)
A New Approach to Fault-Tolerant Wormhole Routing for Mesh-Connected Parallel Computers
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
An overview of the BlueGene/L Supercomputer
Proceedings of the 2002 ACM/IEEE conference on Supercomputing
User-controllable coherence for high performance shared memory multiprocessors
Proceedings of the ninth ACM SIGPLAN symposium on Principles and practice of parallel programming
A Fault-Tolerant and Deadlock-Free Routing Protocol in 2D Meshes Based on Odd-Even Turn Model
IEEE Transactions on Computers
Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
Power-driven Design of Router Microarchitectures in On-chip Networks
Proceedings of the 36th annual IEEE/ACM International Symposium on Microarchitecture
A New Approach to Fault-Tolerant Wormhole Routing for Mesh-Connected Parallel Computers
IEEE Transactions on Computers
On fault tolerance of 3-dimensional mesh networks
Journal of Computer Science and Technology
Analytically Modeling a Fault-Tolerant Messaging Protocol
IEEE Transactions on Computers
Characterizing a new class of threads in scientific applications for high end supercomputers
Proceedings of the 18th annual international conference on Supercomputing
IBM Journal of Research and Development
IBM Systems Journal - Deep computing for the life sciences
Computational biology and high-performance computing
Communications of the ACM - Bioinformatics
Optimizing NANOS OpenMP for the IBM Cyclops Multithreaded Architecture
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01
A Framework for Measuring Supercomputer Productivity
International Journal of High Performance Computing Applications
Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials
International Journal of High Performance Computing Applications
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
SCMP: a single-chip message-passing parallel computer
The Journal of Supercomputing - Special issue: Parallel and distributed processing and applications
Performance characterization of molecular dynamics techniques for biomolecular simulations
Proceedings of the eleventh ACM SIGPLAN symposium on Principles and practice of parallel programming
Chip multiprocessing and the cell broadband engine
Proceedings of the 3rd conference on Computing frontiers
Fault-Tolerant Routing Algorithm in Meshes with Solid Faults
The Journal of Supercomputing
Fault-tolerant wormhole routing with 2 virtual channels in meshes
Journal of Computer Science and Technology
Blue matter: approaching the limits of concurrency for classical molecular dynamics
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Proceedings of the 2006 ACM/IEEE conference on Supercomputing
Probabilistic analysis on mesh network fault tolerance
Journal of Parallel and Distributed Computing
Zonal methods for the parallel execution of range-limited N-body simulations
Journal of Computational Physics
A novel ab-initio genetic-based approach for protein folding prediction
Proceedings of the 9th annual conference on Genetic and evolutionary computation
The blue gene/L supercomputer: a hardware and software story
International Journal of Parallel Programming
The cell broadband engine: exploiting multiple levels of parallelism in a chip multiprocessor
International Journal of Parallel Programming
Exploiting multilevel parallelism using OpenMP on a massive multithreaded architecture
Journal of Embedded Computing - Issues in embedded single-chip multicore architectures
Massively parallel molecular dynamics simulations of lysozyme unfolding
IBM Journal of Research and Development
IBM Journal of Research and Development
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
IBM Journal of Research and Development
Genetic algorithms and solutions of an interesting differential equation
Proceedings of the 10th annual conference on Genetic and evolutionary computation
A unified fault-tolerant routing scheme for a class of cluster networks
Journal of Systems Architecture: the EUROMICRO Journal
Deadlock-Free Adaptive Routing in 2D Tori with a New Turn Model
ICA3PP '08 Proceedings of the 8th international conference on Algorithms and Architectures for Parallel Processing
DFS Based Partial Pathways in GA for Protein Structure Prediction
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Effect of increasing chip density on the evolution of computer architectures
IBM Journal of Research and Development
Packaging the Blue Gene/L supercomputer
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
IBM Journal of Research and Development
Overview of molecular dynamics techniques and early scientific results from the Blue Gene project
IBM Journal of Research and Development
Lower bounds on the connectivity probability for 2-D mesh networks
WiCOM'09 Proceedings of the 5th International Conference on Wireless communications, networking and mobile computing
Evaluation of OpenMP for the cyclops multithreaded architecture
WOMPAT'03 Proceedings of the OpenMP applications and tools 2003 international conference on OpenMP shared memory parallel programming
Progress in scaling biomolecular simulations to petaflop scale platforms
Euro-Par'06 Proceedings of the CoreGRID 2006, UNICORE Summit 2006, Petascale Computational Biology and Bioinformatics conference on Parallel processing
Fast PGAS connected components algorithms
Proceedings of the Third Conference on Partitioned Global Address Space Programing Models
Adaptive parallel computing for large-scale distributed and parallel applications
Proceedings of the First International Workshop on Data Dissemination for Large Scale Complex Critical Infrastructures
Exploiting 162-Nanosecond End-to-End Communication Latency on Anton
Proceedings of the 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis
The potential of on-chip multiprocessing for QCD machines
HiPC'05 Proceedings of the 12th international conference on High Performance Computing
Upper bounds on the connection probability for 2-D meshes and tori
Journal of Parallel and Distributed Computing
Performance measurements of the 3D FFT on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Performance effects of node mappings on the IBM bluegene/l machine
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Efficient computation of fitness function by pruning in hydrophobic-hydrophilic model
ISBMDA'05 Proceedings of the 6th International conference on Biological and Medical Data Analysis
Fault tolerance analysis of mesh networks with uniform versus nonuniform node failure probability
Information Processing Letters
Blue matter: strong scaling of molecular dynamics on blue gene/l
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
AI'06 Proceedings of the 19th Australian joint conference on Artificial Intelligence: advances in Artificial Intelligence
IBM Blue Gene/Q system software stack
IBM Journal of Research and Development
TM: a new and simple topology for interconnection networks
The Journal of Supercomputing
| Hi-index | 0.01 |
In December 1999, IBM announced the start of a five-year effort to build a massively parallel computer, to be applied to the study of biomolecular phenomena such as protein folding. The project has two main goals: to advance our understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively parallel machine architecture and software. This project should enable biomolecular simulations that are orders of magnitude larger than current technology permits. Major areas of investigation include: how to most effectively utilize this novel platform to meet our scientific goals, how to make such massively parallel machines more usable, and how to achieve performance targets, with reasonable cost, through novel machine architectures. This paper provides an overview of the Blue Gene project at IBM Research. It includes some of the plans that have been made, the intended goals, and the anticipated challenges regarding the scientific work, the software application, and the hardware design.