|
|
|
|
|
|
New approaches to applications, tools for parallelization, and architectures exemplified by the Blue Gene/L system have allowed massively parallel systems to address an increasingly broad range of applications. Topics for this diverse issue include molecular dynamics, geophysical imaging, drug discovery, quantum chromodynamics, nuclear fusion, neuron modeling, climate simulation, turbulence, and an introduction to the new Blue Gene/P architecture.
|
|
|
|
|
|
|
|
Applications of Massively Parallel Systems
|
|
|
|
|
|
|
|
Message from the Vice President, Systems, IBM Research Division
|
|
Tilak Agerwala
|
|
|
|
|
|
|
|
|
Preface
|
|
F. Mintzer, Guest Editor
|
p. 3
|
|
|
|
|
|
|
|
Advances in Rosetta protein structure prediction on massively parallel systems
|
|
S. Raman, B. Qian, D. Baker, and R. C. Walker
|
p. 7
|
|
|
|
|
|
|
|
Massively parallel molecular dynamics simulations of lysozyme unfolding
|
|
R. Zhou, M. Eleftheriou, C.-C. Hon, R. S. Germain, A. K. Royyuru, and B. J. Berne
|
p. 19
|
|
|
|
|
|
|
|
Brain-scale simulation of the neocortex on the IBM Blue Gene/L supercomputer
|
|
M. Djurfeldt, M. Lundqvist, C. Johansson, M. Rehn, Ö. Ekeberg, and A. Lansner
|
p. 31
|
|
|
|
|
|
|
|
Identifying, tabulating, and analyzing contacts between branched neuron morphologies
|
|
J. Kozloski, K. Sfyrakis, S. Hill, F. Schürmann, C. Peck, and H. Markram
|
p. 43
|
|
|
|
|
|
|
|
Ligand discovery on massively parallel systems
|
|
S. R. Shave, P. Taylor, M. Walkinshaw, L. Smith, J. Hardy, and A. Trew
|
p. 57
|
|
|
|
|
|
|
|
EUDOC on the IBM Blue Gene/L system: Accelerating the transfer of drug discoveries from laboratory to patient
|
|
Y.-P. Pang, T. J. Mullins, B. A. Swartz, J. S. McAllister, B. E. Smith, C. J. Archer, R. G. Musselman, A. E. Peters, B. P. Wallenfelt, and K. W. Pinnow
|
p. 69
|
|
|
|
|
|
|
|
A massively parallel implementation of the common azimuth pre-stack depth migration
|
|
H. Calandra, F. Bothorel, and P. Vezolle
|
p. 83
|
|
|
|
|
|
|
|
Massively parallel electrical-conductivity imaging of hydrocarbons using the IBM Blue Gene/L supercomputer
|
|
M. Commer, G. A. Newman, J. J. Carazzone, T. A. Dickens, K. E. Green, L. A. Wahrmund, D. E. Willen, and J. Shiu
|
p. 93
|
|
|
|
|
|
|
|
Large-scale gyrokinetic particle simulation of microturbulence in magnetically confined fusion plasmas
|
|
S. Ethier, W. M. Tang, R. Walkup, and L. Oliker
|
p. 105
|
|
|
|
|
|
|
|
Scaling climate simulation applications on the IBM Blue Gene/L system
|
|
J. M. Dennis and H. M. Tufo
|
p. 117
|
|
|
|
|
|
|
|
Terascale turbulence computation using the FLASH3 application framework on the IBM Blue Gene/L system
|
|
R. T. Fisher, L. P. Kadanoff, D. Q. Lamb, A. Dubey, T. Plewa, A. Calder, F. Cattaneo, P. Constantin, I. Foster, M. E. Papka, S. I. Abarzhi, S. M. Asida, P. M. Rich, C. C. Glendenin, K. Antypas, D. J. Sheeler, L. B. Reid, B. Gallagher, and S. G. Needham
|
p. 127
|
|
|
|
|
|
|
|
Architecture of Qbox: A scalable first-principles molecular dynamics code
|
|
F. Gygi
|
p. 137
|
|
|
|
|
|
|
|
Blue Matter: Scaling of N-body simulations to one atom per node
|
|
B. G. Fitch, A. Rayshubskiy, M. Eleftheriou, T. J. C. Ward, M. E. Giampapa, M. C. Pitman, J. W. Pitera, W. C. Swope, and R. S. Germain
|
p. 145
|
|
|
|
|
|
|
|
Fine-grained parallelization of the Car–Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer
|
|
E. Bohm, A. Bhatele, L. V. Kalé, M. E. Tuckerman, S. Kumar, J. A. Gunnels, and G. J. Martyna
|
p. 159
|
|
|
|
|
|
|
|
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
|
|
S. Kumar, C. Huang, G. Zheng, E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, and L. V. Kalé
|
p. 177
|
|
|
|
|
|
|
|
Massively parallel quantum chromodynamics
|
|
P. Vranas, M. A. Blumrich, D. Chen, A. Gara, M. E. Giampapa, P. Heidelberger, V. Salapura, J. C. Sexton, R. Soltz, and G. Bhanot
|
p. 189
|
|
|
|
|
|
|
|
Overview of the IBM Blue Gene/P project
|
|
IBM Blue Gene team
|
p. 199
|
|
