Scalable I/O of large-scale molecular dynamics simulations: A data-compression algorithm

Citation
A. Omeltchenko et al., Scalable I/O of large-scale molecular dynamics simulations: A data-compression algorithm, COMP PHYS C, 131(1-2), 2000, pp. 78-85
Citations number
24
Categorie Soggetti
Physics
Journal title
COMPUTER PHYSICS COMMUNICATIONS
ISSN journal
00104655 → ACNP
Volume
131
Issue
1-2
Year of publication
2000
Pages
78 - 85
Database
ISI
SICI code
0010-4655(20000901)131:1-2<78:SIOLMD>2.0.ZU;2-A
Abstract
Disk space, input/output (I/O) speed, and data-transfer bandwidth present a major bottleneck in large-scale molecular dynamics simulations, which requ ire storing positions and velocities of multimillion atoms. A data compress ion algorithm is designed for scalable I/O of molecular dynamics data. The algorithm uses octree indexing and sorts atoms accordingly on the resulting space-filling curve. By storing differences of successive atomic coordinat es and using an adaptive, variable-length encoding to handle exceptional va lues, the I/O size is reduced by an order-of-magnitude with user-controlled error bound. (C) 2000 Elsevier Science B.V. All rights reserved.