Out-of-Core Solution of Eigenproblems for Macromolecular Simulations

被引：1

作者：

Aliaga, Jose I. ^{[1
]}

Davidovic, Davor ^{[2
]}

Quintana-Orti, Enrique S. ^{[1
]}

机构：

[1] Univ Jaume 1, Dept Ingn & Ciencia Comp, Castellon de La Plana 12071, Spain

[2] Rudjer Boskovic Inst, CIR, Zagreb 10000, Croatia

来源：

PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2013), PT I | 2014年 / 8384卷

关键词：

Macromolecular motion simulation; Eigenvalue problems; Out-of-core computing; Multicore processors; GPUs; NORMAL-MODE ANALYSIS;

D O I：

10.1007/978-3-642-55224-3_46

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

We consider the solution of large-scale eigenvalue problems that appear in the motion simulation of complex macromolecules on desktop platforms. To tackle the dimension of the matrices that are involved in these problems, we formulate out-of-core (OOC) variants of the two selected eigensolvers, that basically decouple the performance of the solver from the storage capacity. Furthermore, we contend with the high computational complexity of the solvers by off-loading the arithmeticallyintensive parts of the algorithms to a hardware graphics accelerator.

引用

页码：490 / 499

页数：10

共 50 条

[31] Out-of-core Algorithms for Binary Partition Hierarchies
Josselin Lefèvre
Jean Cousty
Benjamin Perret
Harold Phelippeau
Journal of Mathematical Imaging and Vision, 2025, 67 (2)
[32] The design of a new out-of-core multifrontal solver
Reid, John K.
Scott, Jennifer A.
APPLIED PARALLEL COMPUTING: STATE OF THE ART IN SCIENTIFIC COMPUTING, 2007, 4699 : 598 - +
[33] Towards Out-of-core Neural Networks on Microcontrollers
Miao, Hongyu
Lin, Felix Xiaozhu
2022 IEEE/ACM 7TH SYMPOSIUM ON EDGE COMPUTING (SEC 2022), 2022, : 1 - 13
[34] Out-of-core scheduling methods in cluster computing
Zhou, Z. (zzhou0328@whu.edu.cn), 1600, Huazhong University of Science and Technology (41):
[35] An efficient algorithm for out-of-core matrix transposition
Suh, J
Prasanna, VK
IEEE TRANSACTIONS ON COMPUTERS, 2002, 51 (04) : 420 - 438
[36] Getting more from out-of-core columnsort
Chaudhry, G
Cormen, TH
ALGORITHM ENGINEERING AND EXPERIMENTS, 2002, 2409 : 143 - 154
[37] Out-of-core simplification with guaranteed error tolerance
Borodin, P
Guthe, M
Klein, R
VISION, MODELING, AND VISUALIZATION 2003, 2003, : 309 - 316
[38] Out-of-core simplification of large polygonal models
Lindstrom, P
SIGGRAPH 2000 CONFERENCE PROCEEDINGS, 2000, : 259 - 262
[39] Out-of-core and compressed level set methods
Nielsen, Michael B.
Nilsson, Ola
Soderstrom, Andreas
Museth, Ken
ACM TRANSACTIONS ON GRAPHICS, 2007, 26 (04):
[40] Out-of-Core Multigrid Solver for Streaming Meshes
Shi, Xiaohan
Bao, Hujun
Zhou, Kun
ACM TRANSACTIONS ON GRAPHICS, 2009, 28 (05): : 1 - 7

← 1 2 3 4 5 →