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Out-of-core solution of eigenproblems for macromolecular simulations

Aliaga, José Ignacio; Davidović, Davor; Quintana-Ortí, Enrique S. (2014) Out-of-core solution of eigenproblems for macromolecular simulations. In: Wyrzykowski, Roman; Dongarra, Jack; Karczewski, Konrad; Waśniewski, Jerzy, (eds.) Parallel Processing and Applied Mathematics. pp. 490-499 .

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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 arithmetically-intensive parts of the algorithms to a hardware graphics accelerator.

Item Type: Conference or workshop item published in conference proceedings (UNSPECIFIED)
Uncontrolled Keywords: Macromolecular motion simulation; eigenvalue problems; out-of-core computing; multicore processors; GPUs
Subjects: NATURAL SCIENCES > Mathematics > Algebra
NATURAL SCIENCES > Mathematics > Numerical Mathematics
TECHNICAL SCIENCES > Computing > Program Engineering
Divisions: Center for Informatics and Computing
Project titleProject leaderProject codeProject type
Depositing User: Davor Davidović
Date Deposited: 12 Jun 2014 11:43
DOI: 10.1007/978-3-642-55224-3

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