Parallel solution of large-scale eigenvalue problem for master equation in protein folding dynamics

DOI10.1016/J.JPDC.2007.09.002MaRDI QIDQ436775zbMATH OpenOpenAlexFDO

Authors Yiming Li, Shao-Ming Yu, Yih-Lang Li

Publication date 26 July 2012

Published in Journal of Parallel and Distributed Computing (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jpdc.2007.09.002

zbMATH Keywords

MPIparallelizationJacobi-Davidson methodimplicitly restarted Arnoldi methodPC-based Linux clusterQR method

Mathematics Subject Classification ID

Parallel numerical computation (65Y05) Biochemistry, molecular biology (92C40) Numerical computation of eigenvalues and eigenvectors of matrices (65F15)

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Cites work

• scientific article; zbMATH DE number 782058 (Why is no real title available?)
• A Block Orthogonalization Procedure with Constant Synchronization Requirements
• A Jacobi--Davidson Iteration Method for Linear Eigenvalue Problems
• Deflation Techniques for an Implicitly Restarted Arnoldi Iteration
• Dynamic Thick Restarting of the Davidson, and the Implicitly Restarted Arnoldi Methods
• Implicit Application of Polynomial Filters in a k-Step Arnoldi Method
• Jacobi--Davidson Style QR and QZ Algorithms for the Reduction of Matrix Pencils
• Reorthogonalization and Stable Algorithms for Updating the Gram-Schmidt QR Factorization
• \(QR\)-like algorithms for eigenvalue problems

Describes a project that uses

Uses Software

• IRAM
• JDQR
• eigs

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