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

DOI10.1016/j.jpdc.2007.09.002zbMath1243.92022OpenAlexW2022132154MaRDI QIDQ436775

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

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

MPIQR methodparallelizationJacobi-Davidson methodimplicitly restarted Arnoldi methodPC-based Linux cluster

Mathematics Subject Classification ID

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

Uses Software

• eigs
• JDQR
• IRAM

Cites Work

• Unnamed Item
• \(QR\)-like algorithms for eigenvalue problems
• Implicit Application of Polynomial Filters in a k-Step Arnoldi Method
• Reorthogonalization and Stable Algorithms for Updating the Gram-Schmidt QR Factorization
• Jacobi--Davidson Style QR and QZ Algorithms for the Reduction of Matrix Pencils
• Dynamic Thick Restarting of the Davidson, and the Implicitly Restarted Arnoldi Methods
• A Jacobi--Davidson Iteration Method for Linear Eigenvalue Problems
• Deflation Techniques for an Implicitly Restarted Arnoldi Iteration
• A Block Orthogonalization Procedure with Constant Synchronization Requirements

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