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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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Linear solver type property for algorithms where applicable #3

Closed jonrkarr closed 3 years ago

jonrkarr commented 13 years ago

Some algorithms depend on a linear solver, and some implementations let the users pick this type of linear solver (e.g. IDA, which provides direct solvers along with solvers based on Krylov Subspace methods. I suggest Generalised Minimal Residual (GMRES) be a subset of Krylov Subspace Solvers, and Scaled, Preconditioned GMR (SPGMR) be treated as a specific type of GMRES; under Krylov Subspace Methods, Biconjugate Gradient Stabilized Methods, with the scaled, preconditioned variant, a minimum residual method, and a quasi-minimum residual (QMR), with transpose-free QMR (TFQMR) as a type of QMR, and the scaled, preconditioned variant SPTQMR as a variant of that).

Reported by: a1kmm

jonrkarr commented 13 years ago

Fixed in revision 163. 'Linearity of equation' (KISAO_0000376) characteristic was added and below are the KiSAO identifiers for the suggested Krylov subspace solvers: Krylov Subspace method KISAO_0000354 Generalised Minimal Residual (GMRES) KISAO_0000353 Scaled, Preconditioned GMR (SPGMR) KISAO_0000386 Biconjugate Gradient Stabilized Methods KISAO_0000392 scaled, preconditioned variant of Biconjugate Gradient Stabilized Method KISAO_0000392 and uses some 'preconditioning technique' minimum residual method KISAO_0000388 quasi-minimum residual (QMR) KISAO_0000389 transpose-free QMR (TFQMR) KISAO_0000396 scaled, preconditioned variant SPTQMR KISAO_0000396 and uses some 'preconditioning technique'

Original comment by: annazhukova

jonrkarr commented 13 years ago

Original comment by: annazhukova