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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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KLU solver #29

Closed jonrkarr closed 3 years ago

jonrkarr commented 7 years ago

As of version 2.6 the CVODES solver by SUNDIALS supports the sparse linear solver KLU from SuiteSparse (http://faculty.cse.tamu.edu/davis/suitesparse.html). Especially for large scale systems with sparse interactions it is important to specify this as linear solver as it will typically yield a substantial computational speedup.

I am not sure whether "algorithm characteristic" is correct. It should be treated the same as other linear solvers such as GMRES.

name: KLU ("Clark Kent" LU factorization algorithm) type: algorithm characteristic short description: sparse left-looking LU factorization, using a block triangular form reference: Davis, Timothy A., and Ekanathan Palamadai Natarajan. "Algorithm 907: KLU, a direct sparse solver for circuit simulation problems." ACM Transactions on Mathematical Software (TOMS) 37.3 (2010): 36.

Reported by: *anonymous

jonrkarr commented 7 years ago

Thank you for the term suggestion! I have added KLU as an algorithm (KISAO_0000497). It is available since version 2.3.12.

Original comment by: annazhukova

jonrkarr commented 7 years ago

Original comment by: annazhukova