Proposals:Sparse Linear Solvers

The Problem

ITK requires functionalities for solving large sparse linear systems.

The current solution obtained though VXL must be replaced because it relies internally on code whose Copyright is held by ACM, and is subject to a license that precludes commercial use.

Some interesting threads from the mailing lists about this issue:

• Replacing Sparse Matrix Linear Solver : due to Licensing issues
• Scope of VTK and it's potential as a common research language
• Scope of VTK and it's potential as a common research language (continued)

Previous Review

Tom Vercauteren previously gathered the following list of options.

ITK_Release_4.0#3rd_Party_Libraries

Options

Comparative Table

Name	License	Size	Support Sparse	Support Dense	Language	Coverage	Valgrind	CMakeified	Dashboard
SuiteSparse	LGPL / GPL		Yes		C/C++ (with Fortran and Matlab interfaces)	Unknown	Unknown
TAUCS google code page	MIT		Yes		C	Unknown	Unknown
SuperLU	BSD		Yes		C	Unknown	Unknown
Eigen	LGPL v3 (headers only)	3.8 Mb	Yes	Yes	C++	Unknown	Unknown	Yes	Yes
Boost uBLAS + Numeric Bindings or user contributions	Boost License but need to check binded libs		Yes	Yes	C++	Unknown	Unknown	Under development	Yes for uBLAS
ARPACK++	BSD	Templates	Yes		C++	Unknown	No
ARPACK	New BSD	1.5 Mb	Yes		FORTRAN	Unknown	No
MUMPS	Public Domain	11 Mb	Yes		FORTRAN 90	Unknown	Unknown
lapack	BSD	86 Mb	No	Yes	Fortran	??	Unknown	Yes	??
clapack	BSD	22 Mb	No	Yes	C	80%	Unknown	Yes	Yes
PLASMA	BSD	13 Mb	No	Yes	C + FORTRAN			Yes
OpenNL	?, BSD	2.8 Mb	Yes		C, C++, CUDA	Unknown	Unknown	Yes
LSQR	CPL (& BSD?)		Yes	No	C, Fortran			Yes (already in ITK)	Part of ITK dashboard
OpenNL	BSD	5.0Mb	Yes	??	C	0% (no tests)	Unknown (no tests)	Yes

SuiteSparse

• License: LGPL / GPL (depending on the submodules, e.g. CSparse and SuiteSparseQR)
• Home: http://www.cise.ufl.edu/research/sparse/SuiteSparse

TAUCS

• License: MIT
• Home: http://code.google.com/p/taucs/

SuperLU

• License: BSD
• Home: http://crd.lbl.gov/~xiaoye/SuperLU/

Eigen

• License: LGPL v3 headers only (The authors claim it is compatible with BSD software)
• Home: http://eigen.tuxfamily.org/index.php?title=Main_Page
• Cdash dashboard here
• Support for both sparse and dense matrices and algorithms
• Python bindings are available with BSD licence

MUMPS

• License:
• http://graal.ens-lyon.fr/MUMPS/
• Requires
  • BLAS

Boost uBLAS + Numeric Bindings

• uBLAS hompage
  • Boost Software License
• Numeric bindings
  • License: seems to be BSD (but links to MUMPS, UMFPack, so better check with them directly)
  • Packaged version of the old hand-written version of boost bindings
  • Trunk version of the automatically generated boost bindings
    • Things might be moving towards a real release
• Alternatives to the numeric bindings for uBLAS could be to rely on:
  • Some user contributions. This contains code for Cholesky decomposition, GMRES method, etc.
  • ublasJama a public domain port of JAMA (Java Matrix Package) for uBLAS

ARPACK++

• C++ Template API for sparse matrix containers and API to ARPACK FORTRAN library solvers
• License: BSD
• http://www.ime.unicamp.br/~chico/arpack++/

ARPACK

• to solve large scale eigenvalue problems
• License: New BSD
• http://www.caam.rice.edu/software/ARPACK/

lapack

• http://icl.cs.utk.edu/lapack-forum/viewtopic.php?f=2&t=1746
• Source Code
  • svn co http://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk
  • svn co http://icl.cs.utk.edu/svn/scalapack-dev
  • svn co https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk lapack
• Dashboard: http://my.cdash.org/index.php?project=LAPACK
• Main maintainer Site:
  • Innovative Computing Laboratory
  • University of Tennessee from Denver, Colorado

clapack

• Dashboard: http://my.cdash.org/index.php?project=CLAPACK
• License:
• Source code release: http://www.netlib.org/clapack/clapack-3.2.1-CMAKE.tgz
• Home page: https://icl.eecs.utk.edu/
• Repository:
  • https://icl.cs.utk.edu/svn/lapack-dev/lapack/trunk/
  • The code is generated from the FORTRAN version of lapack. The generation process is not under source control.
• Main maintainer Site:
  • Innovative Computing Laboratory
  • University of Tennessee from Denver, Colorado

PLASMA

• Home Page: http://icl.cs.utk.edu/plasma/index.html
• License: BSD

OpenNL

• Home Page: http://alice.loria.fr/index.php/software/4-library/23-opennl.html
• License: BSD
  • (as specified in the header of source files)
• Size: 5.0 Mb

LSQR

• Home Page: http://www.stanford.edu/group/SOL/software/lsqr.html
• Already in ITK through the VXL-VNL-netlib chain
• License: CPL but looks to be also licensable under BSD