View source for Lis (linear algebra library)

{{Short description|Parallel software library for linear algebra}}
{{Infobox software
| name                   = Lis
| title                  = 
| logo                   = Irises screen 1.jpg
| logo size              = 160px
| logo caption           = 
| screenshot             = <!-- [[File: ]] -->
| caption                = 
| collapsible            = 
| author                 = 
| developer              = 
| released               = 
| discontinued           = 
| latest release version = 2.1.7
| latest release date    = {{Start date|2024|12|17}}
| latest preview version = 
| latest preview date    = <!-- {{Start date and age|YYYY|MM|DD|df=yes/no}} -->
| language               = [[C (programming language)|C]], [[Fortran]]
| operating system       = [[Cross-platform]]
| platform               = 
| size                   = 
| genre                  = [[Software library]]
| license                = [[New BSD License]]
| website                = [https://www.ssisc.org/lis/index.en.html www.ssisc.org/lis/]
}}
'''Lis''' ('''Library of Iterative Solvers''' for linear systems; pronounced ''lis'']) is a [[scalability|scalable]] [[parallel computing|parallel]] software library to solve [[discretization|discretized]] [[system of linear equations|linear equation]]s and [[Eigenvalue, eigenvector and eigenspace|eigenvalue problems]] that mainly arise from the [[numerical analysis|numerical solution]] of [[partial differential equation]]s using [[iterative method]]s.<ref>{{Cite book
|author=Akira Nishida 
|year=2010
|chapter=Experience in Developing an Open Source Scalable Software Infrastructure in Japan
|title=Computational Science and Its Applications – ICCSA 2010 
|volume=6017
|series=Lecture Notes in Computer Science 6017
|pages=87–98
|publisher=Springer
|doi=10.1007/978-3-642-12165-4_36
|isbn=978-3-642-12164-7 
}}</ref><ref>{{Cite book
|author1=Hisashi Kotakemori |author2=Hidehiko Hasegawa |author3=Tamito Kajiyama |author4=Akira Nukada |author5=Reiji Suda |author6=Akira Nishida  |name-list-style=amp |year=2008
|chapter=Performance Evaluation of Parallel Sparse Matrix-Vector Products on SGI Altix 3700
|title=OpenMP Shared Memory Parallel Programming 
|series=Lecture Notes in Computer Science 4315
|pages=153–163
|publisher=Springer
|doi=10.1007/978-3-540-68555-5_13 
|isbn=978-3-540-68554-8 
}}</ref><ref>{{Cite book
|author1=Hisashi Kotakemori |author2=Hidehiko Hasegawa |author3=Akira Nishida  |name-list-style=amp |year=2005
|chapter=Performance Evaluation of a Parallel Iterative Method Library using OpenMP
|title=Proceedings of the 8th International Conference on High Performance Computing in Asia Pacific Region (HPC Asia 2005)
|pages=432–436
|publisher=IEEE
|doi=10.1109/HPCASIA.2005.74
|isbn=0-7695-2486-9
|s2cid=6402585 }}</ref> Although it is designed for parallel computers, the library can be used without being conscious of [[parallel computing|parallel processing]].

== Features ==
'''Lis''' provides facilities for:
* [[Configure script|Automatic program configuration]]
* [[Non-Uniform Memory Access|NUMA]] aware hybrid implementation with [[Message Passing Interface|MPI]] and [[OpenMP]]
* Exchangeable dense and [[sparse matrix]] [[data structure|storage format]]s
* Basic [[linear algebra]] operations for dense and sparse matrices
* Parallel [[iterative method]]s for [[system of linear equations|linear equation]]s and [[Eigenvalue, eigenvector and eigenspace|eigenvalue problems]]
* Parallel [[preconditioner]]s for iterative methods
* [[Quadruple-precision floating-point format|Quadruple precision]] [[floating point]] operations
* [[profiling (computer programming)|Performance analysis]]
* [[Command-line interface]] to solvers and benchmarks

== Example ==
A [[C (programming language)|C]] program to solve the linear equation <math>Ax=b</math> is written as follows:
<syntaxhighlight lang=c>
#include <stdio.h>
#include "lis_config.h"
#include "lis.h"

LIS_INT main(LIS_INT argc, char* argv[])
{
  LIS_MATRIX  A;
  LIS_VECTOR  b, x;
  LIS_SOLVER  solver;
  LIS_INT     iter;
  double      time;

  lis_initialize(&argc, &argv);

  lis_matrix_create(LIS_COMM_WORLD, &A);
  lis_vector_create(LIS_COMM_WORLD, &b);
  lis_vector_create(LIS_COMM_WORLD, &x);

  lis_input_matrix(A, argv[1]);
  lis_input_vector(b, argv[2]);
  lis_vector_duplicate(A, &x);

  lis_solver_create(&solver);
  lis_solver_set_optionC(solver);
  lis_solve(A, b, x, solver);

  lis_solver_get_iter(solver, &iter);
  lis_solver_get_time(solver, &time);
  printf("number of iterations = %d\n", iter);
  printf("elapsed time = %e\n", time);

  lis_output_vector(x, LIS_FMT_MM, argv[3]);

  lis_solver_destroy(solver);
  lis_matrix_destroy(A);
  lis_vector_destroy(b);
  lis_vector_destroy(x);

  lis_finalize();

  return 0;
}
</syntaxhighlight>

== System requirements ==
Installing '''Lis''' requires a C compiler. If you wish to use the Fortran interface, a Fortran compiler is needed, and the [[Multigrid method|algebraic multigrid]] preconditioner requires a Fortran 90 compiler.<ref>{{Cite book
|author1=Akihiro Fujii |author2=Akira Nishida |author3=Yoshio Oyanagi  |name-list-style=amp |year=2005
|chapter=Evaluation of Parallel Aggregate Creation Orders : Smoothed Aggregation Algebraic Multigrid Method
|title=High Performance Computational Science and Engineering
|pages=99–122
|publisher=Springer
|doi=10.1007/0-387-24049-7_6  
|isbn=1-4419-3684-X 
|s2cid=118053459 }}</ref> 
For parallel computing environments, an OpenMP or MPI library is necessary. Lis supports both the [[Matrix Market exchange formats|Matrix Market]] and [[Harwell-Boeing file format|Harwell-Boeing]] formats for importing and exporting user data.

== Packages that use Lis ==
* [[Gerris (software)|Gerris]]
* [[OpenModelica]]
* [http://www.opengeosys.org/ OpenGeoSys]
* [http://www.sicopolis.net/ SICOPOLIS]
* [http://stomp.pnnl.gov/ STOMP]
* [http://dl.acm.org/citation.cfm?id=2634291 Diablo]
* [https://kiva.readthedocs.io/en/latest/ Kiva]
* [https://notus-cfd.org/ Notus]
* [https://www.hamady.org/solis.html Solis]
* [https://web.tecgraf.puc-rio.br/gema/ GeMA]
* [https://www.opencfs.org/ openCFS]
* [https://www.numgeo.de/ numgeo]
* [https://github.com/nikola-m/freeCappuccino freeCappuccino]
* [https://github.com/WildSmilodon/Andromeda Andromeda]
* [https://palma-ice.github.io/yelmo-docs/ Yelmo]

== See also ==
{{Portal|Free and open-source software}}
* [[List of numerical libraries]]
* [[Conjugate gradient method]]
* [[Biconjugate gradient stabilized method|Biconjugate gradient stabilized method (BiCGSTAB)]]
* [[Generalized minimal residual method|Generalized minimal residual method (GMRES)]]
* [[Eigenvalue algorithm]]
* [[Lanczos algorithm]]
* [[Arnoldi iteration]]
* [[Krylov subspace]]
* [[Multigrid method]]

== References ==
{{reflist}}

== External links ==
* {{Official website|https://www.ssisc.org/lis/index.en.html}}
* [https://github.com/anishida/lis/tree/develop Development repository on GitHub]
* [http://www.netlib.org/utk/people/JackDongarra/la-sw.html Prof. Jack Dongarra's freely available linear algebra software page]
* [http://www.netlib.org/linalg/lis Netlib repository] (Courtesy of [[Netlib|Netlib Project]])
<!-- * [http://apps.fedoraproject.org/packages/lis Fedora packages] (Courtesy of [[Fedora Project]]) (currently seems to be unavailable) -->
* [https://rpms.remirepo.net/rpmphp/zoom.php?rpm=lis Fedora packages] (Courtesy of [[Fedora Project]])
* [http://packages.gentoo.org/package/sci-libs/lis Gentoo packages] (Courtesy of [[Gentoo Linux|Gentoo Linux Project]])
* [https://aur.archlinux.org/packages/lis/ AUR packages] (Courtesy of [[Arch Linux|Arch Linux Community]])
* [https://codeberg.org/FreeBSD/freebsd-ports/src/math/lis FreeBSD packages] (Courtesy of [[FreeBSD|FreeBSD Project]])
* [https://github.com/brewsci/homebrew-science/blob/master/Formula/lis.rb Packages for macOS (Homebrew)] (Courtesy of [[Homebrew (package management software)|Homebrew Project]])
* [https://ports.macports.org/port/lis/summary Packages for macOS (MacPorts)] (Courtesy of [[MacPorts|MacPorts Project]])
* [http://sourceforge.net/projects/whpc/files/ Packages for Windows] (Courtesy of WHPC Project)
* [https://github.com/msys2/MINGW-packages/tree/master/mingw-w64-lis Packages for Mingw-w64] (Courtesy of [[Mingw-w64|Mingw-w64 Project]])
* [https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/lis/package.py Spack packages] (Courtesy of [[Lawrence Livermore National Laboratory]])

{{Numerical linear algebra}}

[[Category:Numerical libraries]]
[[Category:Numerical linear algebra]]
[[Category:Scientific simulation software]]
[[Category:C (programming language) libraries]]
[[Category:Fortran libraries]]
[[Category:Free simulation software]]
[[Category:Free software programmed in C]]
[[Category:Free software programmed in Fortran]]