SuiteSparse: A Suite of Sparse matrix packages at http://www.suitesparse.com
Oct 20, 2019. SuiteSparse VERSION 5.6.0
Now includes GraphBLAS and a new interface to the SuiteSparse Matrix Collection (ssget), via MATLAB and a Java GUI, to http://sparse.tamu.edu.
Primary author of SuiteSparse (codes and algorithms, excl. METIS): Tim Davis
Code co-authors, in alphabetical order (not including METIS):
Patrick Amestoy, David Bateman, Yanqing Chen, Iain Duff, Les Foster,
William Hager, Scott Kolodziej, Stefan Larimore, Ekanathan Palamadai,
Sivasankaran Rajamanickam, Sanjay Ranka, Wissam Sid-Lakhdar, Nuri Yeralan.
Additional algorithm designers: Esmond Ng and John Gilbert.
Refer to each package for license, copyright, and author information. All codes are authored or co-authored by Timothy A. Davis.
NOTE: Use of the Intel MKL BLAS is strongly recommended. A recent OpenBLAS can result in severe performance degradation. The reason for this is being investigated, and this may be resolved in the near future. Ignore the comments about OpenBLAS in the various user guides; those are out of date.
Packages in SuiteSparse, and files in this directory:
GraphBLAS graph algorithms in the language of linear algebra.
https://graphblas.org
A stand-alone package that uses cmake to compile; see
GraphBLAS/README.txt. The rest of SuiteSparse still uses
'make'. A cmake setup for all of SuiteSparse is in progress.
author: Tim Davis
AMD approximate minimum degree ordering. This is the built-in AMD
function in MATLAB.
authors: Tim Davis, Patrick Amestoy, Iain Duff
bin where the metis-5.1.0 programs are placed when METIS is compiled
BTF permutation to block triangular form
authors: Tim Davis, Ekanathan Palamadai
CAMD constrained approximate minimum degree ordering
authors: Tim Davis, Patrick Amestoy, Iain Duff, Yanqing Chen
CCOLAMD constrained column approximate minimum degree ordering
authors: Tim Davis, Sivasankaran Rajamanickam, Stefan Larimore.
Algorithm design collaborators: Esmond Ng, John Gilbert
(for COLAMD)
ChangeLog a summary of changes to SuiteSparse. See */Doc/ChangeLog
for details for each package.
CHOLMOD sparse Cholesky factorization. Requires AMD, COLAMD, CCOLAMD,
the BLAS, and LAPACK. Optionally uses METIS. This is chol and
x=A\b in MATLAB.
author for all modules: Tim Davis
CHOLMOD/Modify module authors: Tim Davis and William W. Hager
COLAMD column approximate minimum degree ordering. This is the
built-in COLAMD function in MATLAB.
authors (of the code): Tim Davis and Stefan Larimore
Algorithm design collaborators: Esmond Ng, John Gilbert
Contents.m a list of contents for 'help SuiteSparse' in MATLAB.
CSparse a concise sparse matrix package, developed for my
book, "Direct Methods for Sparse Linear Systems",
published by SIAM. Intended primarily for teaching.
It does have a 'make install' but I recommend using
CXSparse instead. In particular, both CSparse and CXSparse
have the same include filename: cs.h.
This package is used for the built-in DMPERM in MATLAB.
author: Tim Davis
CSparse_to_CXSparse
a Perl script to create CXSparse from CSparse and
CXSparse_newfiles
author: David Bateman, Motorola
CXSparse CSparse Extended. Includes support for complex matrices
and both int or long integers. Use this instead of CSparse
for production use; it creates a libcsparse.so (or *dylib on
the Mac) with the same name as CSparse. It is a superset
of CSparse. Any code that links against CSparse should
also be able to link against CXSparse instead.
author: Tim Davis, David Bateman
CXSparse_newfiles
Files unique to CXSparse
author: Tim Davis, David Bateman
share 'make' places documentation for each package here
include 'make' places user-visible include fomes for each package here
KLU sparse LU factorization, primarily for circuit simulation.
Requires AMD, COLAMD, and BTF. Optionally uses CHOLMOD,
CAMD, CCOLAMD, and METIS.
authors: Tim Davis, Ekanathan Palamadai
LDL a very concise LDL' factorization package
author: Tim Davis
lib 'make' places shared libraries for each package here
Makefile to compile all of SuiteSparse (except GraphBLAS)
make compiles SuiteSparse libraries and runs demos
make install compiles SuiteSparse and installs in /usr/local
make uninstall undoes 'make install'
make library compiles SuiteSparse libraries (not demos)
make distclean removes all files not in distribution, including
./bin, ./share, ./lib, and ./include.
make purge same as 'make distclean'
make clean removes all files not in distribution, but
keeps compiled libraries and demoes, ./lib,
./share, and ./include.
make config displays parameter settings; does not compile
Each individual package also has each of the above 'make'
targets. Doing 'make config' in each package */Lib directory
displays the exact shared and static library names.
Things you don't need to do:
make cx creates CXSparse from CSparse
make docs creates user guides from LaTeX files
make cov runs statement coverage tests (Linux only)
make metis compiles METIS (also done by 'make')
MATLAB_Tools various m-files for use in MATLAB
author: Tim Davis (all parts)
for spqr_rank: author Les Foster and Tim Davis
Contents.m list of contents
dimacs10 loads matrices for DIMACS10 collection
Factorize object-oriented x=A\b for MATLAB
find_components finds connected components in an image
GEE simple Gaussian elimination
getversion.m determine MATLAB version
gipper.m create MATLAB archive
hprintf.m print hyperlinks in command window
LINFACTOR predecessor to Factorize package
MESHND nested dissection ordering of regular meshes
pagerankdemo.m illustrates how PageRank works
SFMULT C=S*F where S is sparse and F is full
shellgui display a seashell
sparseinv sparse inverse subset
spok check if a sparse matrix is valid
spqr_rank SPQR_RANK package. MATLAB toolbox for rank
deficient sparse matrices: null spaces,
reliable factorizations, etc. With Leslie
Foster, San Jose State Univ.
SSMULT C=A*B where A and B are both sparse
SuiteSparseCollection for the SuiteSparse Matrix Collection
waitmex waitbar for use inside a mexFunction
The SSMULT and SFMULT functions are the basis for the
built-in C=A*B functions in MATLAB.
Mongoose graph partitioning.
authors: Nuri Yeralan, Scott Kolodziej, William Hager, Tim Davis
metis-5.1.0 a modified version of METIS. See the README.txt files for
details.
author: George Karypis; not an integral component of
SuiteSparse, however. This is just a copy included with
SuiteSparse via the open-source license provided by
George Karypis
RBio read/write sparse matrices in Rutherford/Boeing format
author: Tim Davis
README.txt this file
SPQR sparse QR factorization. This the built-in qr and x=A\b in
MATLAB.
author of the CPU code: Tim Davis
author of GPU modules: Tim Davis, Nuri Yeralan,
Wissam Sid-Lakhdar, Sanjay Ranka
SPQR/GPUQREngine: GPU support package for SPQR
(not built into MATLAB, however)
authors: Tim Davis, Nuri Yeralan, Sanjay Ranka,
Wissam Sid-Lakhdar
SuiteSparse_config configuration file for all the above packages. The
SuiteSparse_config/SuiteSparse_config.mk is included in the
Makefile's of all packages. CSparse and MATLAB_Tools do not
use SuiteSparse_config.
author: Tim Davis
SuiteSparse_GPURuntime GPU support package for SPQR and CHOLMOD
(not builtin to MATLAB, however).
SuiteSparse_install.m install SuiteSparse for MATLAB
SuiteSparse_test.m exhaustive test for SuiteSparse in MATLAB
ssget MATLAB interface to the SuiteSparse Matrix Collection
(formerly called the UF Sparse Matrix Collection).
Includes a UFget function for backward compatibility.
author: Tim Davis
UMFPACK sparse LU factorization. Requires AMD and the BLAS.
This is the built-in lu and x=A\b in MATLAB.
author: Tim Davis
algorithm design collaboration: Iain Duff
Some codes optionally use METIS 5.1.0. This package is located in SuiteSparse in the metis-5.1.0 directory. Its use is optional, so you can remove it before compiling SuiteSparse, if you desire. The use of METIS will improve the ordering quality. METIS has been slightly modified for use in SuiteSparse; see the metis-5.1.0/README.txt file for details. SuiteSparse can use the unmodified METIS 5.1.0, however. To use your own copy of METIS, or a pre-installed copy of METIS use 'make MY_METIS_LIB=-lmymetis' or 'make MY_METIS_LIB=/my/stuff/metis-5.1.0/whereeveritis/libmetis.so MY_METIS_INC=/my/stuff/metis-5.1.0/include'. If you want to use METIS in MATLAB, however, you MUST use the version provided here, in SuiteSparse/metis-5.1.0. The MATLAB interface to METIS required some small changes in METIS itself to get it to work. The original METIS 5.1.0 will segfault MATLAB.
Refer to each package for license, copyright, and author information. All codes are authored or co-authored by Timothy A. Davis. email: [email protected]
Licenses for each package are located in the following files, all in PACKAGENAME/Doc/License.txt:
AMD/Doc/License.txt
BTF/Doc/License.txt
CAMD/Doc/License.txt
CCOLAMD/Doc/License.txt
CHOLMOD/Doc/License.txt
COLAMD/Doc/License.txt
CSparse/Doc/License.txt
CXSparse/Doc/License.txt
GPUQREngine/Doc/License.txt
KLU/Doc/License.txt
LDL/Doc/License.txt
MATLAB_Tools/Doc/License.txt
Mongoose/Doc/License.txt
RBio/Doc/License.txt
SPQR/Doc/License.txt
SuiteSparse_GPURuntime/Doc/License.txt
ssget/Doc/License.txt
UMFPACK/Doc/License.txt
GraphBLAS/Doc/License.txt
These files are also present, but they are simply copies of the above license files for CXSparse and ssget:
CXSparse_newfiles/Doc/License.txt
CSparse/MATLAB/ssget/Doc/License.txt
CXSparse/MATLAB/ssget/Doc/License.txt
METIS 5.0.1 is distributed with SuiteSparse, and is Copyright (c) by George Karypis. Please refer to that package for its License.
Uncompress the SuiteSparse.zip or SuiteSparse.tar.gz archive file (they contain the same thing), then in the MATLAB Command Window, cd to the SuiteSparse directory and type SuiteSparse_install. All packages will be compiled, and several demos will be run. To run a (long!) exhaustive test, do SuiteSparse_test.
For just GraphBLAS, do this:
cd GraphBLAS/build ; cmake .. ; make ; cd ../Demo ; ./demo
cd ../build ; sudo make install
For all other packages, type 'make' in this directory. All libraries will be created and copied into SuiteSparse/lib. All include files need by the applications that use SuiteSparse are copied into SuiteSparse/include. All user documenation is copied into SuiteSparse/share/doc.
When compiling the libraries, do NOT use the INSTALL=... options for installing. Just do:
make
or to compile just the libraries without running the demos, do:
make library
Any program that uses SuiteSparse can thus use a simpler rule as compared to earlier versions of SuiteSparse. If you add /home/myself/SuiteSparse/lib to your library search patch, you can do the following (for example):
S = /home/myself/SuiteSparse
cc myprogram.c -I$(S)/include -lumfpack -lamd -lcholmod -lsuitesparseconfig -lm
To change the C and C++ compilers, and to compile in parallel use:
AUTOCC=no CC=gcc CX=g++ JOBS=32 make
for example, which changes the compiler to gcc and g++, and runs make with 'make -j32', in parallel with 32 jobs.
Now you can install the libraries, if you wish, in a location other than SuiteSparse/lib, SuiteSparse/include, and SuiteSparse/share/doc, using 'make install INSTALL=...'
Do 'make install' if you want to install the libraries and include files in SuiteSparse/lib and SuiteSparse/include, and the documentation in SuiteSparse/doc/suitesparse-VERSION. This will work on Linux/Unix and the Mac. It should automatically detect if you have the Intel compilers or not, and whether or not you have CUDA. If this fails, see the SuiteSparse_config/SuiteSparse_config.mk file. There are many options that you can either list on the 'make' command line, or you can just edit that file. For example, to compile with your own BLAS:
make BLAS=-lmyblaslibraryhere
NOTE: Use of the Intel MKL BLAS is strongly recommended. The OpenBLAS can result in severe performance degradation, in CHOLMOD in particular.
To list all configuration options (but not compile anything), do:
make config
Any parameter you see in the output of 'make config' with an equal sign can be modified at the 'make' command line.
If you do "make install" by itself, then the packages are all installed in SuiteSparse/lib (libraries), SuiteSparse/include (include *.h files), and SuiteSparse/doc/suitesparse-VERSION (documentation). If you want to install elsewhere, do:
make install INSTALL=/my/path
which puts the files in /my/path/lib, /my/path/include, and /my/path/doc. If you want to selectively put the libraries, include files, and doc files in different locations, do:
make install INSTALL_LIB=/my/libs INSTALL_INCLUDE=/myotherstuff/include INSTALL_DOC=/mydocs
for example. Any term not defined will be set to its default, so if you don't want to install the documentation, but wish to install the libraries and includes in /usr/local/lib and /usr/local/include, do:
make install INSTALL_DOC=/tmp/doc
which copies the documentation to /tmp/doc where you can then remove it later.
Both the static (.a) and shared (.so) libraries are compiled. The *.a libraries are left in the package Lib folder (AMD/Lib/libamd.a for example). The main exception to this rule is the SuiteSparse_config library, which is in SuiteSparse/libsuiteSparseconfig.a. SuiteSparse_config is required by all packages. The (extremely) optional xerbla library is also an exception, but it is highly unlikely that you need that library.
The 'make uninstall' takes the same command-line arguments.
(1) Use the right BLAS and LAPACK libraries. Determine where your BLAS and LAPACK libraries are. If the default 'make' does not find them, use 'make BLAS=-lmyblaslibraryhere LAPACK=-lmylapackgoeshere'
(2) Install Intel's Threading Building Blocks (TBB). This is optionally used by SuiteSparseQR. Refer to the User Guide in SuiteSparse/SPQR/Doc/spqr_user_guide.pdf for details.
(3) Determine what other command line options you need for 'make'. All options can be set at the 'make' command line without the need to edit this file. Browse that file to see what options you can control. If you choose different options and wish to recompile, be sure to do 'make distclean' in this directory first, to remove all files not in the original distribution.
(4) Type "make" in this directory. All packages will be be compiled. METIS 5.1.0 will be compiled if you have it (note that METIS require CMake to build it). Several demos will be run. To compile just the libraries, without running any demos, use "make library". The libraries will appear in /Lib/.so.* (*.dylib for the Mac). Include files, as needed by user programs that use CHOLMOD, AMD, CAMD, COLAMD, CCOLAMD, BTF, KLU, UMFPACK, LDL, etc. are in /Include/.h. The include files required by user programs are then copied into SuiteSparse/include, and the compiled libraries are copied into SuiteSparse/lib. Documentation is copied into SuiteSparse/doc. The GraphBLAS libraries are created by cmake and placed in GraphBLAS/build. NOTE: on Linux, you may see some errors when you compile METIS ('make: *** No rule to make target 'w'.). You can safely ignore those errors.
(6) To install, type "make install". This will place copies of all libraries in SuiteSparse/lib, and all include files in SuiteSparse/include, and all documentation in SuiteSparse/doc/suitesparse-VERSION. You can change the install location by "make install INSTALL=/my/path" which puts the libraries in /my/path/lib, the include files in /my/path/include, and documentation in /my/path/doc. These directories are created if they do not already exist.
(7) To uninstall, type "make uninstall", which reverses "make install" by removing the SuiteSparse libraries, include files, and documentation from the place they were installed. If you pass INSTALL_***= options to 'make install', you must pass the same to 'make uninstall'.