May 17, 2021. SuiteSparse VERSION 5.10.1
Now includes GraphBLAS, SLIP_LU, 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, Jinhao Chen. Yanqing Chen, Iain Duff, Les Foster, William Hager, Scott Kolodziej, Chris Lourenco, Stefan Larimore, Erick Moreno-Centeno, 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.
About the BLAS and LAPACK libraries
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 Ignore the comments about OpenBLAS in the various user guides; those are out of date.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 SLIP_LU solves sparse linear systems in exact arithmetic. Requires the GNU GMP and MPRF libraries. 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 make compiles SuiteSparse libraries and runs demos make install compiles SuiteSparse and installs in the current directory (./lib, ./include). Use "sudo make INSTALL=/usr/local" to install in /usr/local/lib and /usr/local/include. 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.
QUICK START FOR MATLAB USERS (Linux, Mac, or Windows):
Uncompress the SuiteSparse.zip or SuiteSparse.tar.gz archive file (they contain the same thing). Next, compile the GraphBLAS library (see instructions in GraphBLAS/Doc). 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.
QUICK START FOR THE C/C++ LIBRARIES:
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.
Be sure to first install all required libraries: BLAS and LAPACK for UMFPACK, CHOLMOD, and SPQR, and GMP and MPFR for SLIP_LU. Be sure to use the latest libraries; SLIP_LU requires MPFR 4.0 for example.
When compiling the libraries, do NOT use the INSTALL=... options for installing. Just do:
or to compile just the libraries without running the demos, do:
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$(S)/include -lumfpack -lamd -lcholmod -lsuitesparseconfig -lm
To change the C and C++ compilers, and to compile in parallel use:
AUTOCC=no CC=gcc CX=g++ JOBS=32 make
for example, which changes the compiler to gcc and g++, and runs make with 'make -j32', in parallel with 32 jobs.
Now you can install the libraries, if you wish, in a location other than SuiteSparse/lib, SuiteSparse/include, and SuiteSparse/share/doc, using 'make install INSTALL=...'
Do 'make install' if you want to install the libraries and include files in SuiteSparse/lib and SuiteSparse/include, and the documentation in SuiteSparse/doc/suitesparse-VERSION. This will work on Linux/Unix and the Mac. It should automatically detect if you have the Intel compilers or not, and whether or not you have CUDA. If this fails, see the SuiteSparse_config/SuiteSparse_config.mk file. There are many options that you can either list on the 'make' command line, or you can just edit that file. For example, to compile with your own BLAS:
NOTE: Use of the Intel MKL BLAS is strongly recommended. The OpenBLAS can result in severe performance degradation, in CHOLMOD in particular.
To list all configuration options (but not compile anything), do:
Any parameter you see in the output of 'make config' with an equal sign can be modified at the 'make' command line.
If you do "make install" by itself, then the packages are all installed in SuiteSparse/lib (libraries), SuiteSparse/include (include .h files), and SuiteSparse/doc/suitesparse-VERSION (documentation). To install in /usr/local, the default location for Linux, do:
make library sudo make install INSTALL=/usr/local
If you want to install elsewhere, say in /my/path, first ensure that /my/path is in your LD_LIBRARY_PATH. How to do that depends on your system, but in the bash shell, add this to your ~/.bashrc file:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/my/path export LD_LIBRARY_PATH
You may also need to add SuiteSparse/lib to your path. If your copy of SuiteSparse is in /home/me/SuiteSparse, for example, then add this to your ~/.bashrc file:
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/me/SuiteSparse/lib:/my/path export LD_LIBRARY_PATH
Then do the following (use "sudo make ..." if needed):
make library 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 lib.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'.