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Added stripped version of ccolamd with files from UFconfig

release/4.3a0
Alex Cunningham 2011-06-02 14:35:19 +00:00
parent 3236a83f60
commit 2d0984e9b4
12 changed files with 6448 additions and 0 deletions
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Jan 25, 2011: version 2.7.3
* minor fix to "make install"
* fixed stats [CCOLAMD_EMPTY_ROW] output
Nov 30, 2009: version 2.7.2
* added "make install" and "make uninstall"
Nov 1, 2007: version 2.7.1
* minor changes to MATLAB test code
May 31, 2007: version 2.7.0
* ported to 64-bit MATLAB
* subdirectories added (Source/, Include/, Lib/, Doc/, MATLAB/, Demo/)
Dec 12, 2006, version 2.5.2
* minor MATLAB clean up
Apr 30, 2006: version 2.5
* ccolamd_recommended modified. Now returns size_t; 0 on error, > 0
if successful. Version number updated to synchronize with COLAMD.
* long replaced with UF_long integer, which is long except on WIN64
Nov 15, 2005
* ccolamd_global.c added to ccolamd_make.m (version is still 1.0).
Oct 10, 2005
* changed definition of ccolamd_printf to "extern"
Version 1.0, released (Aug. 30, 2005)
* CCOLAMD version 1.0 is derived from COLAMD version 2.4. Refer to the
COLAMD ChangeLog file for the changes made to COLAMD since
COLAMD Version 1.0.

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#-------------------------------------------------------------------------------
# CCOLAMD Makefile
#-------------------------------------------------------------------------------
default: libccolamd.a
include ../../UFconfig/UFconfig.mk
I = -I../Include -I../../UFconfig
INC = ../Include/ccolamd.h ../../UFconfig/UFconfig.h
SRC = ../Source/ccolamd.c ../Source/ccolamd_global.c
# creates libccolamd.a, a C-callable COLAMD library
libccolamd.a: $(SRC) $(INC)
$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd_global.c
$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd.c
$(CC) $(CFLAGS) $(I) -c ../Source/ccolamd.c -DDLONG -o ccolamd_l.o
$(AR) libccolamd.a ccolamd.o ccolamd_l.o ccolamd_global.o
ccode: libccolamd.a
library: libccolamd.a
clean:
- $(RM) $(CLEAN)
purge: distclean
distclean: clean
- $(RM) libccolamd.a

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CCOLAMD: constrained column approximate minimum degree ordering
Copyright (C) 2005-2011, Univ. of Florida. Authors: Timothy A. Davis,
Sivasankaran Rajamanickam, and Stefan Larimore. Closely based on COLAMD by
Davis, Stefan Larimore, in collaboration with Esmond Ng, and John Gilbert.
http://www.cise.ufl.edu/research/sparse
-------------------------------------------------------------------------------
The CCOLAMD column approximate minimum degree ordering algorithm computes
a permutation vector P such that the LU factorization of A (:,P)
tends to be sparser than that of A. The Cholesky factorization of
(A (:,P))'*(A (:,P)) will also tend to be sparser than that of A'*A.
CSYMAMD is a symmetric minimum degree ordering method based on CCOLAMD, also
available as a MATLAB-callable function. It constructs a matrix M such
that M'*M has the same pattern as A, and then uses CCOLAMD to compute a column
ordering of M.
Requires UFconfig, in the ../UFconfig directory relative to this directory.
To compile and install the ccolamd m-files and mexFunctions, just cd to
CCOLAMD/MATLAB and type ccolamd_install in the MATLAB command window.
A short demo will run. Optionally, type ccolamd_test to run an extensive tests.
Type "make" in Unix in the CCOLAMD directory to compile the C-callable
library and to run a short demo.
If you have MATLAB 7.2 or earlier, you must first edit UFconfig/UFconfig.h to
remove the "-largeArrayDims" option from the MEX command (or just use
ccolamd_install.m inside MATLAB).
Other "make" targets:
make mex compiles MATLAB mexFunctions only
make libccolamd.a compiles a C-callable library containing ccolamd
make clean removes all files not in the distribution, except for
libccolamd.a
make distclean removes all files not in the distribution
To use ccolamd and csymamd within an application written in C, all you need are
ccolamd.c and ccolamd.h, which are the C-callable ccolamd/csymamd codes.
See ccolamd.c for more information on how to call ccolamd from a C program.
It contains a complete description of the C-interface to CCOLAMD and CSYMAMD.
Copyright (c) 1998-2007 by the University of Florida.
All Rights Reserved.
Licensed under the GNU LESSER GENERAL PUBLIC LICENSE.
-------------------------------------------------------------------------------
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-------------------------------------------------------------------------------
Related papers:
T. A. Davis and W. W. Hager, Rajamanickam, Multiple-rank updates
to a supernodal sparse Cholesky factorization, submitted.
T. A. Davis, W. W. Hager, S. Rajamanickam, and Y. Chen, CHOLMOD: a
sparse Cholesky update/downdate package, submitted. CHOLMOD's
nested dissection ordering relies on CCOLAMD and CSYMAMD to order
the matrix after graph partitioning is used to find the ordering
constraints.
T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, An approximate column
minimum degree ordering algorithm, ACM Transactions on Mathematical
Software, vol. 30, no. 3., pp. 353-376, 2004.
T. A. Davis, J. R. Gilbert, S. Larimore, E. Ng, Algorithm 836: COLAMD,
an approximate column minimum degree ordering algorithm, ACM
Transactions on Mathematical Software, vol. 30, no. 3., pp. 377-380,
2004.
"An approximate minimum degree column ordering algorithm",
S. I. Larimore, MS Thesis, Dept. of Computer and Information
Science and Engineering, University of Florida, Gainesville, FL,
1998. CISE Tech Report TR-98-016. Available at
ftp://ftp.cise.ufl.edu/cis/tech-reports/tr98/tr98-016.ps
via anonymous ftp.
Approximate Deficiency for Ordering the Columns of a Matrix,
J. L. Kern, Senior Thesis, Dept. of Computer and Information
Science and Engineering, University of Florida, Gainesville, FL,
1999. Available at http://www.cise.ufl.edu/~davis/Kern/kern.ps
Authors: Timothy A. Davis, Sivasankaran Rajamanickam, and Stefan Larimore.
Closely based on COLAMD by Stefan I. Larimore and Timothy A. Davis,
University of Florida, in collaboration with John Gilbert, Xerox PARC
(now at UC Santa Barbara), and Esmong Ng, Lawrence Berkeley National
Laboratory (much of this work he did while at Oak Ridge National
Laboratory).
CCOLAMD files:
Demo simple demo
Doc additional documentation (see ccolamd.c for more)
Include include file
Lib compiled C-callable library
Makefile primary Unix Makefile
MATLAB MATLAB functions
README.txt this file
Source C source code
./Demo:
ccolamd_example.c simple example
ccolamd_example.out output of colamd_example.c
ccolamd_l_example.c simple example, long integers
ccolamd_l_example.out output of colamd_l_example.c
Makefile Makefile for C demos
./Doc:
ChangeLog change log
lesser.txt license
./Include:
ccolamd.h include file
./Lib:
Makefile Makefile for C-callable library
./MATLAB:
ccolamd.m MATLAB interface for ccolamd
ccolamd_demo.m simple demo
ccolamd_install.m compile and install ccolamd and csymamd
ccolamd_make.m compile colamd2 and symamd2
ccolamdmex.c MATLAB mexFunction for ccolamd
ccolamd_test.m extensive test
ccolamdtestmex.c test function for ccolamd
Contents.m contents of the MATLAB directory
luflops.m test code
Makefile Makefile for MATLAB functions
csymamd.m MATLAB interface for csymamd
csymamdmex.c MATLAB mexFunction for csymamd
symamdtestmex.c test function for csymamd
./Source:
ccolamd.c primary source code
ccolamd_global.c globally defined function pointers (malloc, free, ...)

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/* ========================================================================== */
/* === UFconfig ============================================================= */
/* ========================================================================== */
/* Copyright (c) 2009, University of Florida. No licensing restrictions
* apply to this file or to the UFconfig directory. Author: Timothy A. Davis.
*/
#include "UFconfig.h"
/* -------------------------------------------------------------------------- */
/* UFmalloc: malloc wrapper */
/* -------------------------------------------------------------------------- */
void *UFmalloc /* pointer to allocated block of memory */
(
size_t nitems, /* number of items to malloc (>=1 is enforced) */
size_t size_of_item, /* sizeof each item */
int *ok, /* TRUE if successful, FALSE otherwise */
UFconfig *config /* SuiteSparse-wide configuration */
)
{
void *p ;
if (nitems < 1) nitems = 1 ;
if (nitems * size_of_item != ((double) nitems) * size_of_item)
{
/* Int overflow */
*ok = 0 ;
return (NULL) ;
}
if (!config || config->malloc_memory == NULL)
{
/* use malloc by default */
p = (void *) malloc (nitems * size_of_item) ;
}
else
{
/* use the pointer to malloc in the config */
p = (void *) (config->malloc_memory) (nitems * size_of_item) ;
}
*ok = (p != NULL) ;
return (p) ;
}
/* -------------------------------------------------------------------------- */
/* UFfree: free wrapper */
/* -------------------------------------------------------------------------- */
void *UFfree /* always returns NULL */
(
void *p, /* block to free */
UFconfig *config /* SuiteSparse-wide configuration */
)
{
if (p)
{
if (!config || config->free_memory == NULL)
{
/* use free by default */
free (p) ;
}
else
{
/* use the pointer to free in the config */
(config->free_memory) (p) ;
}
}
return (NULL) ;
}

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/* ========================================================================== */
/* === UFconfig.h =========================================================== */
/* ========================================================================== */
/* Configuration file for SuiteSparse: a Suite of Sparse matrix packages
* (AMD, COLAMD, CCOLAMD, CAMD, CHOLMOD, UMFPACK, CXSparse, and others).
*
* UFconfig.h provides the definition of the long integer. On most systems,
* a C program can be compiled in LP64 mode, in which long's and pointers are
* both 64-bits, and int's are 32-bits. Windows 64, however, uses the LLP64
* model, in which int's and long's are 32-bits, and long long's and pointers
* are 64-bits.
*
* SuiteSparse packages that include long integer versions are
* intended for the LP64 mode. However, as a workaround for Windows 64
* (and perhaps other systems), the long integer can be redefined.
*
* If _WIN64 is defined, then the __int64 type is used instead of long.
*
* The long integer can also be defined at compile time. For example, this
* could be added to UFconfig.mk:
*
* CFLAGS = -O -D'UF_long=long long' -D'UF_long_max=9223372036854775801' \
* -D'UF_long_idd="lld"'
*
* This file defines UF_long as either long (on all but _WIN64) or
* __int64 on Windows 64. The intent is that a UF_long is always a 64-bit
* integer in a 64-bit code. ptrdiff_t might be a better choice than long;
* it is always the same size as a pointer.
*
* This file also defines the SUITESPARSE_VERSION and related definitions.
*
* Copyright (c) 2007, University of Florida. No licensing restrictions
* apply to this file or to the UFconfig directory. Author: Timothy A. Davis.
*/
#ifndef _UFCONFIG_H
#define _UFCONFIG_H
#ifdef __cplusplus
extern "C" {
#endif
#include <limits.h>
#include <stdlib.h>
/* ========================================================================== */
/* === UF_long ============================================================== */
/* ========================================================================== */
#ifndef UF_long
#ifdef _WIN64
#define UF_long __int64
#define UF_long_max _I64_MAX
#define UF_long_idd "I64d"
#else
#define UF_long long
#define UF_long_max LONG_MAX
#define UF_long_idd "ld"
#endif
#define UF_long_id "%" UF_long_idd
#endif
/* ========================================================================== */
/* === UFconfig parameters and functions ==================================== */
/* ========================================================================== */
/* SuiteSparse-wide parameters will be placed in this struct. So far, they
are only used by RBio. */
typedef struct UFconfig_struct
{
void *(*malloc_memory) (size_t) ; /* pointer to malloc */
void *(*realloc_memory) (void *, size_t) ; /* pointer to realloc */
void (*free_memory) (void *) ; /* pointer to free */
void *(*calloc_memory) (size_t, size_t) ; /* pointer to calloc */
} UFconfig ;
void *UFmalloc /* pointer to allocated block of memory */
(
size_t nitems, /* number of items to malloc (>=1 is enforced) */
size_t size_of_item, /* sizeof each item */
int *ok, /* TRUE if successful, FALSE otherwise */
UFconfig *config /* SuiteSparse-wide configuration */
) ;
void *UFfree /* always returns NULL */
(
void *p, /* block to free */
UFconfig *config /* SuiteSparse-wide configuration */
) ;
/* ========================================================================== */
/* === SuiteSparse version ================================================== */
/* ========================================================================== */
/* SuiteSparse is not a package itself, but a collection of packages, some of
* which must be used together (UMFPACK requires AMD, CHOLMOD requires AMD,
* COLAMD, CAMD, and CCOLAMD, etc). A version number is provided here for the
* collection itself. The versions of packages within each version of
* SuiteSparse are meant to work together. Combining one packge from one
* version of SuiteSparse, with another package from another version of
* SuiteSparse, may or may not work.
*
* SuiteSparse Version 3.6.1 contains the following packages:
*
* AMD version 2.2.2
* BTF version 1.1.2
* CAMD version 2.2.2
* CCOLAMD version 2.7.3
* CHOLMOD version 1.7.3
* COLAMD version 2.7.3
* CSparse version 2.2.5
* CSparse3 version 3.0.1
* CXSparse version 2.2.5
* KLU version 1.1.2
* LDL version 2.0.3
* RBio version 2.0.1
* SPQR version 1.2.2 (also called SuiteSparseQR)
* UFcollection version 1.5.0
* UFconfig version number is the same as SuiteSparse
* UMFPACK version 5.5.1
* LINFACTOR version 1.1.0
* MESHND version 1.1.1
* SSMULT version 2.0.2
* MATLAB_Tools no specific version number
*
* Other package dependencies:
* BLAS required by CHOLMOD and UMFPACK
* LAPACK required by CHOLMOD
* METIS 4.0.1 required by CHOLMOD (optional) and KLU (optional)
*/
#define SUITESPARSE_DATE "May 10, 2011"
#define SUITESPARSE_VER_CODE(main,sub) ((main) * 1000 + (sub))
#define SUITESPARSE_MAIN_VERSION 3
#define SUITESPARSE_SUB_VERSION 6
#define SUITESPARSE_SUBSUB_VERSION 1
#define SUITESPARSE_VERSION \
SUITESPARSE_VER_CODE(SUITESPARSE_MAIN_VERSION,SUITESPARSE_SUB_VERSION)
#ifdef __cplusplus
}
#endif
#endif

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#===============================================================================
# UFconfig.mk: common configuration file for the SuiteSparse
#===============================================================================
# This file contains all configuration settings for all packages authored or
# co-authored by Tim Davis at the University of Florida:
#
# Package Version Description
# ------- ------- -----------
# AMD 1.2 or later approximate minimum degree ordering
# COLAMD 2.4 or later column approximate minimum degree ordering
# CCOLAMD 1.0 or later constrained column approximate minimum degree ordering
# CAMD any constrained approximate minimum degree ordering
# UMFPACK 4.5 or later sparse LU factorization, with the BLAS
# CHOLMOD any sparse Cholesky factorization, update/downdate
# KLU 0.8 or later sparse LU factorization, BLAS-free
# BTF 0.8 or later permutation to block triangular form
# LDL 1.2 or later concise sparse LDL'
# LPDASA any linear program solve (dual active set algorithm)
# CXSparse any extended version of CSparse (int/long, real/complex)
# SuiteSparseQR any sparse QR factorization
#
# The UFconfig directory and the above packages should all appear in a single
# directory, in order for the Makefile's within each package to find this file.
#
# To enable an option of the form "# OPTION = ...", edit this file and
# delete the "#" in the first column of the option you wish to use.
#------------------------------------------------------------------------------
# Generic configuration
#------------------------------------------------------------------------------
# C compiler and compiler flags: These will normally not give you optimal
# performance. You should select the optimization parameters that are best
# for your system. On Linux, use "CFLAGS = -O3 -fexceptions" for example.
CC = cc
CFLAGS = -O3 -fexceptions
# C++ compiler (also uses CFLAGS)
CPLUSPLUS = g++
# ranlib, and ar, for generating libraries
RANLIB = ranlib
AR = ar cr
# copy, delete, and rename a file
CP = cp -f
RM = rm -f
MV = mv -f
# Fortran compiler (not normally required)
F77 = f77
F77FLAGS = -O
F77LIB =
# C and Fortran libraries
LIB = -lm
# For compiling MATLAB mexFunctions (MATLAB 7.5 or later)
MEX = mex -O -largeArrayDims -lmwlapack -lmwblas
# For compiling MATLAB mexFunctions (MATLAB 7.3 and 7.4)
# MEX = mex -O -largeArrayDims -lmwlapack
# For MATLAB 7.2 or earlier, you must use one of these options:
# MEX = mex -O -lmwlapack
# MEX = mex -O
# Which version of MAKE you are using (default is "make")
# MAKE = make
# MAKE = gmake
# For "make install"
INSTALL_LIB = /usr/local/lib
INSTALL_INCLUDE = /usr/local/include
#------------------------------------------------------------------------------
# BLAS and LAPACK configuration:
#------------------------------------------------------------------------------
# UMFPACK and CHOLMOD both require the BLAS. CHOLMOD also requires LAPACK.
# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
# LAPACK is at http://www.netlib.org/lapack/ . You can use the standard
# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
# on a 2.5Ghz dual-core AMD Opteron.
# These settings will probably not work, since there is no fixed convention for
# naming the BLAS and LAPACK library (*.a or *.so) files.
# This is probably slow ... it might connect to the Standard Reference BLAS:
BLAS = -lblas -lgfortran
LAPACK = -llapack
# NOTE: this next option for the "Goto BLAS" has nothing to do with a "goto"
# statement. Rather, the Goto BLAS is written by Dr. Kazushige Goto.
# Using the Goto BLAS:
# BLAS = -lgoto -lgfortran -lgfortranbegin
# Using non-optimized versions:
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
# LAPACK = -llapack_plain
# BLAS = -lblas_plain -lgfortran -lgfortranbegin
# LAPACK = -llapack
# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
# the BLAS. Also, the standard xerbla requires the Fortran I/O library, and
# stops the application program if an error occurs. A C version of xerbla
# distributed with this software (UFconfig/xerbla/libcerbla.a) includes a
# Fortran-callable xerbla routine that prints nothing and does not stop the
# application program. This is optional.
# XERBLA = ../../UFconfig/xerbla/libcerbla.a
# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
# use this option:
XERBLA =
# If you wish to use the Fortran UFconfig/xerbla/xerbla.f instead, use this:
# XERBLA = ../../UFconfig/xerbla/libxerbla.a
#------------------------------------------------------------------------------
# METIS, optionally used by CHOLMOD
#------------------------------------------------------------------------------
# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
# compile CHOLMOD with the -DNPARTITION flag. You must also use the
# "METIS =" option, below.
# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
# You may wish to use an absolute path. METIS is optional. Compile
# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
METIS_PATH = ../../metis-4.0
METIS = ../../metis-4.0/libmetis.a
# If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
# options:
# METIS_PATH =
# METIS =
#------------------------------------------------------------------------------
# UMFPACK configuration:
#------------------------------------------------------------------------------
# Configuration flags for UMFPACK. See UMFPACK/Source/umf_config.h for details.
#
# -DNBLAS do not use the BLAS. UMFPACK will be very slow.
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
# LAPACK and the BLAS (defaults to 'int')
# -DNSUNPERF do not use the Sun Perf. Library (default is use it on Solaris)
# -DNPOSIX do not use POSIX routines sysconf and times.
# -DGETRUSAGE use getrusage
# -DNO_TIMER do not use any timing routines
# -DNRECIPROCAL do not multiply by the reciprocal
# -DNO_DIVIDE_BY_ZERO do not divide by zero
UMFPACK_CONFIG =
#------------------------------------------------------------------------------
# CHOLMOD configuration
#------------------------------------------------------------------------------
# CHOLMOD Library Modules, which appear in libcholmod.a:
# Core requires: none
# Check requires: Core
# Cholesky requires: Core, AMD, COLAMD. optional: Partition, Supernodal
# MatrixOps requires: Core
# Modify requires: Core
# Partition requires: Core, CCOLAMD, METIS. optional: Cholesky
# Supernodal requires: Core, BLAS, LAPACK
#
# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
# Tcov requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
# optional: Partition
# Valgrind same as Tcov
# Demo requires: Core, Check, Cholesky, MatrixOps, Supernodal
# optional: Partition
#
# Configuration flags:
# -DNCHECK do not include the Check module. License GNU LGPL
# -DNCHOLESKY do not include the Cholesky module. License GNU LGPL
# -DNPARTITION do not include the Partition module. License GNU LGPL
# also do not include METIS.
# -DNGPL do not include any GNU GPL Modules in the CHOLMOD library:
# -DNMATRIXOPS do not include the MatrixOps module. License GNU GPL
# -DNMODIFY do not include the Modify module. License GNU GPL
# -DNSUPERNODAL do not include the Supernodal module. License GNU GPL
#
# -DNPRINT do not print anything.
# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
# LAPACK and the BLAS (defaults to 'int')
# -DNSUNPERF for Solaris only. If defined, do not use the Sun
# Performance Library
CHOLMOD_CONFIG =
#------------------------------------------------------------------------------
# SuiteSparseQR configuration:
#------------------------------------------------------------------------------
# The SuiteSparseQR library can be compiled with the following options:
#
# -DNPARTITION do not include the CHOLMOD partition module
# -DNEXPERT do not include the functions in SuiteSparseQR_expert.cpp
# -DTIMING enable timing and flop counts
# -DHAVE_TBB enable the use of Intel's Threading Building Blocks (TBB)
# default, without timing, without TBB:
SPQR_CONFIG =
# with timing and TBB:
# SPQR_CONFIG = -DTIMING -DHAVE_TBB
# with timing
# SPQR_CONFIG = -DTIMING
# This is needed for IBM AIX: (but not for and C codes, just C++)
# SPQR_CONFIG = -DBLAS_NO_UNDERSCORE
# with TBB, you must select this:
# TBB = -ltbb
# without TBB:
TBB =
# with timing, you must include the timing library:
# RTLIB = -lrt
# without timing
RTLIB =
#------------------------------------------------------------------------------
# Linux
#------------------------------------------------------------------------------
# Using default compilers:
# CC = gcc
# CFLAGS = -O3 -fexceptions
# alternatives:
# CFLAGS = -g -fexceptions \
-Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi \
-funit-at-a-time
# CFLAGS = -O3 -fexceptions \
-Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
# CFLAGS = -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
# CFLAGS = -O3
# CFLAGS = -O3 -g -fexceptions
# CFLAGS = -g -fexceptions \
-Wall -W -Wshadow \
-Wredundant-decls -Wdisabled-optimization -ansi
# consider:
# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
# -frename-registers -ffast-math -funroll-loops
# Using the Goto BLAS:
# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
# Using Intel's icc and ifort compilers:
# (does not work for mexFunctions unless you add a mexopts.sh file)
# F77 = ifort
# CC = icc
# CFLAGS = -O3 -xN -vec_report=0
# CFLAGS = -g
# old (broken): CFLAGS = -ansi -O3 -ip -tpp7 -xW -vec_report0
# 64bit:
# F77FLAGS = -O -m64
# CFLAGS = -O3 -fexceptions -m64
# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
# LAPACK = -llapack64
# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
# F77 = gfortran
# BLAS = -lgoto_opteron64 -lgfortran
# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
# F77 = gfortran
# BLAS = -lgoto -lgfortran
#------------------------------------------------------------------------------
# Mac
#------------------------------------------------------------------------------
# As recommended by macports, http://suitesparse.darwinports.com/
# I've tested them myself on Mac OSX 10.6.1 (Snow Leopard), on my MacBook Air.
# F77 = gfortran
# CFLAGS = -O3 -fno-common -no-cpp-precomp -fexceptions
# BLAS = -framework Accelerate
# LAPACK = -framework Accelerate
# Using netlib.org LAPACK and BLAS compiled by gfortran, with and without
# optimzation:
# BLAS = -lblas_plain -lgfortran
# LAPACK = -llapack_plain
# BLAS = -lblas_optimized -lgfortran
# LAPACK = -llapack_optimized
#------------------------------------------------------------------------------
# Solaris
#------------------------------------------------------------------------------
# 32-bit
# CFLAGS = -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
# 64-bit
# CFLAGS = -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
# The Sun Performance Library includes both LAPACK and the BLAS:
# BLAS = -xlic_lib=sunperf
# LAPACK =
#------------------------------------------------------------------------------
# Compaq Alpha
#------------------------------------------------------------------------------
# 64-bit mode only
# CFLAGS = -O2 -std1
# BLAS = -ldxml
# LAPACK =
#------------------------------------------------------------------------------
# Macintosh
#------------------------------------------------------------------------------
# CC = gcc
# CFLAGS = -O3 -fno-common -no-cpp-precomp -fexceptions
# LIB = -lstdc++
# BLAS = -framework Accelerate
# LAPACK = -framework Accelerate
#------------------------------------------------------------------------------
# IBM RS 6000
#------------------------------------------------------------------------------
# BLAS = -lessl
# LAPACK =
# 32-bit mode:
# CFLAGS = -O4 -qipa -qmaxmem=16384 -qproto
# F77FLAGS = -O4 -qipa -qmaxmem=16384
# 64-bit mode:
# CFLAGS = -O4 -qipa -qmaxmem=16384 -q64 -qproto
# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
# AR = ar -X64
#------------------------------------------------------------------------------
# SGI IRIX
#------------------------------------------------------------------------------
# BLAS = -lscsl
# LAPACK =
# 32-bit mode
# CFLAGS = -O
# 64-bit mode (32 bit int's and 64-bit long's):
# CFLAGS = -64
# F77FLAGS = -64
# SGI doesn't have ranlib
# RANLIB = echo
#------------------------------------------------------------------------------
# AMD Opteron (64 bit)
#------------------------------------------------------------------------------
# BLAS = -lgoto_opteron64 -lg2c
# LAPACK = -llapack_opteron64
# SUSE Linux 10.1, AMD Opteron
# F77 = gfortran
# BLAS = -lgoto_opteron64 -lgfortran
# LAPACK = -llapack_opteron64
#------------------------------------------------------------------------------
# remove object files and profile output
#------------------------------------------------------------------------------
CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno

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/* ========================================================================== */
/* === CCOLAMD/ccolamd.h ==================================================== */
/* ========================================================================== */
/* ----------------------------------------------------------------------------
* CCOLAMD Copyright (C), Univ. of Florida. Authors: Timothy A. Davis,
* Sivasankaran Rajamanickam, and Stefan Larimore
* See License.txt for the Version 2.1 of the GNU Lesser General Public License
* http://www.cise.ufl.edu/research/sparse
* -------------------------------------------------------------------------- */
/*
* You must include this file (ccolamd.h) in any routine that uses ccolamd,
* csymamd, or the related macros and definitions.
*/
#ifndef CCOLAMD_H
#define CCOLAMD_H
/* make it easy for C++ programs to include CCOLAMD */
#ifdef __cplusplus
extern "C" {
#endif
/* for size_t definition: */
#include <stdlib.h>
/* ========================================================================== */
/* === CCOLAMD version ====================================================== */
/* ========================================================================== */
/* All versions of CCOLAMD will include the following definitions.
* As an example, to test if the version you are using is 1.3 or later:
*
* if (CCOLAMD_VERSION >= CCOLAMD_VERSION_CODE (1,3)) ...
*
* This also works during compile-time:
*
* #if CCOLAMD_VERSION >= CCOLAMD_VERSION_CODE (1,3)
* printf ("This is version 1.3 or later\n") ;
* #else
* printf ("This is an early version\n") ;
* #endif
*/
#define CCOLAMD_DATE "Jan 25, 2011"
#define CCOLAMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
#define CCOLAMD_MAIN_VERSION 2
#define CCOLAMD_SUB_VERSION 7
#define CCOLAMD_SUBSUB_VERSION 3
#define CCOLAMD_VERSION \
CCOLAMD_VERSION_CODE(CCOLAMD_MAIN_VERSION,CCOLAMD_SUB_VERSION)
/* ========================================================================== */
/* === Knob and statistics definitions ====================================== */
/* ========================================================================== */
/* size of the knobs [ ] array. Only knobs [0..3] are currently used. */
#define CCOLAMD_KNOBS 20
/* number of output statistics. Only stats [0..10] are currently used. */
#define CCOLAMD_STATS 20
/* knobs [0] and stats [0]: dense row knob and output statistic. */
#define CCOLAMD_DENSE_ROW 0
/* knobs [1] and stats [1]: dense column knob and output statistic. */
#define CCOLAMD_DENSE_COL 1
/* knobs [2]: aggressive absorption option */
#define CCOLAMD_AGGRESSIVE 2
/* knobs [3]: LU or Cholesky factorization option */
#define CCOLAMD_LU 3
/* stats [2]: memory defragmentation count output statistic */
#define CCOLAMD_DEFRAG_COUNT 2
/* stats [3]: ccolamd status: zero OK, > 0 warning or notice, < 0 error */
#define CCOLAMD_STATUS 3
/* stats [4..6]: error info, or info on jumbled columns */
#define CCOLAMD_INFO1 4
#define CCOLAMD_INFO2 5
#define CCOLAMD_INFO3 6
/* stats [7]: number of originally empty rows */
#define CCOLAMD_EMPTY_ROW 7
/* stats [8]: number of originally empty cols */
#define CCOLAMD_EMPTY_COL 8
/* stats [9]: number of rows with entries only in dense cols */
#define CCOLAMD_NEWLY_EMPTY_ROW 9
/* stats [10]: number of cols with entries only in dense rows */
#define CCOLAMD_NEWLY_EMPTY_COL 10
/* error codes returned in stats [3]: */
#define CCOLAMD_OK (0)
#define CCOLAMD_OK_BUT_JUMBLED (1)
#define CCOLAMD_ERROR_A_not_present (-1)
#define CCOLAMD_ERROR_p_not_present (-2)
#define CCOLAMD_ERROR_nrow_negative (-3)
#define CCOLAMD_ERROR_ncol_negative (-4)
#define CCOLAMD_ERROR_nnz_negative (-5)
#define CCOLAMD_ERROR_p0_nonzero (-6)
#define CCOLAMD_ERROR_A_too_small (-7)
#define CCOLAMD_ERROR_col_length_negative (-8)
#define CCOLAMD_ERROR_row_index_out_of_bounds (-9)
#define CCOLAMD_ERROR_out_of_memory (-10)
#define CCOLAMD_ERROR_invalid_cmember (-11)
#define CCOLAMD_ERROR_internal_error (-999)
/* ========================================================================== */
/* === Prototypes of user-callable routines ================================= */
/* ========================================================================== */
/* define UF_long */
#include "UFconfig.h"
size_t ccolamd_recommended /* returns recommended value of Alen, */
/* or 0 if input arguments are erroneous */
(
int nnz, /* nonzeros in A */
int n_row, /* number of rows in A */
int n_col /* number of columns in A */
) ;
size_t ccolamd_l_recommended /* returns recommended value of Alen, */
/* or 0 if input arguments are erroneous */
(
UF_long nnz, /* nonzeros in A */
UF_long n_row, /* number of rows in A */
UF_long n_col /* number of columns in A */
) ;
void ccolamd_set_defaults /* sets default parameters */
( /* knobs argument is modified on output */
double knobs [CCOLAMD_KNOBS] /* parameter settings for ccolamd */
) ;
void ccolamd_l_set_defaults /* sets default parameters */
( /* knobs argument is modified on output */
double knobs [CCOLAMD_KNOBS] /* parameter settings for ccolamd */
) ;
int ccolamd /* returns (1) if successful, (0) otherwise*/
( /* A and p arguments are modified on output */
int n_row, /* number of rows in A */
int n_col, /* number of columns in A */
int Alen, /* size of the array A */
int A [ ], /* row indices of A, of size Alen */
int p [ ], /* column pointers of A, of size n_col+1 */
double knobs [CCOLAMD_KNOBS],/* parameter settings for ccolamd */
int stats [CCOLAMD_STATS], /* ccolamd output statistics and error codes */
int cmember [ ] /* Constraint set of A, of size n_col */
) ;
UF_long ccolamd_l /* same as ccolamd, but with UF_long integers */
(
UF_long n_row,
UF_long n_col,
UF_long Alen,
UF_long A [ ],
UF_long p [ ],
double knobs [CCOLAMD_KNOBS],
UF_long stats [CCOLAMD_STATS],
UF_long cmember [ ]
) ;
int csymamd /* return (1) if OK, (0) otherwise */
(
int n, /* number of rows and columns of A */
int A [ ], /* row indices of A */
int p [ ], /* column pointers of A */
int perm [ ], /* output permutation, size n_col+1 */
double knobs [CCOLAMD_KNOBS],/* parameters (uses defaults if NULL) */
int stats [CCOLAMD_STATS], /* output statistics and error codes */
void * (*allocate) (size_t, size_t), /* pointer to calloc (ANSI C) or */
/* mxCalloc (for MATLAB mexFunction) */
void (*release) (void *), /* pointer to free (ANSI C) or */
/* mxFree (for MATLAB mexFunction) */
int cmember [ ], /* Constraint set of A */
int stype /* 0: use both parts, >0: upper, <0: lower */
) ;
UF_long csymamd_l /* same as csymamd, but with UF_long integers */
(
UF_long n,
UF_long A [ ],
UF_long p [ ],
UF_long perm [ ],
double knobs [CCOLAMD_KNOBS],
UF_long stats [CCOLAMD_STATS],
void * (*allocate) (size_t, size_t),
void (*release) (void *),
UF_long cmember [ ],
UF_long stype
) ;
void ccolamd_report
(
int stats [CCOLAMD_STATS]
) ;
void ccolamd_l_report
(
UF_long stats [CCOLAMD_STATS]
) ;
void csymamd_report
(
int stats [CCOLAMD_STATS]
) ;
void csymamd_l_report
(
UF_long stats [CCOLAMD_STATS]
) ;
/* ========================================================================== */
/* === Prototypes of "expert" routines ====================================== */
/* ========================================================================== */
/* These routines are meant to be used internally, or in a future version of
* UMFPACK. They appear here so that UMFPACK can use them, but they should not
* be called directly by the user.
*/
int ccolamd2
( /* A and p arguments are modified on output */
int n_row, /* number of rows in A */
int n_col, /* number of columns in A */
int Alen, /* size of the array A */
int A [ ], /* row indices of A, of size Alen */
int p [ ], /* column pointers of A, of size n_col+1 */
double knobs [CCOLAMD_KNOBS],/* parameter settings for ccolamd */
int stats [CCOLAMD_STATS], /* ccolamd output statistics and error codes */
/* each Front_ array is of size n_col+1: */
int Front_npivcol [ ], /* # pivot cols in each front */
int Front_nrows [ ], /* # of rows in each front (incl. pivot rows) */
int Front_ncols [ ], /* # of cols in each front (incl. pivot cols) */
int Front_parent [ ], /* parent of each front */
int Front_cols [ ], /* link list of pivot columns for each front */
int *p_nfr, /* total number of frontal matrices */
int InFront [ ], /* InFront [row] = f if row in front f */
int cmember [ ] /* Constraint set of A */
) ;
UF_long ccolamd2_l /* same as ccolamd2, but with UF_long integers */
(
UF_long n_row,
UF_long n_col,
UF_long Alen,
UF_long A [ ],
UF_long p [ ],
double knobs [CCOLAMD_KNOBS],
UF_long stats [CCOLAMD_STATS],
UF_long Front_npivcol [ ],
UF_long Front_nrows [ ],
UF_long Front_ncols [ ],
UF_long Front_parent [ ],
UF_long Front_cols [ ],
UF_long *p_nfr,
UF_long InFront [ ],
UF_long cmember [ ]
) ;
void ccolamd_apply_order
(
int Front [ ],
const int Order [ ],
int Temp [ ],
int nn,
int nfr
) ;
void ccolamd_l_apply_order
(
UF_long Front [ ],
const UF_long Order [ ],
UF_long Temp [ ],
UF_long nn,
UF_long nfr
) ;
void ccolamd_fsize
(
int nn,
int MaxFsize [ ],
int Fnrows [ ],
int Fncols [ ],
int Parent [ ],
int Npiv [ ]
) ;
void ccolamd_l_fsize
(
UF_long nn,
UF_long MaxFsize [ ],
UF_long Fnrows [ ],
UF_long Fncols [ ],
UF_long Parent [ ],
UF_long Npiv [ ]
) ;
void ccolamd_postorder
(
int nn,
int Parent [ ],
int Npiv [ ],
int Fsize [ ],
int Order [ ],
int Child [ ],
int Sibling [ ],
int Stack [ ],
int Front_cols [ ],
int cmember [ ]
) ;
void ccolamd_l_postorder
(
UF_long nn,
UF_long Parent [ ],
UF_long Npiv [ ],
UF_long Fsize [ ],
UF_long Order [ ],
UF_long Child [ ],
UF_long Sibling [ ],
UF_long Stack [ ],
UF_long Front_cols [ ],
UF_long cmember [ ]
) ;
int ccolamd_post_tree
(
int root,
int k,
int Child [ ],
const int Sibling [ ],
int Order [ ],
int Stack [ ]
) ;
UF_long ccolamd_l_post_tree
(
UF_long root,
UF_long k,
UF_long Child [ ],
const UF_long Sibling [ ],
UF_long Order [ ],
UF_long Stack [ ]
) ;
#ifndef EXTERN
#define EXTERN extern
#endif
EXTERN int (*ccolamd_printf) (const char *, ...) ;
#ifdef __cplusplus
}
#endif
#endif

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#------------------------------------------------------------------------------
# CCOLAMD Makefile
#------------------------------------------------------------------------------
VERSION = 2.7.3
default: demos
include ../UFconfig/UFconfig.mk
# Compile all C code, including the C-callable routine and the mexFunctions.
# Do not the MATLAB interface.
demos:
( cd Lib ; $(MAKE) )
( cd Demo ; $(MAKE) )
# Compile all C code, including the C-callable routine and the mexFunctions.
all:
( cd Lib ; $(MAKE) )
( cd Demo ; $(MAKE) )
( cd MATLAB ; $(MAKE) )
# compile just the C-callable libraries (not mexFunctions or Demos)
library:
( cd Lib ; $(MAKE) )
# remove object files, but keep the compiled programs and library archives
clean:
( cd Lib ; $(MAKE) clean )
( cd Demo ; $(MAKE) clean )
( cd MATLAB ; $(MAKE) clean )
# clean, and then remove compiled programs and library archives
purge:
( cd Lib ; $(MAKE) purge )
( cd Demo ; $(MAKE) purge )
( cd MATLAB ; $(MAKE) purge )
distclean: purge
# get ready for distribution
dist: purge
( cd Demo ; $(MAKE) dist )
ccode: library
lib: library
# compile the MATLAB mexFunction
mex:
( cd MATLAB ; $(MAKE) )
# install CCOLAMD
install:
$(CP) Lib/libccolamd.a $(INSTALL_LIB)/libccolamd.$(VERSION).a
( cd $(INSTALL_LIB) ; ln -sf libccolamd.$(VERSION).a libccolamd.a )
$(CP) Include/ccolamd.h $(INSTALL_INCLUDE)
# uninstall CCOLAMD
uninstall:
$(RM) $(INSTALL_LIB)/libccolamd*.a
$(RM) $(INSTALL_INCLUDE)/ccolamd.h

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/* ========================================================================== */
/* === ccolamd_global.c ===================================================== */
/* ========================================================================== */
/* ----------------------------------------------------------------------------
* CCOLAMD Copyright (C), Univ. of Florida. Authors: Timothy A. Davis,
* Sivasankaran Rajamanickam, and Stefan Larimore
* See License.txt for the Version 2.1 of the GNU Lesser General Public License
* http://www.cise.ufl.edu/research/sparse
* -------------------------------------------------------------------------- */
/* Global variables for CCOLAMD */
#ifndef NPRINT
#ifdef MATLAB_MEX_FILE
#include "mex.h"
int (*ccolamd_printf) (const char *, ...) = mexPrintf ;
#else
#include <stdio.h>
int (*ccolamd_printf) (const char *, ...) = printf ;
#endif
#else
int (*ccolamd_printf) (const char *, ...) = ((void *) 0) ;
#endif

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# Makefile for UFconfig.c
VERSION = 3.6.0
default: ccode
include UFconfig.mk
ccode: libufconfig.a
all: libufconfig.a
libufconfig.a: UFconfig.c UFconfig.h
$(CC) $(CFLAGS) -c UFconfig.c
$(AR) libufconfig.a UFconfig.o
- $(RM) UFconfig.o
distclean: purge
purge: clean
- $(RM) *.o *.a
clean:
- $(RM) -r $(CLEAN)
# install UFconfig
install:
$(CP) libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a
( cd $(INSTALL_LIB) ; ln -sf libufconfig.$(VERSION).a libufconfig.a )
$(CP) UFconfig.h $(INSTALL_INCLUDE)
# uninstall UFconfig
uninstall:
$(RM) $(INSTALL_LIB)/libufconfig*.a
$(RM) $(INSTALL_INCLUDE)/UFconfig.h