added CCOLAMD, changed colamd compile from C++ to C compiler, added extern accordingly
Michael Kaess
parent
e73f56f817
commit
39d18328e6
33
.cproject
33
.cproject
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@ -12,8 +12,7 @@
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<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>
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<extension id="org.eclipse.cdt.core.MakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
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</extensions>
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</storageModule>
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<storageModule moduleId="cdtBuildSystem" version="4.0.0">
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@ -300,6 +299,22 @@
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</storageModule>
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<storageModule moduleId="org.eclipse.cdt.make.core.buildtargets">
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<buildTargets>
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<target name="all" path="colamd" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>all</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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<runAllBuilders>true</runAllBuilders>
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</target>
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<target name="clean" path="colamd" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>clean</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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<runAllBuilders>true</runAllBuilders>
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</target>
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<target name="install" path="wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments>-j2</buildArguments>
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@ -318,7 +333,6 @@
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</target>
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<target name="clean" path="wrap" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>clean</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -478,6 +492,7 @@
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</target>
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<target name="testBayesTree.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testBayesTree.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -485,7 +500,6 @@
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</target>
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<target name="testSymbolicBayesNet.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testSymbolicBayesNet.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -493,6 +507,7 @@
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</target>
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<target name="testSymbolicFactorGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testSymbolicFactorGraph.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -684,6 +699,7 @@
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</target>
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<target name="testGraph.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testGraph.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -739,7 +755,6 @@
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</target>
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<target name="testSimulated2D.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testSimulated2D.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -787,6 +802,7 @@
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</target>
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<target name="testErrors.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testErrors.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -794,6 +810,7 @@
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</target>
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<target name="testDSF.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testDSF.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -809,6 +826,7 @@
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</target>
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<target name="testConstraintOptimizer.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testConstraintOptimizer.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -816,7 +834,6 @@
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</target>
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<target name="testBTree.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testBTree.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -824,6 +841,7 @@
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</target>
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<target name="testSimulated2DOriented.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testSimulated2DOriented.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>false</useDefaultCommand>
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@ -831,7 +849,6 @@
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</target>
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<target name="testDSFVector.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testDSFVector.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -839,7 +856,6 @@
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</target>
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<target name="testSPQRUtil.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testSPQRUtil.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -847,7 +863,6 @@
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</target>
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<target name="testInference.run" path="cpp" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
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<buildCommand>make</buildCommand>
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<buildArguments/>
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<buildTarget>testInference.run</buildTarget>
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<stopOnError>true</stopOnError>
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<useDefaultCommand>true</useDefaultCommand>
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@ -5,9 +5,8 @@
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all: libcolamd.a
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CC ?= gcc
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CXX ?= g++
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CXXFLAGS += -O2
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CXXFLAGS += -fPIC
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CFLAGS += -O2
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CFLAGS += -fPIC
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sources = $(shell ls *.c)
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@ -17,11 +16,9 @@ library = libcolamd.a
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#Note: hack was added to ensure that flags are acutally used for compilation
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# This should probably be fixed, but will work for 64 bit machines now
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$(library):
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$(CXX) $(CXXFLAGS) -c -o colamd.o colamd.c
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$(CXX) $(CXXFLAGS) -c -DDLONG -o colamd_l.o colamd.c
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$(CXX) $(CXXFLAGS) -c -o colamd_global.o colamd_global.c
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ar crsv $@ colamd.o colamd_l.o colamd_global.o
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$(library): colamd.o colamd_global.o ccolamd.o ccolamd_global.o
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$(CC) $(CFLAGS) -c -DDLONG -o colamd_l.o colamd.c
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ar crsv $@ $^ colamd_l.o
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ranlib $(library)
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clean:
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,365 @@
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/* ========================================================================== */
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/* === CCOLAMD/ccolamd.h ==================================================== */
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/* ========================================================================== */
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/* ----------------------------------------------------------------------------
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* CCOLAMD Copyright (C), Univ. of Florida. Authors: Timothy A. Davis,
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* Sivasankaran Rajamanickam, and Stefan Larimore
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* See License.txt for the Version 2.1 of the GNU Lesser General Public License
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* http://www.cise.ufl.edu/research/sparse
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* -------------------------------------------------------------------------- */
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/*
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* You must include this file (ccolamd.h) in any routine that uses ccolamd,
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* csymamd, or the related macros and definitions.
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*/
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#ifndef CCOLAMD_H
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#define CCOLAMD_H
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/* make it easy for C++ programs to include CCOLAMD */
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#ifdef __cplusplus
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extern "C" {
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#endif
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/* for size_t definition: */
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#include <stdlib.h>
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/* ========================================================================== */
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/* === CCOLAMD version ====================================================== */
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/* ========================================================================== */
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/* All versions of CCOLAMD will include the following definitions.
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* As an example, to test if the version you are using is 1.3 or later:
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*
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* if (CCOLAMD_VERSION >= CCOLAMD_VERSION_CODE (1,3)) ...
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*
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* This also works during compile-time:
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*
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* #if CCOLAMD_VERSION >= CCOLAMD_VERSION_CODE (1,3)
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* printf ("This is version 1.3 or later\n") ;
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* #else
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* printf ("This is an early version\n") ;
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* #endif
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*/
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#define CCOLAMD_DATE "Nov 30, 2009"
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#define CCOLAMD_VERSION_CODE(main,sub) ((main) * 1000 + (sub))
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#define CCOLAMD_MAIN_VERSION 2
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#define CCOLAMD_SUB_VERSION 7
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#define CCOLAMD_SUBSUB_VERSION 2
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#define CCOLAMD_VERSION \
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CCOLAMD_VERSION_CODE(CCOLAMD_MAIN_VERSION,CCOLAMD_SUB_VERSION)
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/* ========================================================================== */
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/* === Knob and statistics definitions ====================================== */
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/* ========================================================================== */
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/* size of the knobs [ ] array. Only knobs [0..3] are currently used. */
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#define CCOLAMD_KNOBS 20
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/* number of output statistics. Only stats [0..10] are currently used. */
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#define CCOLAMD_STATS 20
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/* knobs [0] and stats [0]: dense row knob and output statistic. */
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#define CCOLAMD_DENSE_ROW 0
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/* knobs [1] and stats [1]: dense column knob and output statistic. */
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#define CCOLAMD_DENSE_COL 1
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/* knobs [2]: aggressive absorption option */
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#define CCOLAMD_AGGRESSIVE 2
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/* knobs [3]: LU or Cholesky factorization option */
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#define CCOLAMD_LU 3
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/* stats [2]: memory defragmentation count output statistic */
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#define CCOLAMD_DEFRAG_COUNT 2
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/* stats [3]: ccolamd status: zero OK, > 0 warning or notice, < 0 error */
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#define CCOLAMD_STATUS 3
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/* stats [4..6]: error info, or info on jumbled columns */
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#define CCOLAMD_INFO1 4
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#define CCOLAMD_INFO2 5
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#define CCOLAMD_INFO3 6
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/* stats [7]: number of originally empty rows */
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#define CCOLAMD_EMPTY_ROW 7
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/* stats [8]: number of originally empty cols */
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#define CCOLAMD_EMPTY_COL 8
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/* stats [9]: number of rows with entries only in dense cols */
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#define CCOLAMD_NEWLY_EMPTY_ROW 9
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/* stats [10]: number of cols with entries only in dense rows */
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#define CCOLAMD_NEWLY_EMPTY_COL 10
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/* error codes returned in stats [3]: */
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#define CCOLAMD_OK (0)
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#define CCOLAMD_OK_BUT_JUMBLED (1)
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#define CCOLAMD_ERROR_A_not_present (-1)
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#define CCOLAMD_ERROR_p_not_present (-2)
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#define CCOLAMD_ERROR_nrow_negative (-3)
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#define CCOLAMD_ERROR_ncol_negative (-4)
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#define CCOLAMD_ERROR_nnz_negative (-5)
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#define CCOLAMD_ERROR_p0_nonzero (-6)
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#define CCOLAMD_ERROR_A_too_small (-7)
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#define CCOLAMD_ERROR_col_length_negative (-8)
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#define CCOLAMD_ERROR_row_index_out_of_bounds (-9)
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#define CCOLAMD_ERROR_out_of_memory (-10)
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#define CCOLAMD_ERROR_invalid_cmember (-11)
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#define CCOLAMD_ERROR_internal_error (-999)
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/* ========================================================================== */
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/* === Prototypes of user-callable routines ================================= */
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/* ========================================================================== */
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/* define UF_long */
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#include "UFconfig.h"
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size_t ccolamd_recommended /* returns recommended value of Alen, */
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/* or 0 if input arguments are erroneous */
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(
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int nnz, /* nonzeros in A */
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int n_row, /* number of rows in A */
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int n_col /* number of columns in A */
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) ;
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size_t ccolamd_l_recommended /* returns recommended value of Alen, */
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/* or 0 if input arguments are erroneous */
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(
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UF_long nnz, /* nonzeros in A */
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UF_long n_row, /* number of rows in A */
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UF_long n_col /* number of columns in A */
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) ;
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void ccolamd_set_defaults /* sets default parameters */
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( /* knobs argument is modified on output */
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double knobs [CCOLAMD_KNOBS] /* parameter settings for ccolamd */
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) ;
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void ccolamd_l_set_defaults /* sets default parameters */
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( /* knobs argument is modified on output */
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double knobs [CCOLAMD_KNOBS] /* parameter settings for ccolamd */
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) ;
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int ccolamd /* returns (1) if successful, (0) otherwise*/
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( /* A and p arguments are modified on output */
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int n_row, /* number of rows in A */
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int n_col, /* number of columns in A */
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int Alen, /* size of the array A */
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int A [ ], /* row indices of A, of size Alen */
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int p [ ], /* column pointers of A, of size n_col+1 */
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double knobs [CCOLAMD_KNOBS],/* parameter settings for ccolamd */
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int stats [CCOLAMD_STATS], /* ccolamd output statistics and error codes */
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int cmember [ ] /* Constraint set of A, of size n_col */
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) ;
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UF_long ccolamd_l /* same as ccolamd, but with UF_long integers */
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(
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UF_long n_row,
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UF_long n_col,
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UF_long Alen,
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UF_long A [ ],
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UF_long p [ ],
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double knobs [CCOLAMD_KNOBS],
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UF_long stats [CCOLAMD_STATS],
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UF_long cmember [ ]
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) ;
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int csymamd /* return (1) if OK, (0) otherwise */
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(
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int n, /* number of rows and columns of A */
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int A [ ], /* row indices of A */
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int p [ ], /* column pointers of A */
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int perm [ ], /* output permutation, size n_col+1 */
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double knobs [CCOLAMD_KNOBS],/* parameters (uses defaults if NULL) */
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int stats [CCOLAMD_STATS], /* output statistics and error codes */
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void * (*allocate) (size_t, size_t), /* pointer to calloc (ANSI C) or */
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/* mxCalloc (for MATLAB mexFunction) */
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void (*release) (void *), /* pointer to free (ANSI C) or */
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/* mxFree (for MATLAB mexFunction) */
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int cmember [ ], /* Constraint set of A */
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int stype /* 0: use both parts, >0: upper, <0: lower */
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) ;
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UF_long csymamd_l /* same as csymamd, but with UF_long integers */
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(
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UF_long n,
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UF_long A [ ],
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UF_long p [ ],
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UF_long perm [ ],
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double knobs [CCOLAMD_KNOBS],
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UF_long stats [CCOLAMD_STATS],
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void * (*allocate) (size_t, size_t),
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void (*release) (void *),
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UF_long cmember [ ],
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UF_long stype
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) ;
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void ccolamd_report
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(
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int stats [CCOLAMD_STATS]
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) ;
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void ccolamd_l_report
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(
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UF_long stats [CCOLAMD_STATS]
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) ;
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void csymamd_report
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(
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int stats [CCOLAMD_STATS]
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) ;
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void csymamd_l_report
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(
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UF_long stats [CCOLAMD_STATS]
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) ;
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/* ========================================================================== */
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/* === Prototypes of "expert" routines ====================================== */
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/* ========================================================================== */
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/* These routines are meant to be used internally, or in a future version of
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* UMFPACK. They appear here so that UMFPACK can use them, but they should not
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* be called directly by the user.
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*/
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int ccolamd2
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( /* A and p arguments are modified on output */
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int n_row, /* number of rows in A */
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int n_col, /* number of columns in A */
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int Alen, /* size of the array A */
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int A [ ], /* row indices of A, of size Alen */
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int p [ ], /* column pointers of A, of size n_col+1 */
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double knobs [CCOLAMD_KNOBS],/* parameter settings for ccolamd */
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int stats [CCOLAMD_STATS], /* ccolamd output statistics and error codes */
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/* each Front_ array is of size n_col+1: */
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int Front_npivcol [ ], /* # pivot cols in each front */
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int Front_nrows [ ], /* # of rows in each front (incl. pivot rows) */
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int Front_ncols [ ], /* # of cols in each front (incl. pivot cols) */
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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
|
||||
|
|
@ -0,0 +1,25 @@
|
|||
/* ========================================================================== */
|
||||
/* === 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
|
||||
|
||||
|
|
@ -15,6 +15,10 @@
|
|||
#include <stdexcept>
|
||||
#include <functional>
|
||||
|
||||
extern "C" {
|
||||
#include <colamd/colamd.h>
|
||||
}
|
||||
|
||||
#include <boost/foreach.hpp>
|
||||
#include <boost/tuple/tuple.hpp>
|
||||
#include <boost/format.hpp>
|
||||
|
|
|
|||
|
|
@ -11,8 +11,6 @@
|
|||
#include <boost/numeric/ublas/io.hpp>
|
||||
#include <boost/assign/std/list.hpp> // for operator += in Ordering
|
||||
|
||||
#include <colamd/colamd.h>
|
||||
|
||||
#include "GaussianFactorGraph.h"
|
||||
#include "GaussianFactorSet.h"
|
||||
#include "FactorGraph-inl.h"
|
||||
|
|
|
|||
Loading…
Reference in New Issue