Fixed bug in BP (introduced in commit b8f96214...) and added regression test for...
[libdai.git] / Makefile
index 79addfd..d76c56f 100644 (file)
--- a/Makefile
+++ b/Makefile
-#   Copyright (C) 2006-2008  Joris Mooij  [joris dot mooij at tuebingen dot mpg dot de]
-#   Radboud University Nijmegen, The Netherlands /
-#   Max Planck Institute for Biological Cybernetics, Germany
-#   
-#   This file is part of libDAI.
+# This file is part of libDAI - http://www.libdai.org/
 #
-#   libDAI is free software; you can redistribute it and/or modify
-#   it under the terms of the GNU General Public License as published by
-#   the Free Software Foundation; either version 2 of the License, or
-#   (at your option) any later version.
+# libDAI is licensed under the terms of the GNU General Public License version
+# 2, or (at your option) any later version. libDAI is distributed without any
+# warranty. See the file COPYING for more details.
 #
-#   libDAI 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 General Public License for more details.
-#
-#   You should have received a copy of the GNU General Public License
-#   along with libDAI; if not, write to the Free Software
-#   Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-
-
-# Enable/disable various approximate inference methods
-WITH_BP=true
-WITH_MF=true
-WITH_HAK=true
-WITH_LC=true
-WITH_TREEEP=true
-WITH_JTREE=true
-WITH_MR=true
-WITH_GIBBS=true
-# Build with debug info?
-DEBUG=true
-# Build matlab interface?
-WITH_MATLAB=
-# New/old matlab version?
-NEW_MATLAB=true
-# Windows or linux (default)?
-WINDOWS=
-
-# Directories
+# Copyright (C) 2006-2010  Joris Mooij  [joris dot mooij at libdai dot org]
+# Copyright (C) 2006-2007  Radboud University Nijmegen, The Netherlands
+
+
+# Load the platform independent build configuration file
+include Makefile.ALL
+
+# Load the local configuration from Makefile.conf
+include Makefile.conf
+
+# Set version and date
+DAI_VERSION="git HEAD"
+DAI_DATE="May 12, 2010, or later"
+
+# Directories of libDAI sources
+# Location of libDAI headers
 INC=include/dai
+# Location of libDAI source files
 SRC=src
+# Destination directory of libDAI library
 LIB=lib
 
-# Extensions (library, object, executable, matlab compiled MEX file)
-LE=.a
-OE=.o
-EE=
-ME=.mexglx
+# Set final compiler flags
+ifdef DEBUG
+  CCFLAGS:=$(CCFLAGS) $(CCDEBUGFLAGS)
+else
+  CCFLAGS:=$(CCFLAGS) $(CCNODEBUGFLAGS)
+endif
 
-# Libraries
-LIBS=-ldai
+# Define build targets
+TARGETS:=lib tests utils examples
+ifdef WITH_MATLAB
+  TARGETS:=$(TARGETS) matlabs
+endif
+TARGETS:=$(TARGETS) unittests testregression testem
+ifdef WITH_DOC
+  TARGETS:=$(TARGETS) doc
+endif
 
-# We use the BOOST Program Options library
-BOOSTLIBS=-lboost_program_options
+# Define conditional build targets
+NAMES:=graph dag bipgraph varset daialg alldai clustergraph factor factorgraph properties regiongraph util weightedgraph exceptions exactinf evidence emalg
+ifdef WITH_BP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_BP
+  NAMES:=$(NAMES) bp
+endif
+ifdef WITH_FBP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_FBP
+  NAMES:=$(NAMES) fbp
+endif
+ifdef WITH_TRWBP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_TRWBP
+  NAMES:=$(NAMES) trwbp
+endif
+ifdef WITH_MF
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_MF
+  NAMES:=$(NAMES) mf
+endif
+ifdef WITH_HAK
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_HAK
+  NAMES:=$(NAMES) hak
+endif
+ifdef WITH_LC
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_LC
+  NAMES:=$(NAMES) lc
+endif
+ifdef WITH_TREEEP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_TREEEP
+  NAMES:=$(NAMES) treeep
+endif
+ifdef WITH_JTREE
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_JTREE
+  NAMES:=$(NAMES) jtree
+endif
+ifdef WITH_MR
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_MR
+  NAMES:=$(NAMES) mr
+endif
+ifdef WITH_GIBBS
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_GIBBS
+  NAMES:=$(NAMES) gibbs
+endif
+ifdef WITH_CBP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_CBP
+  NAMES:=$(NAMES) bbp cbp bp_dual
+endif
+ifdef WITH_DECMAP
+  WITHFLAGS:=$(WITHFLAGS) -DDAI_WITH_DECMAP
+  NAMES:=$(NAMES) decmap
+endif
 
-# Compile using GNU C++ Compiler
-CC=g++
-# Output filename option
-CCO=-o
+# Define standard libDAI header dependencies, source file names and object file names
+HEADERS=$(foreach name,graph dag bipgraph index var factor varset smallset prob daialg properties alldai enum exceptions util,$(INC)/$(name).h)
+SOURCES:=$(foreach name,$(NAMES),$(SRC)/$(name).cpp)
+OBJECTS:=$(foreach name,$(NAMES),$(name)$(OE))
 
-# Flags for the C++ compiler
-CCFLAGS=-O3 -Wno-deprecated -Wall -W -Wextra -fpic -Iinclude -Llib
-CCDEBUGFLAGS=-g -DDAI_DEBUG
+# Setup final command for C++ compiler
+ifneq ($(OS),WINDOWS)
+  CC:=$(CC) $(CCINC) $(CCFLAGS) $(WITHFLAGS) $(CCLIB)
+else
+  CC:=$(CC) $(CCINC) $(CCFLAGS) $(WITHFLAGS)
+  LIBS:=$(LIBS) $(CCLIB)
+endif
 
-# Build targets
-TARGETS=tests utils $(LIB)/libdai$(LE) examples testregression doc
+# Setup final command for MEX
+ifdef NEW_MATLAB
+  MEXFLAGS:=$(MEXFLAGS) -largeArrayDims
+else
+  MEXFLAGS:=$(MEXFLAGS) -DSMALLMEM
+endif
+MEX:=$(MEX) $(MEXINC) $(MEXFLAGS) $(WITHFLAGS) $(MEXLIB)
 
-ifdef WITH_MATLAB
-       # Replace the following by the directory where Matlab has been installed
-       MATLABDIR=/agbs/share/sw/matlab
-       MEX=$(MATLABDIR)/bin/mex
-       MEXFLAGS=-Iinclude CXX\#$(CC) CXXFLAGS\#'-O3 -Wno-deprecated -Wall -W -Wextra -fpic'
+
+# META TARGETS
+###############
+
+all : $(TARGETS)
+       @echo libDAI built successfully!
+
+examples : examples/example$(EE) examples/example_bipgraph$(EE) examples/example_varset$(EE) examples/example_permute$(EE) examples/example_sprinkler$(EE) examples/example_sprinkler_gibbs$(EE) examples/example_sprinkler_em$(EE) examples/example_imagesegmentation$(EE)
+
+matlabs : matlab/dai$(ME) matlab/dai_readfg$(ME) matlab/dai_writefg$(ME) matlab/dai_potstrength$(ME)
+
+unittests : tests/unit/var_test$(EE) tests/unit/smallset_test$(EE) tests/unit/varset_test$(EE) tests/unit/graph_test$(EE) tests/unit/dag_test$(EE) tests/unit/bipgraph_test$(EE) tests/unit/weightedgraph_test$(EE) tests/unit/enum_test$(EE) tests/unit/enum_test$(EE) tests/unit/util_test$(EE) tests/unit/exceptions_test$(EE) tests/unit/properties_test$(EE) tests/unit/index_test$(EE) tests/unit/prob_test$(EE) tests/unit/factor_test$(EE) tests/unit/factorgraph_test$(EE) tests/unit/clustergraph_test$(EE) tests/unit/regiongraph_test$(EE) tests/unit/daialg_test$(EE) tests/unit/alldai_test$(EE)
+       echo Running unit tests...
+       tests/unit/var_test$(EE)
+       tests/unit/smallset_test$(EE)
+       tests/unit/varset_test$(EE)
+       tests/unit/graph_test$(EE)
+       tests/unit/dag_test$(EE)
+       tests/unit/bipgraph_test$(EE)
+       tests/unit/weightedgraph_test$(EE)
+       tests/unit/enum_test$(EE)
+       tests/unit/util_test$(EE)
+       tests/unit/exceptions_test$(EE)
+       tests/unit/properties_test$(EE)
+       tests/unit/index_test$(EE)
+       tests/unit/prob_test$(EE)
+       tests/unit/factor_test$(EE)
+       tests/unit/factorgraph_test$(EE)
+       tests/unit/clustergraph_test$(EE)
+       tests/unit/regiongraph_test$(EE)
+       tests/unit/daialg_test$(EE)
+       tests/unit/alldai_test$(EE)
+
+tests : tests/testdai$(EE) tests/testem/testem$(EE) tests/testbbp$(EE) $(unittests)
+
+utils : utils/createfg$(EE) utils/fg2dot$(EE) utils/fginfo$(EE) utils/uai2fg$(EE)
+
+lib: $(LIB)/libdai$(LE)
+
+
+# OBJECTS
+##########
+
+%$(OE) : $(SRC)/%.cpp $(INC)/%.h $(HEADERS)
+       $(CC) -c $<
+
+bbp$(OE) : $(SRC)/bbp.cpp $(INC)/bbp.h $(INC)/bp_dual.h $(HEADERS)
+       $(CC) -c $<
+
+cbp$(OE) : $(SRC)/cbp.cpp $(INC)/cbp.h $(INC)/bbp.h $(INC)/bp_dual.h $(HEADERS)
+       $(CC) -c $<
+
+hak$(OE) : $(SRC)/hak.cpp $(INC)/hak.h $(HEADERS) $(INC)/regiongraph.h
+       $(CC) -c $<
+
+jtree$(OE) : $(SRC)/jtree.cpp $(INC)/jtree.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h
+       $(CC) -c $<
+
+treeep$(OE) : $(SRC)/treeep.cpp $(INC)/treeep.h $(HEADERS) $(INC)/weightedgraph.h $(INC)/clustergraph.h $(INC)/regiongraph.h $(INC)/jtree.h
+       $(CC) -c $<
+
+emalg$(OE) : $(SRC)/emalg.cpp $(INC)/emalg.h $(INC)/evidence.h $(HEADERS)
+       $(CC) -c $<
+
+decmap$(OE) : $(SRC)/decmap.cpp $(INC)/decmap.h $(HEADERS)
+       $(CC) -c $<
+
+
+# EXAMPLES
+###########
+
+examples/%$(EE) : examples/%.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS)
+
+examples/example_sprinkler_gibbs$(EE) : examples/example_sprinkler_gibbs.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ifdef WITH_GIBBS
+       $(CC) $(CCO)$@ $< $(LIBS)
+else
+       @echo Skipping $@
+endif
+
+examples/example_imagesegmentation$(EE) : examples/example_imagesegmentation.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       -$(CC) $(CIMGINC) $(CCO)$@ $< $(LIBS) $(CIMGLIBS)
+
+
+# UNIT TESTS
+#############
+
+tests/unit/%$(EE) : tests/unit/%.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ifneq ($(OS),WINDOWS)
+       $(CC) -DBOOST_TEST_DYN_LINK $(CCO)$@ $< $(LIBS) $(BOOSTLIBS_UTF)
+else
+       $(CC) $(CCO)$@ $< $(LIBS) $(BOOSTLIBS_UTF) /SUBSYSTEM:CONSOLE
+endif
+
+
+# TESTS
+########
+
+tests/testdai$(EE) : tests/testdai.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS) $(BOOSTLIBS_PO)
+tests/testem/testem$(EE) : tests/testem/testem.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS) $(BOOSTLIBS_PO)
+tests/testbbp$(EE) : tests/testbbp.cpp $(HEADERS) $(LIB)/libdai$(LE)
+ifdef WITH_CBP
+       $(CC) $(CCO)$@ $< $(LIBS)
+else
+       @echo Skipping $@
 endif
 
 
-include Makefile.shared
+# MATLAB INTERFACE
+###################
+
+matlab/dai$(ME) : $(SRC)/matlab/dai.cpp $(HEADERS) $(SOURCES) $(SRC)/matlab/matlab.cpp
+       $(MEX) -output $@ $< $(SRC)/matlab/matlab.cpp $(SOURCES)
+
+matlab/dai_readfg$(ME) : $(SRC)/matlab/dai_readfg.cpp $(HEADERS) $(SRC)/matlab/matlab.cpp $(SRC)/factorgraph.cpp $(SRC)/exceptions.cpp $(SRC)/bipgraph.cpp $(SRC)/graph.cpp $(SRC)/factor.cpp $(SRC)/util.cpp
+       $(MEX) -output $@ $< $(SRC)/matlab/matlab.cpp $(SRC)/factorgraph.cpp $(SRC)/exceptions.cpp $(SRC)/bipgraph.cpp $(SRC)/graph.cpp $(SRC)/factor.cpp $(SRC)/util.cpp
+
+matlab/dai_writefg$(ME) : $(SRC)/matlab/dai_writefg.cpp $(HEADERS) $(SRC)/matlab/matlab.cpp $(SRC)/factorgraph.cpp $(SRC)/exceptions.cpp $(SRC)/bipgraph.cpp $(SRC)/graph.cpp $(SRC)/factor.cpp $(SRC)/util.cpp
+       $(MEX) -output $@ $< $(SRC)/matlab/matlab.cpp $(SRC)/factorgraph.cpp $(SRC)/exceptions.cpp $(SRC)/bipgraph.cpp $(SRC)/graph.cpp $(SRC)/factor.cpp $(SRC)/util.cpp
+
+matlab/dai_potstrength$(ME) : $(SRC)/matlab/dai_potstrength.cpp $(HEADERS) $(SRC)/matlab/matlab.cpp $(SRC)/exceptions.cpp
+       $(MEX) -output $@ $< $(SRC)/matlab/matlab.cpp $(SRC)/exceptions.cpp
+
 
+# UTILS
+########
 
-$(LIB)/libdai$(LE) : bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)
+utils/createfg$(EE) : utils/createfg.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS) $(BOOSTLIBS_PO)
+
+utils/fg2dot$(EE) : utils/fg2dot.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS)
+
+utils/fginfo$(EE) : utils/fginfo.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS)
+
+utils/uai2fg$(EE) : utils/uai2fg.cpp $(HEADERS) $(LIB)/libdai$(LE)
+       $(CC) $(CCO)$@ $< $(LIBS)
+
+
+# LIBRARY
+##########
+
+ifneq ($(OS),WINDOWS)
+$(LIB)/libdai$(LE) : $(OBJECTS)
        -mkdir -p lib
-       ar rcus $(LIB)/libdai$(LE) bipgraph$(OE) daialg$(OE) alldai$(OE) clustergraph$(OE) factorgraph$(OE) properties$(OE) regiongraph$(OE) util$(OE) weightedgraph$(OE) exceptions$(OE) $(OBJECTS)
+       ar rcus $(LIB)/libdai$(LE) $(OBJECTS)
+else
+$(LIB)/libdai$(LE) : $(OBJECTS)
+       -mkdir lib
+       lib /out:$(LIB)/libdai$(LE) $(OBJECTS)
+endif
+
+
+# REGRESSION TESTS
+###################
 
 testregression : tests/testdai$(EE)
        @echo Starting regression test...this can take a minute or so!
+ifneq ($(OS),WINDOWS)
        cd tests && ./testregression && cd ..
+else
+       cd tests && testregression.bat && cd ..
+endif
+
+testem : tests/testem/testem$(EE)
+       @echo Starting EM tests
+ifneq ($(OS),WINDOWS)
+       cd tests/testem && ./runtests && cd ../..
+else
+       cd tests\testem && runtests && cd ..\..
+endif
+
+
+# DOCUMENTATION
+################
 
 doc : $(INC)/*.h $(SRC)/*.cpp examples/*.cpp doxygen.conf
        doxygen doxygen.conf
 
+README : doc scripts/makeREADME
+       DAI_VERSION=$(DAI_VERSION) DAI_DATE=$(DAI_DATE) scripts/makeREADME
+
+TAGS :
+       etags src/*.cpp include/dai/*.h tests/*.cpp utils/*.cpp
+       ctags src/*.cpp include/dai/*.h tests/*.cpp utils/*.cpp
+
+
+# CLEAN
+########
+
 .PHONY : clean
+ifneq ($(OS),WINDOWS)
 clean :
-       -rm *$(OE)
+       -rm $(OBJECTS)
        -rm matlab/*$(ME)
-       -rm examples/example$(EE) examples/example_bipgraph$(EE) examples/example_varset$(EE)
-       -rm tests/testdai$(EE)
-       -rm utils/fg2dot$(EE) utils/createfg$(EE) utils/fginfo$(EE)
+       -rm examples/example$(EE) examples/example_bipgraph$(EE) examples/example_varset$(EE) examples/example_permute$(EE) examples/example_sprinkler$(EE) examples/example_sprinkler_gibbs$(EE) examples/example_sprinkler_em$(EE) examples/example_imagesegmentation$(EE)
+       -rm tests/testdai$(EE) tests/testem/testem$(EE) tests/testbbp$(EE)
+       -rm tests/unit/var_test$(EE) tests/unit/smallset_test$(EE) tests/unit/varset_test$(EE) tests/unit/graph_test$(EE) tests/unit/dag_test$(EE) tests/unit/bipgraph_test$(EE) tests/unit/weightedgraph_test$(EE) tests/unit/enum_test$(EE) tests/unit/util_test$(EE) tests/unit/exceptions_test$(EE) tests/unit/properties_test$(EE) tests/unit/index_test$(EE) tests/unit/prob_test$(EE) tests/unit/factor_test$(EE) tests/unit/factorgraph_test$(EE) tests/unit/clustergraph_test$(EE) tests/unit/regiongraph_test$(EE) tests/unit/daialg_test$(EE) tests/unit/alldai_test$(EE)
+       -rm factorgraph_test.fg alldai_test.aliases
+       -rm utils/fg2dot$(EE) utils/createfg$(EE) utils/fginfo$(EE) utils/uai2fg$(EE)
        -rm -R doc
        -rm -R lib
+else
+clean :
+       -del *.obj
+       -del *.ilk
+       -del *.pdb
+       -del matlab\*$(ME)
+       -del examples\*$(EE)
+       -del examples\*$(EE).manifest
+       -del examples\*.ilk
+       -del examples\*.pdb
+       -del tests\*$(EE)
+       -del tests\*$(EE).manifest
+       -del tests\*.pdb
+       -del tests\*.ilk
+       -del tests\testem\*$(EE)
+       -del tests\testem\*$(EE).manifest
+       -del tests\testem\*.pdb
+       -del tests\testem\*.ilk
+       -del utils\*$(EE)
+       -del utils\*$(EE).manifest
+       -del utils\*.pdb
+       -del utils\*.ilk
+       -del tests\unit\*_test$(EE)
+       -del tests\unit\*_test$(EE).manifest
+       -del tests\unit\*_test.pdb
+       -del tests\unit\*_test.ilk
+       -del factorgraph_test.fg
+       -del alldai_test.aliases
+       -del $(LIB)\libdai$(LE)
+       -rmdir lib
+endif