#------------------------------------------------------
# Maximum likelihood estimation 
# of migration rate  and effectice population size
# using importance sampling of correlated genealogies
# a Metropolis-Hastings Monte Carlo algorithm        
# n-population version
# 
# In case you want to change something
# edit Makefile.in and run configure again AND
# notify me, so that I can change the configure script.
# 
# this makefile was produced with configure:
# Makefile.in -> configure -> Makefile
#
# $Id: Makefile.in 756 2007-06-27 02:45:26Z beerli $ 
#------------------------------------------------------                 
# Peter Beerli 2002-2003, Seattle
# Peter Beerli 2004-2007 Tallahassee
# beerli@scs.fsu.edu
#-----------------------------------------------------

.SUFFIXES:
.SUFFIXES: .o .c .cpp .h
#######################################################
MIGRATEVERSION    = 2.3
MIGRATESUBVERSION = 
#######################################################
prefix            = 
exec_prefix       = ${prefix}
INSTALLDIR        = ${exec_prefix}/bin #/usr/local/bin
MANPAGEDIR        = ${prefix}/man/man1 #/usr/local/man/man1
# Source of manpage migrate.1 -----------------------
# not up to date
MANPAGE           = migrate.1

#----------------------------------------------------
# programs specified through configure
CC                = cc
INSTALL           = /usr/bin/install -c -o root -g wheel
TAR               = tar
MPICC             = mpicc
#----------------------------------------------------
# compile flags
# outcommented ones are for specific systems or then
# use different modules in the program
# current default is using Mersenne-Twister as random number generator
CPUTYPE           = i386
OSTYPE            = gnu
# use Mersenne twister random number generator
CFLAGS_MT         = -DMERSENNE_TWISTER -DMEXP=19937
MT_FILES          = SFMT.c
# to optimize Mersenne-Twister random number generator use ./configure --enable-sse2 on INTEL
# machines or ./configure --enable-altivec on PowerPC architectures, this will then set the option 
# correctly
HARDWARECFLAGS    = 
COMMONFLAGS       = -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
#
# combine the common flags with the version number and subversion number
COMMONVFLAGS      =  $(COMMONFLAGS)  -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" 
CFLAGS            =  $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\" 
# IBM xlc compiler
# CC              = xlc
# CFLAGS_XLC      = -O3 -Q -qunroll -qalloca -qhot -qipa -qthreaded 
# CFLAGS          = $(CFLAGS_XLC) -D$(CPU) $(COMMONVFLAGS)  -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\"
# INTEL icc compiler
# CC = icc
# CFLAGS          = -fast $(COMMONVFLAGS) -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\\\"\"
#
# flags that are used when multi-threading 
THREADCFLAGS      = -D_REENTRANT -DPTHREADS
# not used currently should replace the fixed random number generator above with configure
#RANDOMCFLAG       = @RANDOMFLAG@
# need to compile the haru pdf library
PRETTYCFLAGS      = -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY
#
# DEBUG FLAGS --- you should not need to use those
# if you have not gcc and want to debug, you need to know
# how to change the cflags yourself: -Wall is not known to all compilers
# on SGI or IBM AIX machines remove the -Wall tag
DEBUGCFLAGS       = -g -Wall  -DDEBUG $(COMMONFLAGS) -DMIGRATEVERSION=\"\\\"debug $(MIGRATEVERSION)\\\"\"
CHECKERCFLAGS     = -g -Wall  $(COMMONFLAGS) -DMIGRATEVERSION=\"\\\"checker $(MIGRATEVERSION)\"\\\"
DMALLOCCFLAGS     = -g -DDMALLOC_FUNC_CHECK -Wall -DHIGHBITS -DHAVE_CONFIG_H  -DMIGRATEVERSION=\"\\\"$(MIGRATEVERSION)\"\\\"
EFENCEFLAGS       = -g -Wall -DHIGHBITS -DHAVE_CONFIG_H -DMIGRATEVERSION=\"\\\"efence $(MIGRATEVERSION)\"\\\"
MEMDEBUGFLAGS     = -g -Wall -DHIGHBITS -DHAVE_CONFIG_H -DMEMEDEBUG
#
# Library flags
LIBS              = -lm 
LDFLAGS           = 
PDFLIB            = -Lharu -lharu -lz -lstdc++ 
OTHERLIBS         =   -pthread   
DMALLOCLIBS       = -lm -ldmalloc
EFENCELIBS        = -lm -lefence
MEMDEBUGLIBS      = -lm -lmemdb
WINLIBS           =  -luser32 -Wl,--subsystem,console 
#----------------------------------------------------
#
NAME              = migrate-n
DMALLOCNAME       = mig.dmalloc
EFENCENAME        = mig.efence
MEMDEBUGNAME      = mig.memdebug
WINNAME           = migrate.exe
CFILES            = aic.c altivec.c bayes.c broyden.c combroyden2.c data.c gammalike.c fst.c \
heating.c inthp.c joint-chains.c laguerre.c lrt.c main.c migrate_mpi.c\
mcmc1.c mcmc2.c menu.c migevents.c options.c profile.c random.c reporter.c   \
spline.c tools.c tree.c sequence.c sighandler.c slice.c sort.c uep.c world.c pretty.c skyline.c watterson.c

CPLUSFILES        = pretty-win32.cpp
 
HFILES            = aic.h altivec.h bayes.h broyden.h combroyden.h data.h definitions.h \
fst.h gammalike.h heating.h integrate.h \
joint-chains.h laguerre.h lrt.h\
mcmc.h mcmc2.h menu.h migration.h migevents.h migrate_mpi.h options.h \
profile.h random.h sequence.h sighandler.h slice.h sort.h \
tools.h tree.h world.h spline.h reporter.h uep.h pretty.h skyline.h watterson.h

SOURCEFILES       = $(CFILES)
ALLSOURCES        = $(CFILES) $(HFILES) $(CPLUSFILES)
CONFIGUREEXEC     = configure configure.in config.guess\
 config.sub config.status install-sh
ADDITIONALFILES   = Makefile.in  conf.h.in conf.h INSTALL $(MANPAGE) $(CONFIGUREEXEC) jamfile
DOCUMENTATION     = README HISTORY HOWTO-PARALLEL migrate.html
EXAMPLEDIR        = example
GRAPHICSDIR       = graphics
TESTSUITE         = testsuite
CONTRIBDIR        = contribution
HARUDIR           = haru
MTDIR             = SFMT-src-1.2
OFILES            = $(CFILES:.c=.o) $(CPLUSFILES:.cpp=.o) $(MT_FILES:.c=.o)
INSTALL_DEPENDS   = $(INSTALLDIR) all 
PRODUCT_DEPENDS   = $(OFILES)

.c.o:
	$(CC) $(CFLAGS) -c $*.c 
.cpp.o:
	$(CC) $(CFLAGS) -c $*.cpp 
#-o $*.o
#
#
#
intro::
	@echo "-----------------------------------------------------"
	@echo "Migrate $(MIGRATEVERSION)"
	@echo "please **read** the documentation"
	@echo "this Makefile will produce an executable: migrate-n"
	@echo "I am interested in getting email about any problems."
	@echo "Please send all compile warning or error messages"
	@echo "   beerli@csit.fsu.edu [Peter Beerli]"
	@echo "----------------------------------------------------"
	$(MAKE) all

all::   
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)"  "LIBS = $(LIBS)";\
	strip $(NAME)

debug::   
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)"

pretty:: haru   
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 

thread-pretty:: haru   
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)" "LDFLAGS = $(LDFLAGS) -fexceptions" 

pretty-debug:: haru   
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) -fexceptions" 
 
dox:
	cat migrate.dox.in | sed 's/MIGRATEVERSION/$(MIGRATEVERSION)/g' | sed 's/MIGRATESUBVERSION/$(MIGRATESUBVERSION)/g' > migrate.dox
	doxygen migrate.dox

thread::   
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)";\
	strip $(NAME) 

mpis-debug::   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(DEBUGCFLAGS) -DHAVE_DEBUGMPI -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT"  "LIBS = $(LIBS)"


mpis::   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT"  "LIBS = $(LIBS)"
 
mpis-thread::   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(LIBS)"

mpis-thread-pretty:: haru   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)"

mpis-pretty:: haru   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(CFLAGS) $(PRETTYCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(PDFLIB) $(LIBS)"

mpis-pretty-debug:: haru   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(DEBUGCFLAGS) $(PRETTYCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(PDFLIB) $(LIBS)"


mpis-thread-pretty-debug:: haru   
	$(MAKE) $(NAME) "CC=$(MPICC)" "CFLAGS = $(DEBUGCFLAGS) $(PRETTYCFLAGS) $(THREADCFLAGS) -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = $(OTHERLIBS) $(PDFLIB) $(LIBS)"


# experimental development
longsum:: 
	@echo "!!!!!!!!!!!!!! DO NOT USE THIS, DOES NOT WORK CORRECTLY YET !!!!!!"
#	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) -DLONGSUM"
quasi-cud:: haru  
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DCUD" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 
quasi-korobov:: haru  
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DKOROBOV" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasi-halton:: haru  
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DHALTON" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasi-weyl:: haru  
	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DWEYL " "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasir-cud::   haru
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DCUD" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasir-korobov::   haru
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DKOROBOV" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasir-halton::   haru
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DHALTON" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

quasir-weyl::   haru
	$(MAKE) $(NAME) "CFLAGS = $(CFLAGS)  $(PRETTYCFLAGS) -DQUASIRANDOM -DWEYL " "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS = -fexceptions" 

altivec::  
	@echo "!!!!!!!!!!!!!! DO NOT USE THIS, DOES NOT WORK CORRECTLY YET !!!!!!"
#       $(MAKE) $(NAME) "CFLAGS = -faltivec -DALTIVEC $(CFLAGS) $(THREADCFLAGS)" "LIBS = $(OTHERLIBS) $(LIBS)";
#        strip $(NAME) ;


win::   
	build-mig windows

efence::   
	$(MAKE) $(EFENCENAME) "CFLAGS = $(EFENCEFLAGS)"

memdebug::   
	$(MAKE) $(MEMDEBUGNAME) "CFLAGS = $(MEMDEBUGFLAGS)"

checker::   
	$(MAKE) $(NAME) "CC=checkergcc" "CFLAGS = $(CHECKERCFLAGS)"

dmalloc::
	$(MAKE) $(DMALLOCNAME) "CFLAGS = $(DMALLOCCFLAGS)"


install:: $(INSTALL_DEPENDS)
	$(INSTALL) $(IFLAGS) $(NAME) $(INSTALLDIR)
	$(INSTALL) $(IFLAGS) $(MANPAGE) $(MANPAGEDIR)

clean::     
	make haru-clean  
	-/bin/rm -rf  $(GARBAGE) *.o gmon.out

distclean::      
	make haru-clean  
	/bin/rm -rf  $(GARBAGE) *.o conf.h gmon.out config.cache \
        config.status Makefile $(NAME) *~ *.log migrate-n \
        mig.efence mig.dmalloc;


zip::
	@echo '  $(TAR) and gzip to ../migrate-$(MIGRATEVERSION).zip.tar.gz'
	-/bin/rm -i ../migrate-$(MIGRATEVERSION).zip.tar.gz 
	$(TAR) cf -  $(ALLSOURCES) $(ADDITIONALFILES) $(GRAPHICSDIR)	\
	$(EXAMPLEDIR) $(CONTRIBDIR) $(DOCUMENTATION) |				\
        gzip > ../migrate-$(MIGRATEVERSION).zip.tar.gz

fix::  
	-/bin/chmod +x $(CONFIGUREEXEC) 	

haru::
	(cd ./haru ; $(MAKE) -f makefile.osx "CC=$(CC)" "CPP=$(CC)")

haru-clean::
	(cd ./haru ; $(MAKE) -f makefile.osx clean)

distrib::
	$(MAKE) srcdistrib;
	$(MAKE) bindistrib;

srcdistrib::
	@echo '  Creating Distribution version $(MIGRATEVERSION)'
	@make haru-clean
	-/bin/chmod +x $(CONFIGUREEXEC) 
	-/bin/rm -i ../migrate-$(MIGRATEVERSION).tar.gz
	-/bin/rm -rf /tmp/migrate-tmp
	-/bin/mkdir -p /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)/src/$(TESTSUITE)  
	-$(TAR) --exclude .svn -cf -  $(ALLSOURCES) $(ADDITIONALFILES) $(MTDIR) $(HARUDIR) copy_mt_to_src | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)/src ; $(TAR) xf -)
	-$(TAR) --exclude .svn -cf -  $(GRAPHICSDIR) $(EXAMPLEDIR) $(CONTRIBDIR) $(DOCUMENTATION) | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION) ; $(TAR) xf -)
	-$(TAR) --exclude .svn -cf -  $(TESTSUITE)/infile* $(TESTSUITE)/parmfile* $(TESTSUITE)/runtest | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)/src/$(TESTSUITE) ; $(TAR) xf -)
	-(cd /tmp/migrate-tmp ; $(TAR) cf - migrate-$(MIGRATEVERSION) | \
	gzip) > ../migrate-$(MIGRATEVERSION).src.tar.gz

winzip::
	@echo '  Creating Windows Distribution version $(MIGRATEVERSION)'
	-/bin/rm -rf /tmp/migrate-tmp
	-/bin/mkdir -p /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)
	-$(TAR) --exclude .svn -cf -  $(WINNAME) $(GRAPHICSDIR) $(EXAMPLEDIR) $(CONTRIBDIR) $(DOCUMENTATION) | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION) ; $(TAR) xf -)
	-(cd /tmp/migrate-tmp ; zip -r migrate-$(MIGRATEVERSION).windows.zip migrate-$(MIGRATEVERSION))
	-cp /tmp/migrate-tmp/migrate-$(MIGRATEVERSION).windows.zip .. 

bindistrib:: $(NAME)
	@make bin-local-distrib "OSTYPE=$(OSTYPE)" "CPUTYPE=$(CPUTYPE)";
	#@make bin-local-distrib "OSTYPE=`uname -s | tr " " "-" `" "CPUTYPE=`uname -m  | tr " " "-" `";

bin-local-distrib:
	@echo '  Creating binary $(OSTYPE)-$(CPUTYPE)-distribution version $(MIGRATEVERSION)'
	-/bin/chmod +x $(CONFIGUREEXEC) 
	-/bin/rm -i ../migrate-$(MIGRATEVERSION).$(OSTYPE)-$(CPUTYPE).tar.gz
	-/bin/rm -rf /tmp/migrate-tmp
	-/bin/mkdir -p /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)/src  
	-$(TAR) cf -  $(ALLSOURCES) $(ADDITIONALFILES) $(HARUDIR) | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION)/src ; $(TAR) xf -)
	-$(TAR) cf - $(NAME) $(GRAPHICSDIR) $(EXAMPLEDIR) $(CONTRIBDIR) $(DOCUMENTATION) | \
	  (cd /tmp/migrate-tmp/migrate-$(MIGRATEVERSION) ; $(TAR) xf -)
	-(cd /tmp/migrate-tmp ; $(TAR) cf - migrate-$(MIGRATEVERSION) | \
	gzip) > ../migrate-$(MIGRATEVERSION).$(OSTYPE)-$(CPUTYPE).tar.gz


help::
	@echo 'Makefile targets, the one with the [*] are suggested targets:'
	@echo '  make        (creates the basic executable)'
	@echo '  make pretty (creates the basic executable with added PDF support) [*]'
	@echo '  make thread (allows parallel processing of heated chains on SMP)'
	@echo '  make thread-pretty (SMP + PDF support: USE THIS ON DUAL_CORE machines)[*]'
#	@echo '  make mpi    (fastnet - assumes you use LAM/MPI, and talk to me)'
#	@echo '  make mpi-thread (fastnet - assumes you use LAM/MPI and pthreads, and talk to me)'
	@echo '  make mpis-pretty (slownet - assumes you use an MPI library [LAM, openmpi, or mpich2])'
#	@echo '  make mpis-thread (slownet - assumes you use MPI-lib and pthreads)'
#	@echo '  make mpis-thread-pretty (like above but with PDF Bayes printing)'
	@echo '  make clean (removes all *.o files but not the Makefile)'
#	@echo '  make distclean (removes all created files)'
	@echo '  make install (installs the executables and man page)'
	@echo '  make pretty-debug (there are more options like this, but check out the Makefile)'

#----------------------------------------------------------
#
$(OFILE_DIR) $(INSTALLDIR):
	mkdir -p $@;

SRCROOT:
	@if [ -n "${$@}" ]; then exit 0; \
	else echo Must define $@; exit 1; fi

$(NAME): $(PRODUCT_DEPENDS)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(LIBS) ;

$(WINNAME): $(PRODUCT_DEPENDS)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(OTHERLIBS) $(WINLIBS) ;


$(EFENCENAME): $(PRODUCT_DEPENDS)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(EFENCELIBS) $(LIBS) ;


$(MEMDEBUGNAME): $(PRODUCT_DEPENDS)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(MEMDEBUGLIBS) $(LIBS) ;


$(DMALLOCNAME): $(PRODUCT_DEPENDS)
	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(OFILES) $(DMALLOCLIBS) $(LIBS) ;


#----------------------------------------------------------------
# test section
# 
#
#
test: pretty
	mkdir test;
	cd test; \
	cp ../example/parmfile* . ;\
	cp ../example/infile.msat . ;\
	../migrate-n parmfile.testml ;\
	../migrate-n parmfile.testbayes ;\
srctest:
	mkdir test;
	make srcdistrib; #@
	mv ../migrate-$(MIGRATEVERSION).src.tar.gz test/ ;
	cd test; \
	tar xzvf migrate-$(MIGRATEVERSION).src.tar.gz ;\
	cd migrate-$(MIGRATEVERSION)/src ;\
	configure ;\
	make pretty;\
	cd ../.. ;\
	cp ../example/parmfile* . ;\
	cp ../example/infile.msat . ;\
	migrate-$(MIGRATEVERSION)/src/migrate-n parmfile.testml ;\
	migrate-$(MIGRATEVERSION)/src/migrate-n parmfile.testbayes ;\
	cd migrate-$(MIGRATEVERSION)/src ;\
	make clean ;\
	make mpis-thread-pretty ;\
	cd ../.. ;\
	lamboot ;\
	mpirun -np 5 migrate-n parmfile.testml ;\
	mpirun -np 5 migrate-n parmfile.testbayes ; 

#
#
#
#
#----------------------------------------------------------------