# Makefile August 2006 by Alexandros Stamatakis
# Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>

CC = gcc 

CFLAGS = -D_USE_PTHREADS  -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops  -D__AVX #-Wall -pedantic -Wunused-parameter -Wredundant-decls  -Wreturn-type  -Wswitch-default -Wunused-value -Wimplicit  -Wimplicit-function-declaration  -Wimplicit-int -Wimport  -Wunused  -Wunused-function  -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast  -Wmissing-declarations -Wmissing-prototypes  -Wnested-externs  -Wold-style-definition -Wstrict-prototypes  -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value  -Wunused-variable -Wformat  -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast


LIBRARIES = -lm -pthread 

RM = rm -f

objs    = axml.o  optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o   classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o  mem_alloc.o eigen.o  

all : raxmlHPC

GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h  #mem_alloc.h compiler.h  gcc.h  ll_asm.h  ll_list.h

raxmlHPC : $(objs)
	$(CC) -o raxmlHPC-PTHREADS-AVX $(objs) $(LIBRARIES) 

avxLikelihood.o : avxLikelihood.c $(GLOBAL_DEPS)
		$(CC) $(CFLAGS) -mavx -c -o avxLikelihood.o avxLikelihood.c

fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)
		   $(CC) $(CFLAGS) -mavx -c -o fastDNAparsimony.o fastDNAparsimony.c

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)
rmqs.o : rmqs.c $(GLOBAL_DEPS)
classify.o : classify.c $(GLOBAL_DEPS)
evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)
bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)
optimizeModel.o : optimizeModel.c $(GLOBAL_DEPS)
multiple.o : multiple.c $(GLOBAL_DEPS)
axml.o : axml.c $(GLOBAL_DEPS)
searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)
topologies.o : topologies.c $(GLOBAL_DEPS)
parsePartitions.o : parsePartitions.c $(GLOBAL_DEPS)
treeIO.o : treeIO.c $(GLOBAL_DEPS)
models.o : models.c $(GLOBAL_DEPS)
rapidBootstrap.o : rapidBootstrap.c $(GLOBAL_DEPS) 
evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)
evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)
newviewGenericSpecial.o : newviewGenericSpecial.c $(GLOBAL_DEPS)
makenewzGenericSpecial.o : makenewzGenericSpecial.c $(GLOBAL_DEPS)
fastSearch.o : fastSearch.c $(GLOBAL_DEPS)
leaveDropping.o : leaveDropping.c $(GLOBAL_DEPS)
ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS)
 mem_alloc.o eigen.o  : mem_alloc.c  $(GLOBAL_DEPS)

eigen.o : eigen.c $(GLOBAL_DEPS)
	$(CC) -c -o eigen.o eigen.c 
clean : 
	$(RM) *.o raxmlHPC-PTHREADS-AVX