makefile.linux

fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memo

#
#     Makefile for serial, PVM and MPI versions of fastDNAml_1_2_2.c
#     Makefile for Linux machines.
#


#*******************************************************************************

# C compilers
#CC         = /usr/local/bin/gcc #Pentium Group
 CC         = /usr/bin/gcc #Gnu
 CCOPT      = -O2
#CCOPT      = -g

# MPI settings
#MPI_ROOT   =
 MPI_ARCH   = LINUX
 MPI_DEVICE = ch_p4
 MPI_INCDIR = -I$(MPI_ROOT)/include
#MPI_INCDIR =   
#MPI_LIBDIR = -L$(MPI_ROOT)/lib/$(MPI_ARCH)/$(MPI_DEVICE) #Gnu
 MPI_LIBDIR = -L$(MPI_ROOT)/lib/$(MPI_DEVICE) #Gnu
#MPI_LIBDIR = -L/usr/mpich/build/LINUX/ch_p4/lib #Portland Group
 MPI_CLIBS  = -lmpich #not needed with mpicc and mpif77
 MPICC      = $(CC)
#MPICC      = mpicc

# PVM settings
 PVM_ARCH   = LINUX
 PVM_ROOT   = /usr/local/pvm3
 PVM_INCDIR = -I$(PVM_ROOT)/include
 PVM_LIBDIR = -L$(PVM_ROOT)/lib/$(PVM_ARCH)
 PVM_CLIBS  = -lpvm3

#*******************************************************************************


 CFLAGS = $(CCOPT) $(MDEP_CFLAGS) $(USER_CFLAGS)
 LFLAGS = 

.SUFFIXES:      .o .c .h

.c.o:
	$(CC) $(CFLAGS) -c $*.c 


 DNAML_FLAGS = 
#DNAML_FLAGS = -DDEBUG
 MPI_LIB_PATH = $(MPI_LIBDIR)
 PVM_LIB_PATH = $(PVM_LIBDIR)

 MASTER_OBJ    = master.o m_fastDNAml.o send_tree.o
 WORKER_OBJ    = worker.o w_fastDNAml.o
 COMMON_OBJ    = getinput.o wgts_categs.o best_tree.o print_tree.o \
  write_tree_string.o str_addElementLen.o str_readTreeLikelihood.o \
  readKeyValue.o str_util.o file_util.o addElementLen.o utilities.o


serial: fastDNAml
mpi: mpi_fastDNAml mpi_foreman mpi_worker mpi_dnaml_mon 
pvm: pvm_fastDNAml pvm_foreman pvm_worker pvm_dnaml_mon 


#  ------------------------   main programs   ----------------------------------
fastDNAml: s_master.o fastDNAml.o $(COMMON_OBJ) comm_seq.o
	$(CC) $(LFLAGS) -o fastDNAml s_master.o fastDNAml.o $(COMMON_OBJ) comm_seq.o -lm



mpi_fastDNAml: $(MASTER_OBJ) $(COMMON_OBJ) comm_mpi.o
	$(MPICC) $(LFLAGS) -o mpi_fastDNAml $(MASTER_OBJ) $(COMMON_OBJ) \
 comm_mpi.o $(MPI_LIB_PATH) $(MPI_CLIBS) -lm
	@ echo "";echo""

mpi_foreman: foreman.o comm_mpi.o str_readTreeLikelihood.o utilities.o readKeyValue.o
	$(MPICC) $(LFLAGS) -o mpi_foreman foreman.o comm_mpi.o str_readTreeLikelihood.o \
  utilities.o  readKeyValue.o $(MPI_LIB_PATH) $(MPI_CLIBS) $(ARCHLIB)
	@ echo "";echo""

mpi_worker: $(WORKER_OBJ) $(COMMON_OBJ) comm_mpi.o
	$(MPICC) $(LFLAGS) -o mpi_worker  $(WORKER_OBJ) $(COMMON_OBJ) \
 comm_mpi.o $(MPI_LIB_PATH) $(MPI_CLIBS) -lm
	@ echo "";echo ""

mpi_dnaml_mon: dnaml_mon.o comm_mpi.o utilities.o
	$(MPICC) $(LFLAGS) -o mpi_dnaml_mon dnaml_mon.o comm_mpi.o utilities.o \
  $(MPI_LIB_PATH) $(MPI_CLIBS)
	@ echo "";echo""



pvm_fastDNAml: $(MASTER_OBJ) $(COMMON_OBJ) comm_pvm.o
	$(CC) $(LFLAGS) -o pvm_fastDNAml $(MASTER_OBJ) $(COMMON_OBJ) \
 comm_pvm.o $(PVM_LIB_PATH) $(PVM_CLIBS) -lm
	@ echo "";echo""

pvm_foreman: foreman.o comm_pvm.o str_readTreeLikelihood.o utilities.o readKeyValue.o
	$(CC) $(LFLAGS) -o pvm_foreman foreman.o comm_pvm.o str_readTreeLikelihood.o \
  utilities.o  readKeyValue.o $(PVM_LIB_PATH) $(PVM_CLIBS) $(ARCHLIB)
	@ echo "";echo""

pvm_worker: $(WORKER_OBJ) $(COMMON_OBJ) comm_pvm.o
	$(CC) $(LFLAGS) -o pvm_worker  $(WORKER_OBJ) $(COMMON_OBJ) \
 comm_pvm.o $(PVM_LIB_PATH) $(PVM_CLIBS) -lm
	@ echo "";echo ""

pvm_dnaml_mon: dnaml_mon.o comm_pvm.o utilities.o
	$(CC) $(LFLAGS) -o pvm_dnaml_mon dnaml_mon.o comm_pvm.o utilities.o \
  $(PVM_LIB_PATH) $(PVM_CLIBS)
	@ echo "";echo""

cmon: cmon.o comm_pvm.o utilities.o
	$(CC) $(LFLAGS) -o cmon cmon.o comm_pvm.o utilities.o \
  $(PVM_LIB_PATH) $(PVM_CLIBS) -lncurses
	@ echo "";echo""



# ----------------------  .o files for main programs  --------------------------

dnaml_mon.o: dnaml_mon.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) dnaml_mon.c

cmon.o: cmon.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) $(PVM_INCDIR) cmon.c

foreman.o: foreman.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) foreman.c

master.o: master.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) master.c

s_master.o: master.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) master.c -o $@

worker.o: worker.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) worker.c

# ----------------------  .o files for all functions  --------------------------

fastDNAml.o: fastDNAml.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) -DSequential fastDNAml.c

m_fastDNAml.o: fastDNAml.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) -DMaster fastDNAml.c -o $@

w_fastDNAml.o: fastDNAml.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) -DSlave fastDNAml.c -o $@

getinput.o: getinput.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) getinput.c

str_util.o: str_util.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) str_util.c

wgts_categs.o: wgts_categs.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) wgts_categs.c

best_tree.o: best_tree.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) best_tree.c

write_tree_string.o: write_tree_string.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) write_tree_string.c

print_tree.o: print_tree.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) print_tree.c

send_tree.o: send_tree.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) send_tree.c

utilities.o: utilities.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) utilities.c

str_readTreeLikelihood.o: str_readTreeLikelihood.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) str_readTreeLikelihood.c

readKeyValue.o: readKeyValue.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) readKeyValue.c

str_addElementLen.o: str_addElementLen.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) str_addElementLen.c

file_util.o: file_util.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) file_util.c

addElementLen.o: addElementLen.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) addElementLen.c

comm_seq.o: comm_seq.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) comm_seq.c

comm_mpi.o: comm_mpi.c
	$(MPICC) $(CFLAGS) -c $(DNAML_FLAGS) $(MPI_INCDIR) comm_mpi.c

comm_pvm.o: comm_pvm.c
	$(CC) $(CFLAGS) -c $(DNAML_FLAGS) $(PVM_INCDIR) comm_pvm.c

# -----------------------------   .h dependencies     --------------------------

fastDNAml.o dnaml_mon.o foreman.o $(MASTER_OBJ) $(WORKER_OBJ) $(COMMON_OBJ) \
comm_seq.o comm_mpi.o comm_pvm.o: \
  fastDNAml_types.h

fastDNAml.o dnaml_mon.o foreman.o $(MASTER_OBJ) $(WORKER_OBJ) $(COMMON_OBJ) \
comm_seq.o comm_mpi.o comm_pvm.o: \
  fastDNAml_funcs.h

fastDNAml.o dnaml_mon.o foreman.o $(MASTER_OBJ) $(WORKER_OBJ) $(COMMON_OBJ) \
comm_seq.o comm_mpi.o comm_pvm.o: \
  fastDNAml_globals.h

foreman.o: \
  foreman.h

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

clean:
	rm -f *.o

realclean:
	rm -rf *.o fastDNAml \
 mpi_fastDNAml mpi_foreman mpi_worker mpi_dnaml_mon \
 pvm_fastDNAml pvm_foreman pvm_worker pvm_dnaml_mon