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Makefile
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Makefile
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#
# Makefile
#
# $Id: Makefile,v 1.3 2007/11/27 18:33:59 sheneman Exp $
#
#
#*****************************************************************************
#
# Copyright (c) 2004, Luke Sheneman
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# + Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# + Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
# + The names of its contributors may not be used to endorse or promote
# products derived from this software without specific prior
# written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
#*****************************************************************************
#
# AUTHOR:
#
# Luke Sheneman
# sheneman@cs.uidaho.edu
#
#*****************************************************************************
# Specify your compiler here
CC = gcc
#CC = cc
# Uncomment the following line to use the GNU getopt_long() instead
# of the built-in getopt_long()
#OPTFLAG = -DUSE_GNU
############################# THE CFLAGS ####################################
#
# NOTE: The optimal selection of compiler flags is important.
# Clearcut was written and developed on a Pentium 4 Linux
# Computer. As such, compiler optimization flags for
# recent versions of GCC on the Pentium 4 platform have been
# well tested and do make a significant impact on overall
# performance.
#
# Several alternative sets of compiler options are listed below.
# Customize the compiler flags (CFLAGS) to match your target system.
#
######################## ALL ARCHITECTURES ##################################
# DEFAULT GCC OPTIMIZATION CONFIGURATION (ALL ARCHITECTURES)
CFLAGS = -O3 -Wall -funroll-loops -fomit-frame-pointer
# BASIC OPTIMIZATION
#CFLAGS = -O3
######################## INTEL PENTIUM OPTIMIZATIONS ########################
# PENTIUM 4 w/SSE GCC OPTIMIZATIONS. REQUIRES GCC >= 3.2
#CFLAGS = -O3 -funroll-loops -march=pentium4 -mcpu=pentium4 -mfpmath=sse -ffast-math -momit-leaf-frame-pointer
# GENERIC i686 OPTIMIZATIONS GCC OPTIMIZATIONS
#CFLAGS = -O3 -funroll-loops -march=i686 -mcpu=i686 -fomit-frame-pointer
# GENERIC Intel C Compiler (ICC) Optimizations
#CFLAGS = -O3 -axP -xP -unroll100 -IPF_fp_fast -IPF_fltacc+ -ip
#############################################################################
######################### POWER PC OPTIMIZATIONS ############################
# MAC OS X POWER PC OPTIMIZATIONS
#CFLAGS = -O3 -funroll-loops -fomit-frame-pointer -mcpu=powerpc -mabi=altivec -mtune=powerpc -maltivec
#############################################################################
# DEBUGGING COMPILER FLAGS
#CFLAGS = -g3
INCDIRS = -I /usr/local/include
DEPEND = makedepend
# *** THE LINK FLAGS ***
#LINKFLAGS = -O3
LIBS = -lm
SRCS = clearcut.c dist.c dmat.c fasta.c cmdargs.c prng.c getopt_long.c
OBJS = clearcut.o dist.o dmat.o fasta.o cmdargs.o prng.o getopt_long.o
HDRS = clearcut.h dist.h dmat.h fasta.h cmdargs.h common.h dayhoff.h getopt_long.h prng.h
all: clearcut
clean:
rm -f *.o a.out *.a clearcut
.c.o: $(SRCS) $(HDRS)
$(CC) -c $(INCDIRS) $(CFLAGS) $(OPTFLAG) $(DEFS) $<
clearcut: $(OBJS) $(LIBOBJS)
$(CC) $(LINKFLAGS) -o $@ $(OBJS) $(LIBDIRS) $(LIBS)