# $ Id: $
#
# makefile for fasta3, fasta3_t Use Makefile.mpi for fasta36_mpi
#
# This file is designed for 64-bit Linux systems using an X86
# architecture with SSE2 extensions.  -D_LARGEFILE64_SOURCE and
# -DBIG_LIB64 require a 64-bit linux system.
# SSE2 extensions are used for ssearch35(_t)
#
# Use Makefile.linux32_sse2 for 32-bit linux x86
#

SHELL=/bin/bash

CC = gcc -g -O -msse2
LIB_DB=

#CC= gcc -pg -g -O -msse2 -ffast-math
#CC = gcc -g -DDEBUG -msse2
#CC=gcc -Wall -pedantic -ansi -g -msse2 -DDEBUG

# EBI uses the following with pgcc, -O3 does not work:
# CC= pgcc -O2 -pipe -mcpu=pentiumpro -march=pentiumpro -fomit-frame-pointer

# this file works for x86 LINUX

# standard options

CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64
# -I/usr/include/mysql -DMYSQL_DB
# -DSUPERFAMNUM -DSFCHAR="'|'" 

#
#(for mySQL databases)  (also requires change to Makefile36m.common or use of Makefile36m.common_mysql)
# run 'mysql_config' so find locations of mySQL files

LIB_M = -lm
# for mySQL databases
# LIB_M = -L/usr/lib64/mysql -lmysqlclient -lm

HFLAGS= -o
NFLAGS= -o

# for Linux
THR_SUBS = pthr_subs2
THR_LIBS = -lpthread
THR_CC =

BIN = ../bin
XDIR = /seqprg/bin
#XDIR = ~/bin/LINUX

# set up files for SSE2/Altivec acceleration
#
include ../make/Makefile.sse_alt

# SSE2 acceleration
#
DROPGSW_O = $(DROPGSW_SSE_O)
DROPLAL_O = $(DROPLAL_SSE_O)
DROPGNW_O = $(DROPGNW_SSE_O)
DROPLNW_O = $(DROPLNW_SSE_O)

# renamed (fasta36)  programs
include ../make/Makefile36m.common
# conventional (fasta3) names
# include ../make/Makefile.common
