makefile

he AutoMix package is a C program for Unix-like systems, implementing the automatic reversible jum

#############################################################################
# Make file for AutoMix sampler
# Written by: David Hastie, University of Bristol
# Last edited: 14/11/04
# 
# If you use the AutoMix sampler please reference the author and work
# as instructed on the website http://www.davidhastie.me.uk/AutoMix
# Initially this reference is likely to be the Ph.D. thesis that introduces 
# the AutoMix sampler. However, this will hopefully change to be a published
# paper in the not too distant future.
#
# All code has only been tested using the GNU compiler gcc.
#############################################################################

# The file contains commands for compiling programs using optimisation and 
# no debugging. Also included are commands for compiling with debugging.
# The executables and object files for the debugging are identified by 
# the final letter "d". For example, amtoy1.exe is the AutoMix sampler for the
# toy problem (see Ph.D. thesis section 5.5.1 for details) and amtoy1d.exe is 
# the version that allows debugging using a debugger such as gdb
# Flags and compiler names should be changed as necessary.

# C compiler
CC=gcc

# Normal optimised flags
CFLAGS=-O3 -o

# Debugging flags
CFLAGSD=-g -o

# Dependency flags
DEPFLAGS=-c

# Dependency flags with debugging
DEPFLAGSD=-g -c

# Libraries
LIB=-lm

# Compiler flags:
#       -g      -- Enable debugging through gdb
#       -O3     -- Optimise progs 
#       -Wall   -- Turn on all warnings
#       -lm     -- Use the maths library
#       -c      -- Compile flag for dependencies


###### Type "make all" to make all files in the folder #####

all: amtoy1 amtoy2 amcpt amcptrs amrb9 amddi amtoy1d amtoy2d amcptd amcptrsd amrb9d amddid

###### Normal (already debugged) progs ############

# Toy example 1
amtoy1: automix.c usertoy1.o sd.o gammafns.o sokal.o
	$(CC) $(CFLAGS) amtoy1 automix.c usertoy1.o sd.o gammafns.o sokal.o $(LIB)

# Toy example 2
amtoy2: automix.c usertoy2.o sd.o gammafns.o sokal.o
	$(CC) $(CFLAGS) amtoy2 automix.c usertoy2.o sd.o gammafns.o sokal.o $(LIB)

# Change point problem
amcpt: automix.c usercpt.o gammafns.o sd.o sokal.o
	$(CC) $(CFLAGS) amcpt automix.c usercpt.o sd.o gammafns.o sokal.o $(LIB)

# Rescaled change point problem
amcptrs: automix.c usercptrs.o gammafns.o sd.o sokal.o
	$(CC) $(CFLAGS) amcptrs automix.c usercptrs.o sd.o gammafns.o sokal.o $(LIB)

# Rb9 problem
amrb9: automix.c userrb9.o gammafns.o sd.o sokal.o 
	$(CC) $(CFLAGS) amrb9 automix.c userrb9.o sd.o gammafns.o sokal.o $(LIB)

# DDI Clinical trial problem
amddi: automix.c ddidata.h userddi.o gammafns.o sd.o sokal.o 
	$(CC) $(CFLAGS) amddi automix.c userddi.o sd.o gammafns.o sokal.o $(LIB)

### AutoMix dependencies (already debugged)

# Calculates loggamma function
gammafns.o: gammafns.c 
	$(CC) $(DEPFLAGS) gammafns.c

# Random number generator
sd.o: sd.c
	$(CC) $(DEPFLAGS) sd.c -DDOUB -DRETS

# Calculates autocorrelation using Sokal's method (Green and Han,92)
sokal.o: sokal.c
	$(CC) $(DEPFLAGS) sokal.c

### User supplied functions (already debugged)

# Toy example 1
usertoy1.o: usertoy1.c
	$(CC) $(DEPFLAGS) usertoy1.c

# Toy example 2
usertoy2.o: usertoy2.c
	$(CC) $(DEPFLAGS) usertoy2.c

# Change point problem
usercpt.o: usercpt.c
	$(CC) $(DEPFLAGS) usercpt.c

# Rescaled change point problem
usercptrs.o: usercptrs.c
	$(CC) $(DEPFLAGS) usercptrs.c

# Rb9 problem
userrb9.o: userrb9.c
	$(CC) $(DEPFLAGS) userrb9.c

# DDI clinical trial problem
userddi.o: userddi.c
	$(CC) $(DEPFLAGS) userddi.c
 
###### Progs to be debugged ############

# Toy example 1
amtoy1d: automix.c usertoy1d.o sdd.o gammafnsd.o sokald.o
	$(CC) $(CFLAGSD) amtoy1d automix.c usertoy1d.o sdd.o gammafnsd.o sokald.o $(LIB)

# Toy example 2
amtoy2d: automix.c usertoy2d.o sdd.o gammafnsd.o sokald.o
	$(CC) $(CFLAGSD) amtoy2d automix.c usertoy2d.o sdd.o gammafnsd.o sokald.o $(LIB)

# Change point problem
amcptd: automix.c usercptd.o gammafnsd.o sdd.o sokald.o
	$(CC) $(CFLAGSD) amcptd automix.c usercptd.o sdd.o gammafnsd.o sokald.o $(LIB)

# Rescaled change point problem
amcptrsd: automix.c usercptrsd.o gammafnsd.o sdd.o sokald.o
	$(CC) $(CFLAGSD) amcptrsd automix.c usercptrsd.o sdd.o gammafnsd.o sokald.o $(LIB)

# Rb9 problem
amrb9d: automix.c userrb9d.o gammafnsd.o sdd.o sokald.o 
	$(CC) $(CFLAGSD) amrb9d automix.c userrb9d.o sdd.o gammafnsd.o sokald.o $(LIB)

# DDI Clinical trial problem
amddid: automix.c ddidata.h userddid.o gammafnsd.o sdd.o sokald.o 
	$(CC) $(CFLAGSD) amddid automix.c userddid.o sdd.o gammafnsd.o sokald.o $(LIB)

# (Old) Toy problems compiled with automix2.c program, implementing
# adaptation through regeneration (automix2.c not included in distribution) 

### AutoMix dependencies (to be debugged)

# Calculates loggamma function
gammafnsd.o: gammafns.c
	cp gammafns.c gammafnsd.c 
	$(CC) $(DEPFLAGSD) gammafnsd.c
	rm gammafnsd.c

# Random number generator
sdd.o: sd.c
	cp sd.c sdd.c
	$(CC) $(DEPFLAGSD) sdd.c -DDOUB -DRETS
	rm sdd.c

# Calculates autocorrelation using Sokal's method (Green and Han,92)
sokald.o: sokal.c
	cp sokal.c sokald.c
	$(CC) $(DEPFLAGSD) sokald.c
	rm sokald.c

### User supplied functions (to be debugged)

# Toy example 1
usertoy1d.o: usertoy1.c
	cp usertoy1.c usertoy1d.c
	$(CC) $(DEPFLAGSD) usertoy1d.c
	rm usertoy1d.c

# Toy example 2
usertoy2d.o: usertoy2.c
	cp usertoy2.c usertoy2d.c
	$(CC) $(DEPFLAGSD) usertoy2d.c
	rm usertoy2d.c

# Change point problem
usercptd.o: usercpt.c
	cp usercpt.c usercptd.c
	$(CC) $(DEPFLAGSD) usercptd.c
	rm usercptd.c

# Rescaled change point problem
usercptrsd.o: usercptrs.c
	cp usercptrs.c usercptrsd.c
	$(CC) $(DEPFLAGSD) usercptrsd.c
	rm usercptrsd.c

# Rb9 problem
userrb9d.o: userrb9.c
	cp userrb9.c userrb9d.c
	$(CC) $(DEPFLAGSD) userrb9d.c
	rm userrb9d.c

# DDI clinical trial problem
userddid.o: userddi.c
	cp userddi.c userddid.c
	$(CC) $(DEPFLAGSD) userddid.c
	rm userddid.c

###### Type "make clean" to remove all executables and object files ####

clean:
	rm *.o
	rm am*