Makefile Makeover -- Almost Complete, Want Feedback - c++

Question

I've been heavily refactoring my makefiles, with help from Beta, Paul R, and Sjoerd (thanks guys!).
Below is my STARTING product:
#Nice, wonderful makefile written by Jason
CC=g++
CFLAGS=-c -Wall
BASE_DIR:=.
SOURCE_DIR:=$(BASE_DIR)/source
BUILD_DIR:=$(BASE_DIR)/build
TEST_DIR:=$(BASE_DIR)/build/tests
MAKEFILE_DIR:=$(BASE_DIR)/makefiles
DATA_DIR:=$(BASE_DIR)/data
DATA_DIR_TESTS:=$(DATA_DIR)/tests
MOLECULE_UT_SOURCES := $(SOURCE_DIR)/molecule_test/main.cc \
$(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/molecule_manager.cpp \
$(SOURCE_DIR)/molecule_manager_main.h \
$(SOURCE_DIR)/molecule_manager_main.cpp \
$(SOURCE_DIR)/molecule_reader.h \
$(SOURCE_DIR)/molecule_reader.cpp \
$(SOURCE_DIR)/molecule_reader_psf_pdb.h \
$(SOURCE_DIR)/molecule_reader_psf_pdb.cpp \
$(SOURCE_DIR)/parameter_manager_lj_molecule.h \
$(SOURCE_DIR)/parameter_manager_lj_molecule.cpp \
$(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parameter_manager.cpp \
$(SOURCE_DIR)/parser.h \
$(SOURCE_DIR)/parser.cpp \
$(SOURCE_DIR)/common.h
MOLECULE_UT_DATA := \
$(DATA_DIR_TESTS)/molecule_test/par_oxalate_and_friends.inp \
$(DATA_DIR_TESTS)/molecule_test/dicarboxy-octane_4.pdb \
$(DATA_DIR_TESTS)/molecule_test/dicarboxy-octane_4.psf
PARAM_UT_SOURCES := $(SOURCE_DIR)/parameter_test/main.cc \
$(SOURCE_DIR)/parameter_manager_lj_molecule.h \
$(SOURCE_DIR)/parameter_manager_lj_molecule.cpp \
$(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parameter_manager.cpp \
$(SOURCE_DIR)/parser.h \
$(SOURCE_DIR)/parser.cpp \
$(SOURCE_DIR)/common.h
PARAM_UT_DATA := $(DATA_DIR_TESTS)/molecule_test/par_oxalate_and_friends.inp
molecule_test : molecule_test_prepare_sources molecule_test_prepare_makefiles \
molecule_test_prepare_data_files
#$(shell cd $(TEST_DIR)/molecule_unit_test/; \
make ./bin/molecule_test)
molecule_test_prepare_sources: molecule_test_dir
#echo Copying sources...
#cp --preserve $(MOLECULE_UT_SOURCES) \
$(TEST_DIR)/molecule_unit_test/source
molecule_test_prepare_makefiles: $(MAKEFILE_DIR)/Makefile.molecule_test
#cp --preserve $(MAKEFILE_DIR)/Makefile.molecule_test \
$(TEST_DIR)/molecule_unit_test/Makefile
molecule_test_prepare_data_files:
cp --preserve $(MOLECULE_UT_DATA) $(TEST_DIR)/molecule_unit_test/bin/
molecule_test_dir:
#if test -d $(BUILD_DIR); then \
echo Build exists...; \
else \
echo Build directory does not exist, making build dir...; \
mkdir $(BUILD_DIR); \
fi
#if test -d $(TEST_DIR); then \
echo Tests exists...; \
else \
echo Tests directory does not exist, making tests dir...; \
mkdir $(TEST_DIR); \
fi
#if test -d $(TEST_DIR)/molecule_unit_test; then \
echo Molecule unit test directory exists...; \
else \
echo Molecule unit test directory does \
not exist, making build dir...; \
mkdir $(TEST_DIR)/molecule_unit_test; \
fi
#if test -d $(TEST_DIR)/molecule_unit_test/source; then \
echo Molecule unit test source directory exists...; \
else \
echo Molecule unit test source directory does \
not exist, making build dir...; \
mkdir $(TEST_DIR)/molecule_unit_test/source; \
fi
#if test -d $(TEST_DIR)/molecule_unit_test/obj; then \
echo Molecule unit test object directory exists...; \
else \
echo Molecule unit test object directory does \
not exist, making object dir...; \
mkdir $(TEST_DIR)/molecule_unit_test/obj; \
fi
#if test -d $(TEST_DIR)/molecule_unit_test/bin; then \
echo Molecule unit test executable directory exists...; \
else \
echo Molecule unit test executable directory does \
not exist, making executable dir...; \
mkdir $(TEST_DIR)/molecule_unit_test/bin; \
fi
param_test : param_test_prepare_sources param_test_prepare_makefiles \
param_test_prepare_data_files
#$(shell cd $(TEST_DIR)/param_unit_test/; \
make ./bin/param_test)
param_test_prepare_sources: param_test_dir
#echo Copying sources...
#cp --preserve $(PARAM_UT_SOURCES) $(TEST_DIR)/param_unit_test/source
param_test_prepare_makefiles: $(MAKEFILE_DIR)/Makefile.param_test
#cp --preserve $(MAKEFILE_DIR)/Makefile.param_test \
$(TEST_DIR)/param_unit_test/Makefile
param_test_prepare_data_files:
cp --preserve $(PARAM_UT_DATA) $(TEST_DIR)/param_unit_test/bin/
param_test_dir:
#if test -d $(BUILD_DIR); then \
echo Build exists...; \
else \
echo Build directory does not exist, making build dir...; \
mkdir $(BUILD_DIR); \
fi
#if test -d $(TEST_DIR); then \
echo Tests exists...; \
else \
echo Tests directory does not exist, making tests dir...; \
mkdir $(TEST_DIR); \
fi
#if test -d $(TEST_DIR)/param_unit_test; then \
echo Param unit test directory exists...; \
else \
echo Param unit test directory does \
not exist, making build dir...; \
mkdir $(TEST_DIR)/param_unit_test; \
fi
#if test -d $(TEST_DIR)/param_unit_test/source; then \
echo Param unit test source directory exists...; \
else \
echo Param unit test source directory does \
not exist, making build dir...; \
mkdir $(TEST_DIR)/param_unit_test/source; \
fi
#if test -d $(TEST_DIR)/param_unit_test/obj; then \
echo Param unit test object directory exists...; \
else \
echo Param unit test object directory does \
not exist, making object dir...; \
mkdir $(TEST_DIR)/param_unit_test/obj; \
fi
#if test -d $(TEST_DIR)/param_unit_test/bin; then \
echo Param unit test executable directory exists...; \
else \
echo Param unit test executable directory does \
not exist, making executable dir...; \
mkdir $(TEST_DIR)/param_unit_test/bin; \
fi
...and the sub makefile:
#Nice, wonderful makefile written by Jason
CC=g++
CFLAGS=-c -Wall
SOURCE_DIR:=./source
OBJ_DIR:=./obj
EXE_DIR:=./bin
$(EXE_DIR)/molecule_test : $(OBJ_DIR)/main.o \
$(OBJ_DIR)/parameter_manager_lj_molecule.o \
$(OBJ_DIR)/parameter_manager.o $(OBJ_DIR)/parser.o \
$(OBJ_DIR)/molecule_manager.o $(OBJ_DIR)/molecule_manager_main.o \
$(OBJ_DIR)/molecule_reader.o \
$(OBJ_DIR)/molecule_reader_psf_pdb.o
#$(CC) $(OBJ_DIR)/main.o $(OBJ_DIR)/parameter_manager.o \
$(OBJ_DIR)/parser.o $(OBJ_DIR)/parameter_manager_lj_molecule.o \
$(OBJ_DIR)/molecule_manager.o $(OBJ_DIR)/molecule_manager_main.o \
$(OBJ_DIR)/molecule_reader.o \
$(OBJ_DIR)/molecule_reader_psf_pdb.o \
-o molecule_test
#mv molecule_test $(EXE_DIR)/
$(OBJ_DIR)/main.o: $(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parameter_manager_lj_molecule.h \
$(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/molecule_manager_main.h \
$(SOURCE_DIR)/molecule_reader.h \
$(SOURCE_DIR)/molecule_reader_psf_pdb.h \
$(SOURCE_DIR)/common.h $(SOURCE_DIR)/main.cc
$(CC) $(CFLAGS) $(SOURCE_DIR)/main.cc
#mv main.o $(OBJ_DIR)/
$(OBJ_DIR)/molecule_reader.o: $(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parameter_manager_lj_molecule.h \
$(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/molecule_manager_main.h \
$(SOURCE_DIR)/molecule_reader.h \
$(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/molecule_reader.cpp
#mv molecule_reader.o $(OBJ_DIR)/
$(OBJ_DIR)/molecule_reader_psf_pdb.o: $(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parameter_manager_lj_molecule.h \
$(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/molecule_manager_main.h \
$(SOURCE_DIR)/molecule_reader.h \
$(SOURCE_DIR)/molecule_reader_psf_pdb.h \
$(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/molecule_reader_psf_pdb.cpp
#mv molecule_reader_psf_pdb.o $(OBJ_DIR)/
$(OBJ_DIR)/molecule_manager.o: $(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/molecule_manager.cpp
#mv molecule_manager.o $(OBJ_DIR)/
$(OBJ_DIR)/molecule_manager_main.o: $(SOURCE_DIR)/molecule_manager.h \
$(SOURCE_DIR)/molecule_manager_main.h \
$(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/molecule_manager_main.cpp
#mv molecule_manager_main.o $(OBJ_DIR)/
$(OBJ_DIR)/parameter_manager_lj_molecule.o: $(SOURCE_DIR)/common.h \
$(SOURCE_DIR)/parameter_manager.h \
$(SOURCE_DIR)/parser.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/parameter_manager_lj_molecule.cpp
#mv parameter_manager_lj_molecule.o $(OBJ_DIR)/
$(OBJ_DIR)/parameter_manager.o: $(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/parameter_manager.cpp
#mv parameter_manager.o $(OBJ_DIR)/
$(OBJ_DIR)/parser.o: $(SOURCE_DIR)/parser.h
#$(CC) $(CFLAGS) $(SOURCE_DIR)/parser.cpp
#mv parser.o $(OBJ_DIR)/
$(OBJ_DIR)/common.o: $(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(SOURCE_DIR)/common.h
mv common.h.gch $(OBJ_DIR)/
With some help from the above users and figuring out a few nifty tricks on my own as well (like use of wildcards), I've refactored the makefiles heavily, plus added comments for posterity.
Here's the top level result:
####################################################
## -------------------------------
## - Monte Carlo Source Makefile -
## -------------------------------
##
## Author: Jason R. Mick
## Date: July 7, 2010
## Company: Wayne State University
##
## CHANGE LOG
## Author Date Description
##
##
##
####################################################
#################################
# These lines set up some basic vars
# such as compiler, flags, and dirs.
#################################
CC=g++
CFLAGS=-c -Wall
BASE_DIR:=.
SOURCE_DIR:=$(BASE_DIR)/source
BUILD_DIR:=$(BASE_DIR)/build
TEST_DIR:=$(BASE_DIR)/build/tests
MAKEFILE_DIR:=$(BASE_DIR)/makefiles
DATA_DIR:=$(BASE_DIR)/data
DATA_DIR_TESTS:=$(DATA_DIR)/tests
#################################
# Note use of wildcards to catch *.h and *.cpp files and all the sub_classes
# ... for future unit tests/classes, follow this approach, please
#################################
MOLECULE_UT_SOURCES := $(SOURCE_DIR)/molecule_test/main.cc \
$(SOURCE_DIR)/molecule_manager* \
$(SOURCE_DIR)/molecule_reader* \
$(SOURCE_DIR)/parameter_manager* \
$(SOURCE_DIR)/parser* \
$(SOURCE_DIR)/common.h
MOLECULE_UT_DATA := \
$(DATA_DIR_TESTS)/molecule_test/par_oxalate_and_friends.inp \
$(DATA_DIR_TESTS)/molecule_test/dicarboxy-octane_4.*
PARAM_UT_SOURCES := $(SOURCE_DIR)/parameter_test/main.cc \
$(SOURCE_DIR)/parameter_manager* \
$(SOURCE_DIR)/parser* \
$(SOURCE_DIR)/common.h
PARAM_UT_DATA := $(DATA_DIR_TESTS)/molecule_test/par_oxalate_and_friends.inp
#################################
# Use sub-make inside subdirectory on test target
# NOTE: # silences output of this call...
#################################
molecule_test : molecule_test_prepare_sources molecule_test_prepare_makefiles \
molecule_test_prepare_data_files
#$(MAKE) -C $(TEST_DIR)/molecule_unit_test/ ./bin/molecule_test
#################################
# NOTE: this target uses --preserve to keep base source modification date
# to prevent unnecessary rebuilds
#################################
molecule_test_prepare_sources: molecule_test_dir
#echo Copying sources...
#cp --preserve $(MOLECULE_UT_SOURCES) \
$(TEST_DIR)/molecule_unit_test/source
molecule_test_prepare_makefiles: $(MAKEFILE_DIR)/Makefile.molecule_test
#cp --preserve $(MAKEFILE_DIR)/Makefile.molecule_test \
$(TEST_DIR)/molecule_unit_test/Makefile
molecule_test_prepare_data_files:
#cp --preserve $(MOLECULE_UT_DATA) $(TEST_DIR)/molecule_unit_test/bin/
#################################
# NOTE: This mkdir command uses -p flag to create any missing parent dirs.
# If all dirs already exist, it also returns no error...
#################################
molecule_test_dir:
mkdir -p $(TEST_DIR)/molecule_unit_test/source
mkdir -p $(TEST_DIR)/molecule_unit_test/obj
mkdir -p $(TEST_DIR)/molecule_unit_test/bin
param_test : param_test_prepare_sources param_test_prepare_makefiles \
param_test_prepare_data_files
#$(MAKE) -C $(TEST_DIR)/param_unit_test/ ./bin/param_test
param_test_prepare_sources: param_test_dir
#echo Copying sources...
#cp --preserve $(PARAM_UT_SOURCES) $(TEST_DIR)/param_unit_test/source
param_test_prepare_makefiles: $(MAKEFILE_DIR)/Makefile.param_test
#cp --preserve $(MAKEFILE_DIR)/Makefile.param_test \
$(TEST_DIR)/param_unit_test/Makefile
param_test_prepare_data_files:
#cp --preserve $(PARAM_UT_DATA) $(TEST_DIR)/param_unit_test/bin/
param_test_dir:
mkdir -p $(TEST_DIR)/param_unit_test/source
mkdir -p $(TEST_DIR)/param_unit_test/obj
mkdir -p $(TEST_DIR)/param_unit_test/bin
Here's the sub-makefile result:
####################################################
## -------------------------------
## - Monte Carlo Source Submake -
## -------------------------------
##
## Author: Jason R. Mick
## Date: July 7, 2010
## Company: Wayne State University
##
## CHANGE LOG
## Author Date Description
##
##
##
####################################################
################################
# These lines set up some basic vars
# such as compiler, flags, and dirs.
################################
CC=g++
CFLAGS=-c -Wall
SOURCE_DIR:=./source
INCDIRS := -I$(SOURCE_DIR)
OBJ_DIR:=./obj
EXE_DIR:=./bin
################################
#This line tells make what directories to search in for rules...
################################
VPATH = $(SOURCE_DIR)
################################
# INFO on the "magic" here:
#$^ is all the prerequisite (.o files), $# is target, and % is wildcard
################################
$(EXE_DIR)/molecule_test : $(OBJ_DIR)/main.o \
$(OBJ_DIR)/parameter_manager_lj_molecule.o \
$(OBJ_DIR)/parameter_manager.o $(OBJ_DIR)/parser.o \
$(OBJ_DIR)/molecule_manager.o $(OBJ_DIR)/molecule_manager_main.o \
$(OBJ_DIR)/molecule_reader.o \
$(OBJ_DIR)/molecule_reader_psf_pdb.o
$(CC) $^ -o $#
################################
# These are extra includes for the general
# rule at the end....
################################
$(OBJ_DIR)/main.o $(OBJ_DIR)/molecule_reader.o \
$(OBJ_DIR)/molecule_reader_psf_pdb.o: \
molecule_manager.h \
molecule_manager_main.h \
parameter_manager.h \
parameter_manager_lj_molecule.h
$(OBJ_DIR)/molecule_manager_main.o: molecule_manager.h
$(OBJ_DIR)/parameter_manager_lj_molecule.o: parser.h
$(OBJ_DIR)/molecule_reader_psf_pdb.o: molecule_reader.h
################################
# Special rule for main object
################################
$(OBJ_DIR)/main.o: $(SOURCE_DIR)/main.cc \
molecule_reader.h \
molecule_reader_psf_pdb.h common.h
$(CC) $(CFLAGS) $(INCDIRS) $< -o $#
################################
# The GENERAL RULE for objects...
# INFO on the "magic" here:
#$< is the first prerequisite (.cpp file), $# is target, and % is wildcard
################################
$(OBJ_DIR)/%.o: $(SOURCE_DIR)/%.cpp $(SOURCE_DIR)/%.h $(SOURCE_DIR)/common.h
$(CC) $(CFLAGS) $(INCDIRS) $< -o $#
... basically I'm pretty satisfied, everything is working, clean, and well documented, but I wanted to see if anyone else has suggestions of things I should change for "best practice" etc. I'm trying to learn as much as I can!! Thanks in advance!!
Cheers,
Jason

Answer 1

I would rethink calling make recursively, and instead #include the submakefiles in the main makefile. It is much easier to get the dependancies to work right, and it allows you to utilize multiple cores for building (using -j). Take a look at Recursive Make Considered Harmful for all the gory details.
Also, take a look at these questions:
What is your experience with non recursive make?
Recursive make friend or foe

Answer 2

(I won't enter into the recursive/non-recursive debate again. 'Nuff said.)
Why copy all of these files around? I understand that you don't want to hardcode a map of your directory structure in the submake, but you can save a lot of time and trouble by giving the submake access to the original files, either by symbolic link:
molecule_test_prepare_sources: molecule_test_dir
#echo linking to sources...
#ln -s $(SOURCE_DIR) $(TEST_DIR)/molecule_unit_test/source
molecule_test_prepare_makefiles: $(MAKEFILE_DIR)/Makefile.molecule_test
#ln -s $< $(TEST_DIR)/molecule_unit_test/Makefile
Or by passing a parameter to the submake:
param_test : param_test_prepare_sources param_test_prepare_makefiles \
param_test_prepare_data_files
#$(MAKE) -C $(TEST_DIR)/param_unit_test/ SOURCE_DIR=$(SOURCE_DIR) \
./bin/param_test # and then use SOURCE_DIR in the submake
The same goes for param_test. I think this actually lets you do away with MOLECULE_UT_SOURCES and PARAM_UT_SOURCES, and good riddance.
(I left out the data directories, because I don't know what this code actually does-- maybe it needs a restriced diet, or modifies its input files or something.)
Finally as a matter of style, almost anywhere you see redundancy you can remove it and make the makefile easier to read. For instance,
$(EXE_DIR)/molecule_test : $(OBJ_DIR)/main.o \
$(OBJ_DIR)/parameter_manager_lj_molecule.o \
$(OBJ_DIR)/parameter_manager.o $(OBJ_DIR)/parser.o \
$(OBJ_DIR)/molecule_manager.o $(OBJ_DIR)/molecule_manager_main.o \
$(OBJ_DIR)/molecule_reader.o \
$(OBJ_DIR)/molecule_reader_psf_pdb.o
$(CC) $^ -o $#
can become
OBJECTS := main \
parameter_manager_lj_molecule \
parameter_manager parser \
molecule_manager molecule_manager_main \
molecule_reader \
molecule_reader_psf_pdb
OBJECTS := $(patsubst %,$(OBJ_DIR)/%.o, $(OBJECTS)
$(EXE_DIR)/molecule_test : $(OBJECTS)
$(CC) $^ -o $#

Answer 3

This isn't the answer you're looking for but have you considered using the "autotools" suite (automake, autoconf, etc.)?
Once you get the hang of it it's quite wonderful to work with. And it has a lot more functionality than pure Make. Functionality such as checking for libraries needed to build, cross-compiling, etc.