How to append lists in makefile using loops - list

I am trying to create a list of targets that depend on one file only. The list I want to create is very long and I may have to add even more elements to it, so I would like to use loops to create that target list. The targets differ mainly by their paths.
I think I just need to find out how to append or add to list in makefile, so I can create the target list I want (TARGETS) in a loop.
Here is what I have so far:
.PHONY: all dircreate dircreate_sub
# Create shortcuts to directories ##############################################
DAT4 = data/4-Year/
DAT2 = data/2-Year/
DEPVARS = a b
# Create directories ###########################################################
dircreate:
mkdir -p \
data/ \
data/4-Year/ \
data/2-Year/
dircreate_sub:
for d in $(DEPVARS); do \
mkdir -p data/4-Year/$$d ; \
mkdir -p data/2-Year/$$d ; \
done;
TARGETS = \
for d in $(DEPVARS); do \
$(DAT4)$$d/train_index.RDS \
$(DAT2)$$d/train_index.RDS \
$(DAT4)$$d/test_index.RDS \
$(DAT2)$$d/test_index.RDS; \
done;
$(TARGETS): \
dataprep.R \
funcs.R \
../core/data/analysis.data.RDS
Rscript $<
all: dircreate dircreate_sub $(TARGETS)

Probably you want something like:
TARGETS := $(foreach d,$(DEPVARS),\
$(DAT4)$d/train_index.RDS \
$(DAT2)$d/train_index.RDS \
$(DAT4)$d/test_index.RDS \
$(DAT2)$d/test_index.RDS)
Note I used := instead of = for efficiency.

You're going to want to use the foreach makefile function:
You could do something like this:
TARGETS := $(foreach depvar,$(DEPVARS),$(DAT4)$$d/train_index.RDS)
TARGETS += $(foreach depvar,$(DEPVARS),$(DAT2)$$d/train_index.RDS)
TARGETS += $(foreach depvar,$(DEPVARS),$(DAT4)$$d/test_index.RDS)
TARGETS += $(foreach depvar,$(DEPVARS),$(DAT2)$$d/test_index.RDS)
or something like this:
TARGETS := $(foreach dat,$(DAT4) $(DAT2),$\
$(foreach filename,train_index.RDS test_index.RDS,$\
$(foreach depvar,$(DEPVARS),$(dat)$(depvar)/$(filename))))
Note: I used the $\ trick to allow going over multiple lines without adding spaces (see here)
if you wanted to do something more complicated, you can always use a shell script to do everything.
TARGETS := $(shell somescript a b c)

Related

how to create a makefile with system header files

I am trying to create a makefile using the help of this thread, I changed the code provided a little bit since I have many *.c files that need to be compiled.
this the project hierarchy:
/coap
Makefile
/src
/src
/coap
/imc
*.h files
/src
*.c files
/system
/imc
client.h
/src
client.c
**makefile**
/files
sdk.sh
I made the first makefile and it seems to work fine, but my problem is with the second one written in bold.
Here, I provide the changes that I made:
program_NAME := coap
program_C_SRCS += \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/address.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/async.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/block.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_asn1.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_cache.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_debug.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_event.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_gnutls.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_hashkey.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_io.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_mbedtls.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_notls.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_openssl.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_prng.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_session.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_tcp.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_time.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/coap_tinydtls.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/encode.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/mem.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/net.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/option.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/pdu.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/resource.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/str.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/subscribe.c \
/home/iat2/Projects/XXXX/package/coap/src/src/coap/src/uri.c
program_C_OBJS := ${program_C_SRCS:.c=.o}
program_OBJS := $(program_C_OBJS)
program_INCLUDE_DIRS :=/home/iat2/Projects/XXXX/package/coap/src/src/coap/imc
program_LIBRARY_DIRS :=
program_LIBRARIES := router
CFLAGS += $(foreach includedir,$(program_INCLUDE_DIRS),-I$(includedir))
LDFLAGS += $(foreach librarydir,$(program_LIBRARY_DIRS),-L$(librarydir))
LDFLAGS += $(foreach library,$(program_LIBRARIES),-l$(library))
.PHONY: all clean distclean
all: $(program_NAME)
$(program_NAME): $(program_OBJS)
$(LINK.cc) $(program_OBJS) -o $(program_NAME)
clean:
#- $(RM) $(program_NAME)
#- $(RM) $(program_OBJS)
distclean: clean
When I try to compile, the log file output is:
fatal error: sys/random.h: No such file or directory
#include <sys/random.h>
and it can't recognize some of the openssl functions written in the coap_openssl.c file.

Modify the buildroot pkg-generic.mk to apply patches to a local package?

Based off my last question here
Buildroot is not applying patches to my package because of the given answer to my previous question... But I would think there would be a way to add in the logic to apply the patches anyways?
Here is the section of code that gets run by build root
# Rsync the source directory if the <pkg>_OVERRIDE_SRCDIR feature is
# used.
$(BUILD_DIR)/%/.stamp_rsynced:
#$(call MESSAGE,"Syncing from source dir $(SRCDIR)")
#test -d $(SRCDIR) || (echo "ERROR: $(SRCDIR) does not exist" ; exit 1)
$(foreach hook,$($(PKG)_PRE_RSYNC_HOOKS),$(call $(hook))$(sep))
rsync -au --chmod=u=rwX,go=rX $(RSYNC_VCS_EXCLUSIONS) $(call qstrip,$(SRCDIR))/ $(#D)
$(foreach hook,$($(PKG)_POST_RSYNC_HOOKS),$(call $(hook))$(sep))
#GV_PATCH : do not touch stamp_rsynced to force rsync
Now right below the rsync section is the piece of code I would like to run to apply patches to my local package, I have already defined the BR2_GLOBAL_PATCH_DIR in my buildroot config and included the directory of my patch package and the patch inside. This is the patch code I would like to run after the rsync.
# Patch
#
# The RAWNAME variable is the lowercased package name, which allows to
# find the package directory (typically package/<pkgname>) and the
# prefix of the patches
#
# For BR2_GLOBAL_PATCH_DIR, only generate if it is defined
$(BUILD_DIR)/%/.stamp_patched: NAMEVER = $(RAWNAME)-$($(PKG)_VERSION)
$(BUILD_DIR)/%/.stamp_patched: PATCH_BASE_DIRS = $(PKGDIR)
$(BUILD_DIR)/%/.stamp_patched: PATCH_BASE_DIRS += $(addsuffix /$(RAWNAME),$(call qstrip,$(BR2_GLOBAL_PATCH_DIR)))
$(BUILD_DIR)/%/.stamp_patched:
#$(call step_start,patch)
#$(call MESSAGE,"Patching")
$(foreach hook,$($(PKG)_PRE_PATCH_HOOKS),$(call $(hook))$(sep))
$(foreach p,$($(PKG)_PATCH),$(APPLY_PATCHES) $(#D) $(DL_DIR) $(notdir $(p))$(sep))
$(Q)( \
for D in $(PATCH_BASE_DIRS); do \
if test -d $${D}; then \
if test -d $${D}/$($(PKG)_VERSION); then \
$(APPLY_PATCHES) $(#D) $${D}/$($(PKG)_VERSION) \*.patch \*.patch.$(ARCH) || exit 1; \
else \
$(APPLY_PATCHES) $(#D) $${D} \*.patch \*.patch.$(ARCH) || exit 1; \
fi; \
fi; \
done; \
)
$(foreach hook,$($(PKG)_POST_PATCH_HOOKS),$(call $(hook))$(sep))
#$(call step_end,patch)
$(Q)touch $#
# Check that all directories specified in BR2_GLOBAL_PATCH_DIR exist.
$(foreach dir,$(call qstrip,$(BR2_GLOBAL_PATCH_DIR)),\
$(if $(wildcard $(dir)),,\
$(error BR2_GLOBAL_PATCH_DIR contains nonexistent directory $(dir))))
Is this possible to do?
I tried adding #$(call step_start,patch) to the first section of code after the #GV_PATCH but it didn't work.
I'm no expert on make files but I figured there is a way to call the patch code? I just don't know how.
The answer is the same as given at the end of your previous question:
# Rsync the source directory if the <pkg>_OVERRIDE_SRCDIR feature is
# used.
$(BUILD_DIR)/%/.stamp_rsynced:
#$(call MESSAGE,"Syncing from source dir $(SRCDIR)")
#test -d $(SRCDIR) || (echo "ERROR: $(SRCDIR) does not exist" ; exit 1)
$(foreach hook,$($(PKG)_PRE_RSYNC_HOOKS),$(call $(hook))$(sep))
rsync -au --chmod=u=rwX,go=rX $(RSYNC_VCS_EXCLUSIONS) $(call qstrip,$(SRCDIR))/ $(#D)
$(foreach hook,$($(PKG)_POST_RSYNC_HOOKS),$(call $(hook))$(sep))
#GV_PATCH : do not touch stamp_rsynced to force rsync
# Apply patches in global patch dir, but no others
$(APPLY_PATCHES) $(#D) $(addsuffix /$(RAWNAME),$(call qstrip,$(BR2_GLOBAL_PATCH_DIR))) \*.patch
By the way, you don't need to remove the stamp file, just use make foo-rebuild - it will also re-sync the package.

How to pass arguments to boilermake

Apologies if this is not the place to post this. I'm not really sure where is.
I'm new to make and after a lot of research I stumbled across boilermake and have implemented it successfully on my project.
I build a release version of my project by default. I would like to know how to build a debug version of my project by supplying a command line argument such as debug. E.g.
make debug
which changes some of the compiler options set in CXXFLAGS in my top-level makefile.
However, I've not been able to get this to work.
Here is my makefile, which is included by the top-level makefile of boilermake.
INCDIRS := \
../component1/include \
../component2/include \
../component3/include
CXXFLAGS := O2 -pipe -std=c++11 -Wall -Wextra -Wold-style-cast -pedantic \
-isystem boost
SUBMAKEFILES := \
../component1/build/component1.mk \
../component2/build/component3.mk \
../component3/build/component4.mk
TARGET := my-project
TGT_LDFLAGS := -L. -L${TARGET_DIR}
TGT_LDLIBS := -lcomponent1 -lcomponent2 -lcomponent3 \
libboost_date_time-mt-sd.a \
libboost_filesystem-mt-sd.a
libcrypto.a \
libssl.a \
-lz \
-ldl \
-lpthread
TGT_PREREQS := \
libcomponent1.a \
libcomponent2.a \
libcomponent3.a
SOURCES := \
main.cpp
Here is the boilermake makefile.
# boilermake: A reusable, but flexible, boilerplate Makefile.
#
# Copyright 2008, 2009, 2010 Dan Moulding, Alan T. DeKok
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# Caution: Don't edit this Makefile! Create your own main.mk and other
# submakefiles, which will be included by this Makefile.
# Only edit this if you need to modify boilermake's behavior (fix
# bugs, add features, etc).
# Note: Parameterized "functions" in this makefile that are marked with
# "USE WITH EVAL" are only useful in conjuction with eval. This is
# because those functions result in a block of Makefile syntax that must
# be evaluated after expansion. Since they must be used with eval, most
# instances of "$" within them need to be escaped with a second "$" to
# accomodate the double expansion that occurs when eval is invoked.
# ADD_CLEAN_RULE - Parameterized "function" that adds a new rule and phony
# target for cleaning the specified target (removing its build-generated
# files).
#
# USE WITH EVAL
#
define ADD_CLEAN_RULE
clean: clean_${1}
.PHONY: clean_${1}
clean_${1}:
$$(strip rm -f ${TARGET_DIR}/${1} $${${1}_OBJS:%.o=%.[do]})
$${${1}_POSTCLEAN}
endef
# ADD_OBJECT_RULE - Parameterized "function" that adds a pattern rule for
# building object files from source files with the filename extension
# specified in the second argument. The first argument must be the name of the
# base directory where the object files should reside (such that the portion
# of the path after the base directory will match the path to corresponding
# source files). The third argument must contain the rules used to compile the
# source files into object code form.
#
# USE WITH EVAL
#
define ADD_OBJECT_RULE
${1}/%.o: ${2}
${3}
endef
# ADD_TARGET_RULE - Parameterized "function" that adds a new target to the
# Makefile. The target may be an executable or a library. The two allowable
# types of targets are distinguished based on the name: library targets must
# end with the traditional ".a" extension.
#
# USE WITH EVAL
#
define ADD_TARGET_RULE
ifeq "$$(suffix ${1})" ".a"
# Add a target for creating a static library.
$${TARGET_DIR}/${1}: $${${1}_OBJS}
#mkdir -p $$(dir $$#)
$$(strip $${AR} $${ARFLAGS} $$# $${${1}_OBJS})
$${${1}_POSTMAKE}
else
# Add a target for linking an executable. First, attempt to select the
# appropriate front-end to use for linking. This might not choose the
# right one (e.g. if linking with a C++ static library, but all other
# sources are C sources), so the user makefile is allowed to specify a
# linker to be used for each target.
ifeq "$$(strip $${${1}_LINKER})" ""
# No linker was explicitly specified to be used for this target. If
# there are any C++ sources for this target, use the C++ compiler.
# For all other targets, default to using the C compiler.
ifneq "$$(strip $$(filter $${CXX_SRC_EXTS},$${${1}_SOURCES}))" ""
${1}_LINKER = $${CXX}
else
${1}_LINKER = $${CC}
endif
endif
$${TARGET_DIR}/${1}: $${${1}_OBJS} $${${1}_PREREQS}
#mkdir -p $$(dir $$#)
$$(strip $${${1}_LINKER} -o $$# $${LDFLAGS} $${${1}_LDFLAGS} \
$${${1}_OBJS} $${LDLIBS} $${${1}_LDLIBS})
$${${1}_POSTMAKE}
endif
endef
# CANONICAL_PATH - Given one or more paths, converts the paths to the canonical
# form. The canonical form is the path, relative to the project's top-level
# directory (the directory from which "make" is run), and without
# any "./" or "../" sequences. For paths that are not located below the
# top-level directory, the canonical form is the absolute path (i.e. from
# the root of the filesystem) also without "./" or "../" sequences.
define CANONICAL_PATH
$(patsubst ${CURDIR}/%,%,$(abspath ${1}))
endef
# COMPILE_C_CMDS - Commands for compiling C source code.
define COMPILE_C_CMDS
#mkdir -p $(dir $#)
$(strip ${CC} -o $# -c -MP -MD ${CFLAGS} ${SRC_CFLAGS} ${INCDIRS} \
${SRC_INCDIRS} ${SRC_DEFS} ${DEFS} $<)
endef
# COMPILE_CXX_CMDS - Commands for compiling C++ source code.
define COMPILE_CXX_CMDS
#mkdir -p $(dir $#)
$(strip ${CXX} -o $# -c -MP -MD ${CXXFLAGS} ${SRC_CXXFLAGS} ${INCDIRS} \
${SRC_INCDIRS} ${SRC_DEFS} ${DEFS} $<)
endef
# INCLUDE_SUBMAKEFILE - Parameterized "function" that includes a new
# "submakefile" fragment into the overall Makefile. It also recursively
# includes all submakefiles of the specified submakefile fragment.
#
# USE WITH EVAL
#
define INCLUDE_SUBMAKEFILE
# Initialize all variables that can be defined by a makefile fragment, then
# include the specified makefile fragment.
TARGET :=
TGT_CFLAGS :=
TGT_CXXFLAGS :=
TGT_DEFS :=
TGT_INCDIRS :=
TGT_LDFLAGS :=
TGT_LDLIBS :=
TGT_LINKER :=
TGT_POSTCLEAN :=
TGT_POSTMAKE :=
TGT_PREREQS :=
SOURCES :=
SRC_CFLAGS :=
SRC_CXXFLAGS :=
SRC_DEFS :=
SRC_INCDIRS :=
SUBMAKEFILES :=
# A directory stack is maintained so that the correct paths are used as we
# recursively include all submakefiles. Get the makefile's directory and
# push it onto the stack.
DIR := $(call CANONICAL_PATH,$(dir ${1}))
DIR_STACK := $$(call PUSH,$${DIR_STACK},$${DIR})
include ${1}
# Initialize internal local variables.
OBJS :=
# Ensure that valid values are set for BUILD_DIR and TARGET_DIR.
ifeq "$$(strip $${BUILD_DIR})" ""
BUILD_DIR := build
endif
ifeq "$$(strip $${TARGET_DIR})" ""
TARGET_DIR := .
endif
# Determine which target this makefile's variables apply to. A stack is
# used to keep track of which target is the "current" target as we
# recursively include other submakefiles.
ifneq "$$(strip $${TARGET})" ""
# This makefile defined a new target. Target variables defined by this
# makefile apply to this new target. Initialize the target's variables.
TGT := $$(strip $${TARGET})
ALL_TGTS += $${TGT}
$${TGT}_CFLAGS := $${TGT_CFLAGS}
$${TGT}_CXXFLAGS := $${TGT_CXXFLAGS}
$${TGT}_DEFS := $${TGT_DEFS}
$${TGT}_DEPS :=
TGT_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${TGT_INCDIRS})
TGT_INCDIRS := $$(call CANONICAL_PATH,$${TGT_INCDIRS})
$${TGT}_INCDIRS := $${TGT_INCDIRS}
$${TGT}_LDFLAGS := $${TGT_LDFLAGS}
$${TGT}_LDLIBS := $${TGT_LDLIBS}
$${TGT}_LINKER := $${TGT_LINKER}
$${TGT}_OBJS :=
$${TGT}_POSTCLEAN := $${TGT_POSTCLEAN}
$${TGT}_POSTMAKE := $${TGT_POSTMAKE}
$${TGT}_PREREQS := $$(addprefix $${TARGET_DIR}/,$${TGT_PREREQS})
$${TGT}_SOURCES :=
else
# The values defined by this makefile apply to the the "current" target
# as determined by which target is at the top of the stack.
TGT := $$(strip $$(call PEEK,$${TGT_STACK}))
$${TGT}_CFLAGS += $${TGT_CFLAGS}
$${TGT}_CXXFLAGS += $${TGT_CXXFLAGS}
$${TGT}_DEFS += $${TGT_DEFS}
TGT_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${TGT_INCDIRS})
TGT_INCDIRS := $$(call CANONICAL_PATH,$${TGT_INCDIRS})
$${TGT}_INCDIRS += $${TGT_INCDIRS}
$${TGT}_LDFLAGS += $${TGT_LDFLAGS}
$${TGT}_LDLIBS += $${TGT_LDLIBS}
$${TGT}_POSTCLEAN += $${TGT_POSTCLEAN}
$${TGT}_POSTMAKE += $${TGT_POSTMAKE}
$${TGT}_PREREQS += $${TGT_PREREQS}
endif
# Push the current target onto the target stack.
TGT_STACK := $$(call PUSH,$${TGT_STACK},$${TGT})
ifneq "$$(strip $${SOURCES})" ""
# This makefile builds one or more objects from source. Validate the
# specified sources against the supported source file types.
BAD_SRCS := $$(strip $$(filter-out $${ALL_SRC_EXTS},$${SOURCES}))
ifneq "$${BAD_SRCS}" ""
$$(error Unsupported source file(s) found in ${1} [$${BAD_SRCS}])
endif
# Qualify and canonicalize paths.
SOURCES := $$(call QUALIFY_PATH,$${DIR},$${SOURCES})
SOURCES := $$(call CANONICAL_PATH,$${SOURCES})
SRC_INCDIRS := $$(call QUALIFY_PATH,$${DIR},$${SRC_INCDIRS})
SRC_INCDIRS := $$(call CANONICAL_PATH,$${SRC_INCDIRS})
# Save the list of source files for this target.
$${TGT}_SOURCES += $${SOURCES}
# Convert the source file names to their corresponding object file
# names.
OBJS := $$(addprefix $${BUILD_DIR}/$$(call CANONICAL_PATH,$${TGT})/,\
$$(addsuffix .o,$$(basename $${SOURCES})))
# Add the objects to the current target's list of objects, and create
# target-specific variables for the objects based on any source
# variables that were defined.
$${TGT}_OBJS += $${OBJS}
$${TGT}_DEPS += $${OBJS:%.o=%.d}
$${OBJS}: SRC_CFLAGS := $${$${TGT}_CFLAGS} $${SRC_CFLAGS}
$${OBJS}: SRC_CXXFLAGS := $${$${TGT}_CXXFLAGS} $${SRC_CXXFLAGS}
$${OBJS}: SRC_DEFS := $$(addprefix -D,$${$${TGT}_DEFS} $${SRC_DEFS})
$${OBJS}: SRC_INCDIRS := $$(addprefix -I,\
$${$${TGT}_INCDIRS} $${SRC_INCDIRS})
endif
ifneq "$$(strip $${SUBMAKEFILES})" ""
# This makefile has submakefiles. Recursively include them.
$$(foreach MK,$${SUBMAKEFILES},\
$$(eval $$(call INCLUDE_SUBMAKEFILE,\
$$(call CANONICAL_PATH,\
$$(call QUALIFY_PATH,$${DIR},$${MK})))))
endif
# Reset the "current" target to it's previous value.
TGT_STACK := $$(call POP,$${TGT_STACK})
TGT := $$(call PEEK,$${TGT_STACK})
# Reset the "current" directory to it's previous value.
DIR_STACK := $$(call POP,$${DIR_STACK})
DIR := $$(call PEEK,$${DIR_STACK})
endef
# MIN - Parameterized "function" that results in the minimum lexical value of
# the two values given.
define MIN
$(firstword $(sort ${1} ${2}))
endef
# PEEK - Parameterized "function" that results in the value at the top of the
# specified colon-delimited stack.
define PEEK
$(lastword $(subst :, ,${1}))
endef
# POP - Parameterized "function" that pops the top value off of the specified
# colon-delimited stack, and results in the new value of the stack. Note that
# the popped value cannot be obtained using this function; use peek for that.
define POP
${1:%:$(lastword $(subst :, ,${1}))=%}
endef
# PUSH - Parameterized "function" that pushes a value onto the specified colon-
# delimited stack, and results in the new value of the stack.
define PUSH
${2:%=${1}:%}
endef
# QUALIFY_PATH - Given a "root" directory and one or more paths, qualifies the
# paths using the "root" directory (i.e. appends the root directory name to
# the paths) except for paths that are absolute.
define QUALIFY_PATH
$(addprefix ${1}/,$(filter-out /%,${2})) $(filter /%,${2})
endef
###############################################################################
#
# Start of Makefile Evaluation
#
###############################################################################
# Older versions of GNU Make lack capabilities needed by boilermake.
# With older versions, "make" may simply output "nothing to do", likely leading
# to confusion. To avoid this, check the version of GNU make up-front and
# inform the user if their version of make doesn't meet the minimum required.
MIN_MAKE_VERSION := 3.81
MIN_MAKE_VER_MSG := boilermake requires GNU Make ${MIN_MAKE_VERSION} or greater
ifeq "${MAKE_VERSION}" ""
$(info GNU Make not detected)
$(error ${MIN_MAKE_VER_MSG})
endif
ifneq "${MIN_MAKE_VERSION}" "$(call MIN,${MIN_MAKE_VERSION},${MAKE_VERSION})"
$(info This is GNU Make version ${MAKE_VERSION})
$(error ${MIN_MAKE_VER_MSG})
endif
# Define the source file extensions that we know how to handle.
C_SRC_EXTS := %.c
CXX_SRC_EXTS := %.C %.cc %.cp %.cpp %.CPP %.cxx %.c++
ALL_SRC_EXTS := ${C_SRC_EXTS} ${CXX_SRC_EXTS}
# Initialize global variables.
ALL_TGTS :=
DEFS :=
DIR_STACK :=
INCDIRS :=
TGT_STACK :=
# Include the main user-supplied submakefile. This also recursively includes
# all other user-supplied submakefiles.
$(eval $(call INCLUDE_SUBMAKEFILE,main.mk))
# Perform post-processing on global variables as needed.
DEFS := $(addprefix -D,${DEFS})
INCDIRS := $(addprefix -I,$(call CANONICAL_PATH,${INCDIRS}))
# Define the "all" target (which simply builds all user-defined targets) as the
# default goal.
.PHONY: all
all: $(addprefix ${TARGET_DIR}/,${ALL_TGTS})
# Add a new target rule for each user-defined target.
$(foreach TGT,${ALL_TGTS},\
$(eval $(call ADD_TARGET_RULE,${TGT})))
# Add pattern rule(s) for creating compiled object code from C source.
$(foreach TGT,${ALL_TGTS},\
$(foreach EXT,${C_SRC_EXTS},\
$(eval $(call ADD_OBJECT_RULE,${BUILD_DIR}/$(call CANONICAL_PATH,${TGT}),\
${EXT},$${COMPILE_C_CMDS}))))
# Add pattern rule(s) for creating compiled object code from C++ source.
$(foreach TGT,${ALL_TGTS},\
$(foreach EXT,${CXX_SRC_EXTS},\
$(eval $(call ADD_OBJECT_RULE,${BUILD_DIR}/$(call CANONICAL_PATH,${TGT}),\
${EXT},$${COMPILE_CXX_CMDS}))))
# Add "clean" rules to remove all build-generated files.
.PHONY: clean
$(foreach TGT,${ALL_TGTS},\
$(eval $(call ADD_CLEAN_RULE,${TGT})))
# Include generated rules that define additional (header) dependencies.
$(foreach TGT,${ALL_TGTS},\
$(eval -include ${${TGT}_DEPS}))
If you make the command as:
make debug=true
Then in one of your makefiles:
ifeq (debug,true)
CXXFLAGS += -DDEBUG
else
CXXFLAGS += -DNDEBUG
endif

Makefile to build C and CPP files

I have been looking for a Makefile to compile a huge project which contains lots of C and C++ files. I have used Eclipse to compile it successfully but I want to go to a standalone Makefile.
I found this generic Makefile that works really well with my project except it can only compile C or C++ files but not both in one run...so it fails at Linking time.
The bits of original Makefile that compile for CPP or C:
SRC_EXT = cpp
OURCES = $(shell find $(SRC_PATH)/ -name '*.$(SRC_EXT)' -printf '%T#\t%p\n' \
SOURCES = $(shell find $(SRC_PATH)/ -name '*.$(CPP_EXT)' -o -name '*.$(C_EXT)' -printf '%T#\t%p\n' \
| sort -k 1nr | cut -f2-)
# fallback in case the above fails
rwildcard = $(foreach d, $(wildcard $1*), $(call rwildcard,$d/,$2) \
$(filter $(subst *,%,$2), $d))
ifeq ($(SOURCES),)
SOURCES := $(call rwildcard, $(SRC_PATH)/, *.$(SRC_EXT))
endif
OBJECTS = $(SOURCES:$(SRC_PATH)/%.$(SRC_EXT)=$(BUILD_PATH)/%.o)
DEPS = $(OBJECTS:.o=.d)
I tried to modify it to be:
SRC_EXT = cpp c
SOURCES = $(shell find $(SRC_PATH)/ -name '*.$(CPP_EXT)' -o -name '*.$(C_EXT)' -printf '%T#\t%p\n' \
| sort -k 1nr | cut -f2-)
# fallback in case the above fails
rwildcard = $(foreach d, $(wildcard $1*), $(call rwildcard,$d/,$2) \
$(filter $(subst *,%,$2), $d))
ifeq ($(SOURCES),)
SOURCES := $(call rwildcard, $(SRC_PATH)/, *.$(SRC_EXT))
endif
But i'm not sure what to do with the OBJECTS directive to make it work with the multiple extensions:
OBJECTS = $(SOURCES:$(SRC_PATH)/%.$(SRC_EXT)=$(BUILD_PATH)/%.o)
Can anybody help with this please?
Thanks
First, replace .cpp by .o, then replace the remaining .c by .o.

Makefile Makeover -- Almost Complete, Want Feedback

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
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
(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 $#
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.