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Makefile
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Makefile
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#############################################################
# Generic Makefile for C/C++ Program
#
# Description:
# ------------
# This is an easily customizable makefile template. The purpose is to
# provide an instant building environment for C/C++ programs.
#
# It searches all the C/C++ source files in the specified directories,
# makes dependencies, compiles and links to form an executable.
#
# Besides its default ability to build C/C++ programs which use only
# standard C/C++ libraries, you can customize the Makefile to build
# those using other libraries. Once done, without any changes you can
# then build programs using the same or less libraries, even if source
# files are renamed, added or removed. Therefore, it is particularly
# convenient to use it to build codes for experimental or study use.
#
# GNU make is expected to use the Makefile. Other versions of makes
# may or may not work.
#
# Usage:
# ------
# 1. Copy the Makefile to your program directory.
# 2. Customize in the "Customizable Section" only if necessary:
# * to use non-standard C/C++ libraries, set pre-processor or compiler
# options to <MY_CFLAGS> and linker ones to <MY_LIBS>
# (See Makefile.gtk+-2.0 for an example)
# * to search sources in more directories, set to <SRCDIRS>
# * to specify your favorite program name, set to <PROGRAM>
# 3. Type make to start building your program.
#
# Make Target:
# ------------
# The Makefile provides the following targets to make:
# http://gcc.gnu.org/onlinedocs/gcc/Optimize-Options.html
# $ make compile and link
# $ make NODEP=yes compile and link without generating dependencies
# $ make objs compile only (no linking)
# $ make tags create tags for Emacs editor
# $ make ctags create ctags for VI editor
# $ make clean clean objects and the executable file
# $ make distclean clean objects, the executable and dependencies
# $ make help get the usage of the makefile
# $ make run execute the main program
#
#===========================================================================
## Customizable Section: adapt those variables to suit your program.
##==========================================================================
# The pre-processor and compiler options.
# -g - turn on debugging (so GDB gives more friendly output)
# -Wall - turns on most warnings
# -O or -O2 - turn on optimizations
# -Ofast Disregard strict standards compliance. -Ofast enables all -O3 optimizations.
# It also enables optimizations that are not valid for all standard-compliant programs.
# It turns on -ffast-math and the Fortran-specific -fno-protect-parens and -fstack-arrays.
# -o <name> - name of the output file
# -c - output an object file (.o)
# -I<include path> - specify an include directory
# -L<library path> - specify a lib directory
# -l<library> - link with library lib<library>.a
# Cantera makefile template
# include /usr/include/cantera/Cantera.mak
# include /opt/cantera/v2.4.0/include/cantera/Cantera.mak
#num of processors
P=12
MY_CFLAGS =
#MPI_ROOT_DIR, mpirun, mpiextc, $(MPI_ROOT_DIR)mpic++ directory
MPI_ROOT_DIR= /usr/bin/
# The linker options.
BOOST_ROOT_INCLUDE= -I/usr/local/include
BOOST_ROOT_LIB= -L/usr/local/lib
OPENMPI_ROOT_INCLUDE= -I/usr/lib/openmpi/include
OPENMPI_ROOT_LIB= -L/usr/lib/openmpi/lib
BOOST_MPI_OPTIONS= -lboost_mpi -lboost_serialization -lboost_program_options -lboost_filesystem -lboost_random -lboost_system -lboost_regex
BOOST_REGEX_DIR= ./include/regex/src
# The link options, directory and libs
MY_LIBS = $(BOOST_ROOT_LIB) $(OPENMPI_ROOT_LIB) $(CANTERA_LIBS) -lgfortran $(BOOST_MPI_OPTIONS)
# The pre-processor options used by the cpp (man cpp for more)
CPPFLAGS = -Wall -fopenmp $(BOOST_ROOT_INCLUDE) $(OPENMPI_ROOT_INCLUDE) $(CANTERA_INCLUDES) -std=c++11
# The options used in linking as well as in any direct use of ld.
LDFLAGS =
# The directories in which source files reside.
# If not specified, only the current directory will be serached.
# Fortran Source directory
FSRC_ROOT_DIR = ./fortran_lib
# FSRCDIRS = $(FSRC_ROOT_DIR) $(FSRC_ROOT_DIR)/dlsode $(FSRC_ROOT_DIR)/chemkin $(FSRC_ROOT_DIR)/cantera
FSRCDIRS = $(FSRC_ROOT_DIR) $(FSRC_ROOT_DIR)/dlsode $(FSRC_ROOT_DIR)/chemkin
# CXX Source directory
# SRCDIRS = . ./src ./src/drivers ./src/tools/debug ./src/relationshipParser ./src/srkin ./src/time ./src/mechanism ./src/odeSolver ./src/statistics ./src/cubicSpline ./src/fileIO/commandLineConfigFileReader ./src/fileIO/CSVFileReader ./src/fileIO/fileIO ./src/pathwayHandler ./src/propagator/superPropagator ./src/propagator/dlsodePropagator ./src/propagator/ssaPropagator ./src/propagator/SOHRPropagator ./src/tools/map_reduce ./src/tools/block_decomposition ./src/tools/sr_libs ./src/tools/matrix ./src/tools/union_find ./src/tools/species_group ./src/tools/pathway_constraint ./src/random ./src/reactionNetwork/superReactionNetwork ./src/reactionNetwork/concreteReactionNetwork ./src/reactionNetwork/reactionNetworkODESolver ./src/search_algorithm/eppstein_algorithm $(FSRC_ROOT_DIR)/cantera $(BOOST_REGEX_DIR)
SRCDIRS = . ./src ./src/drivers ./src/tools/debug ./src/relationshipParser ./src/srkin ./src/time ./src/mechanism ./src/odeSolver ./src/statistics ./src/cubicSpline ./src/fileIO/commandLineConfigFileReader ./src/fileIO/CSVFileReader ./src/fileIO/fileIO ./src/pathwayHandler ./src/propagator/superPropagator ./src/propagator/dlsodePropagator ./src/propagator/ssaPropagator ./src/propagator/SOHRPropagator ./src/tools/map_reduce ./src/tools/block_decomposition ./src/tools/sr_libs ./src/tools/matrix ./src/tools/union_find ./src/tools/species_group ./src/tools/pathway_constraint ./src/random ./src/reactionNetwork/superReactionNetwork ./src/reactionNetwork/concreteReactionNetwork ./src/reactionNetwork/reactionNetworkODESolver ./src/search_algorithm/eppstein_algorithm $(BOOST_REGEX_DIR)
# The executable file name.
# If not specified, current directory name or `a.out' will be used.
PROGRAM = RxnNetwork_PI
## Implicit Section: change the following only when necessary.
##==========================================================================
# The source file types (headers excluded).
# .c indicates C source files, and others C++ ones.
SRCEXTS = .c .C .cc .cpp .CPP .c++ .cxx .cp
# .f indicates Fortran source files
FSRCEXTS = .f .f90 .f95
# The header file types.
HDREXTS = .h .H .hh .hpp .HPP .h++ .hxx .hp
# The pre-processor and compiler options.
# Users can override those variables from the command line.
CFLAGS = -g -Ofast
CXXFLAGS= -g -Ofast
# -w: ignore waring, add cantera libs
# FFLAGS = -g -cpp -ffpe-trap=invalid,zero,overflow,underflow -w -Ofast $(CANTERA_INCLUDES) $(CANTERA_FORTRAN_LIBS)
FFLAGS = -g -cpp -ffpe-trap=invalid,zero,overflow,underflow -w -Ofast
# The C program compiler.
#CC = gcc
#CC = icc
CC = $(MPI_ROOT_DIR)mpic++
# The C++ program compiler.
#CXX = g++
#CXX = icpc
CXX = $(MPI_ROOT_DIR)mpic++
# Un-comment the following line to compile C programs as C++ ones.
#CC = $(CXX)
# The Fortran compiler
#FC = g++
#FC = ifort
FC = $(MPI_ROOT_DIR)mpic++
# The Fortran C/C++ mixed compiler
#FCC = g++
#FCC = ifort
FCC = $(MPI_ROOT_DIR)mpic++
# The command used to delete file.
RM = rm -f
ETAGS = etags
ETAGSFLAGS =
CTAGS = ctags
CTAGSFLAGS =
## Stable Section: usually no need to be changed. But you can add more.
##==========================================================================
SHELL = /bin/sh
EMPTY =
SPACE = $(EMPTY) $(EMPTY)
ifeq ($(PROGRAM),)
CUR_PATH_NAMES = $(subst /,$(SPACE),$(subst $(SPACE),_,$(CURDIR)))
PROGRAM = $(word $(words $(CUR_PATH_NAMES)),$(CUR_PATH_NAMES))
ifeq ($(PROGRAM),)
PROGRAM = a.out
endif
endif
ifeq ($(SRCDIRS),)
SRCDIRS = .
endif
SOURCES = $(foreach d,$(SRCDIRS),$(wildcard $(addprefix $(d)/*,$(SRCEXTS))))
HEADERS = $(foreach d,$(SRCDIRS),$(wildcard $(addprefix $(d)/*,$(HDREXTS))))
SRC_CXX = $(filter-out %.c,$(SOURCES))
# Don't compile ckstrt.f
FSOURCES_ALL = $(foreach d,$(FSRCDIRS),$(wildcard $(addprefix $(d)/*,$(FSRCEXTS))))
# FSOURCES = $(filter-out %ckstrt.f %ckvariables.f %opkddemos.f %math.f %test.f, $(FSOURCES_ALL))
# filter out cantera related files
FSOURCES = $(filter-out %ckstrt.f %ckvariables.f %opkddemos.f %math.f %test.f %use_cantera.f %cantera_ode_solver.f, $(FSOURCES_ALL))
OBJS = $(addsuffix .o, $(basename $(SOURCES)))
FOBJS = $(addsuffix .o, $(basename $(FSOURCES)))
DEPS = $(OBJS:.o=.d)
## Define some useful variables.
DEP_OPT = $(shell if `$(CC) --version | grep "GCC" >/dev/null`; then \
echo "-MM -MP"; else echo "-M"; fi )
DEPEND = $(CC) $(DEP_OPT) $(MY_CFLAGS) $(CFLAGS) $(CPPFLAGS)
DEPEND.d = $(subst -g ,,$(DEPEND))
COMPILE.c = $(CC) $(MY_CFLAGS) $(CFLAGS) $(CPPFLAGS) -c
COMPILE.cxx = $(CXX) $(MY_CFLAGS) $(CXXFLAGS) $(CPPFLAGS) -c
LINK.c = $(CC) $(MY_CFLAGS) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS)
LINK.cxx = $(CXX) $(MY_CFLAGS) $(CXXFLAGS) $(CPPFLAGS) $(LDFLAGS)
COMPILE.f = $(FC) $(FFLAGS)
COMPILE.f.c = $(FCC) $(FCFLAGS)
.PHONY: all objs tags ctags clean distclean help show
# Delete the default suffixes
.SUFFIXES:
all: $(PROGRAM)
# Rules for creating dependency files (.d).
#------------------------------------------
%.d:%.c
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.C
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.cc
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.cpp
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.CPP
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.c++
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.cp
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
%.d:%.cxx
@echo -n $(dir $<) > $@
@$(DEPEND.d) $< >> $@
# Rules for generating object files (.o).
#----------------------------------------
objs:$(OBJS)
%.o:%.c
$(COMPILE.c) $< -o $@
%.o:%.C
$(COMPILE.cxx) $< -o $@
%.o:%.cc
$(COMPILE.cxx) $< -o $@
%.o:%.cpp
$(COMPILE.cxx) $< -o $@
%.o:%.CPP
$(COMPILE.cxx) $< -o $@
%.o:%.c++
$(COMPILE.cxx) $< -o $@
%.o:%.cp
$(COMPILE.cxx) $< -o $@
%.o:%.cxx
$(COMPILE.cxx) $< -o $@
# Rules for generating fortran object files (.o).
#----------------------------------------
fobjs:$(FOBJS)
%.o:%.f
$(COMPILE.f) -c -o $@ $<
%.o:%.f90
$(COMPILE.f) -c -o $@ $<
%.o:%.f95
$(COMPILE.f) -c -o $@ $<
# Rules for generating the tags.
#-------------------------------------
tags: $(HEADERS) $(SOURCES)
$(ETAGS) $(ETAGSFLAGS) $(HEADERS) $(SOURCES)
ctags: $(HEADERS) $(SOURCES)
$(CTAGS) $(CTAGSFLAGS) $(HEADERS) $(SOURCES)
# Rules for generating the executable.
#-------------------------------------
$(PROGRAM):$(OBJS) $(FOBJS)
ifeq ($(SRC_CXX),) # C program
$(LINK.c) $(OBJS) $(MY_LIBS) -o $@
@echo Type ./$@ to execute the program.
else # C++ program # The link options have to be at the end of the command
$(LINK.cxx) $(OBJS) $(FOBJS) $(MY_LIBS) -o $@
@echo Type ./$@ to execute the program.
endif
ifndef NODEP
ifneq ($(DEPS),)
sinclude $(DEPS)
endif
endif
clean:
$(RM) $(FCOBJS) $(FOBJS) $(OBJS) $(PROGRAM) $(PROGRAM).exe
distclean: clean
$(RM) $(DEPS) TAGS
# Show help.
help:
@echo 'Generic Makefile for C/C++ Programs (gcmakefile) version 0.5'
@echo 'Copyright (C) 2007, 2008 whyglinux <whyglinux@hotmail.com>'
@echo 'Copyright (C) 2013, 2014 Shaun.Bai <Shaun.Bai@hotmail.com>'
@echo
@echo 'Usage: make [TARGET]'
@echo 'TARGETS:'
@echo ' all (=make) compile and link.'
@echo ' NODEP=yes make without generating dependencies.'
@echo ' objs compile only (no linking).'
@echo ' tags create tags for Emacs editor.'
@echo ' ctags create ctags for VI editor.'
@echo ' clean clean objects and the executable file.'
@echo ' distclean clean objects, the executable and dependencies.'
@echo ' show show variables (for debug use only).'
@echo ' run execute the main program.'
@echo ' help print this message.'
@echo
@echo 'Report bugs to <bunnysirah AT hotmail DOT com>.'
# Show variables (for debug use only.)
show:
@echo 'PROGRAM :' $(PROGRAM)
@echo 'SRCDIRS :' $(SRCDIRS)
@echo 'HEADERS :' $(HEADERS)
@echo 'SOURCES :' $(SOURCES)
@echo 'SRC_CXX :' $(SRC_CXX)
@echo 'OBJS :' $(OBJS)
@echo 'DEPS :' $(DEPS)
@echo 'DEPEND :' $(DEPEND)
@echo 'COMPILE.c :' $(COMPILE.c)
@echo 'COMPILE.cxx :' $(COMPILE.cxx)
@echo 'link.c :' $(LINK.c)
@echo 'link.cxx :' $(LINK.cxx)
# execute the main program
run:
$(MPI_ROOT_DIR)mpirun -np $(P) ./$(PROGRAM) -c ../SOHR_DATA/input/cmd.cfg
## End of the Makefile ## Suggestions are welcome ## All rights reserved ##
##############################################################