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Merge pull request #73 from stuart-knock/makefile
Extend Makefile
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‎.gitignore

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# Ignore files associated with compiling
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bin/
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obj/
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dep/
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# Ignore files associated with doxygen docs
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Documentation/html/
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Documentation/latex/
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doc/html/
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doc/latex/
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# Ignore NeuroField output files
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*.output

‎Makefile

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# Standard Linux (gcc must be > 4.9) performance
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CXX = g++
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CXXFLAGS = -g -lm -Wall -O3 -Wextra -pedantic -std=c++11 -msse -msse2 -msse3 -mfpmath=sse -march=native -mtune=native -funroll-loops -flto #-m64
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# Mac OS
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# CXX = g++-4.9
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# CXXFLAGS = -lm -Wall -O3 -std=c++11
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# Windows
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# CXX = x86_64-w64-mingw32-g++
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# CXXFLAGS = -lm -Wall -O3 -msse -msse2 -msse3 -mfpmath=sse -funroll-loops -flto -m64 -std=gnu++11 -static -static-libgcc -static-libstdc++
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# Debugging
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# CXX = g++
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# CXXFLAGS = g++ -g -lm -Wall -Wextra -pedantic -std=c++11 -msse -msse2 -msse3
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HEADER = $(wildcard src/*.h)
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CPP = $(wildcard src/*.cpp)
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OBJ = $(addprefix obj/,$(notdir $(CPP:.cpp=.o)))
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# target: default - compile bin/neurofield
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default: bin/neurofield
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debugmode: CXXFLAGS = -g -ggdb3 -lm -Wall -Wextra -pedantic -std=c++11 -msse -msse2 -msse3
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debugmode: bin/neurofield
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bin/neurofield: $(OBJ)
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@mkdir -p bin
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@echo "$(CXX) $(CXXFLAGS) $(OBJ) -o $@"
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@$(CXX) $(CXXFLAGS) $(OBJ) -o $@ || (echo "mycommand failed $$?"; exit 1)
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#Makefile for neurofield
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#
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# Type 'make help' for a list of possible targets with brief descriptions.
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# If you're having problems, the Makefile itself can be debugged using the
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# option -d, eg 'make -d help'. Also 'make info' will display the contents
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# of key variables in the Makefile, to help with debugging.
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#
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#Specify our directories.
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SRCDIR := src/
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OBJDIR := obj/
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BINDIR := bin/
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DOCDIR := doc/
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DEPDIR := dep/
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#Default to *nix, suffix-less, binary.
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BIN := neurofield
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#User-manual files
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USER_MANUAL := NeurofieldManual.pdf
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USER_MANUAL_SRC := NeurofieldManual.tex
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#Default to *nix commands.
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MV := mv -f
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RM := rm -f
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RMDIR := rm -rf
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GREP := egrep
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CAT := cat
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# Standard Linux (gcc must be >= 4.8.5) performance
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ifeq ($(shell uname -s), Linux)
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CXX := g++
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CXXFLAGS := -std=c++11 -lm -Wall -Wextra -pedantic -msse -msse2 -msse3 -mfpmath=sse -march=native -mtune=native -funroll-loops -flto -O3
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DEBUG := -std=c++11 -ggdb3 -Og -lm -Wall -Wextra -pedantic -msse -msse2 -msse3 -mfpmath=sse -march=native -mtune=native -funroll-loops
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DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
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endif
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# Mac OS, default to clang++
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ifeq ($(shell uname -s), Darwin)
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CXX := clang++
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CXXFLAGS := -std=c++11 -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -fdiagnostics-fixit-info -Wdocumentation -march=native -funroll-loops -flto -O3
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DEBUG := -std=c++11 -glldb -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -fdiagnostics-fixit-info -Wdocumentation
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DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
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endif
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# Source and header files
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HEADER := $(wildcard $(SRCDIR)*.h)
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CPP := $(wildcard $(SRCDIR)*.cpp)
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OBJ := $(addprefix $(OBJDIR),$(notdir $(CPP:.cpp=.o)))
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DEP := $(addprefix $(DEPDIR),$(notdir $(CPP:.cpp=.d)))
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#Targets that don't need the dependencies evaluated/included.
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NO_DEPS := make_bin_dir make_obj_dir make_dep_dir help help-dev docs info $(DOCDIR)$(USER_MANUAL) reference-manual user-manual
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NO_DEPS += clean-user-manual clean-reference-manual clean-docs clean-deps clean-objs clean-bin clean clean-all
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# Delete the default suffixes
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.SUFFIXES:
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# Define our suffix list
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.SUFFIXES: .o .d .cpp .h .tex
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.PHONY: neurofield debug all clang make_bin_dir make_obj_dir make_dep_dir help help-dev info docs user-manual reference-manual \
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clean-user-manual clean-reference-manual clean-docs clean-deps clean-objs clean-bin clean clean-all
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# target: neurofield - compile neurofield placing the executable in the bin directory.
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neurofield: $(BINDIR)$(BIN)
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# target: debug - compile neurofield with debugging enabled.
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debug: CXXFLAGS := $(DEBUG)
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debug: neurofield
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# target: all - compile neurofield and build all documentation.
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all: neurofield docs
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# target: clang - Build using clang++, redundant on MacOS as clang++ is default.
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ifeq ($(MAKECMDGOALS), clang)
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CXX := $(shell command -v clang++ 2> /dev/null)
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ifndef CXX
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$(error "You don't appear to have clang++ installed. If it is installed make sure it's in your PATH.")
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endif
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CXXFLAGS := -std=c++11 -Weverything -Wno-c++98-compat -Wno-c++98-compat-pedantic -fdiagnostics-fixit-info -Wdocumentation -march=native -funroll-loops -flto -O3
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DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
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endif
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clang: neurofield
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# target: icc - Build using intel C++ compiler.
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ifeq ($(MAKECMDGOALS), icc)
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CXX := $(shell command -v icc 2> /dev/null)
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ifndef CXX
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$(error "You don't appear to have icc installed. If it is installed make sure it's in your PATH.")
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endif
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#TODO: consider/test -ipp -mkl -unroll-aggressive -static
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CXXFLAGS := -std=c++11 -Wall -Wremarks -Wchecks -Weffec++ -xHost -funroll-loops -ipo -O3
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DEPFLAGS = -std=c++11 -MM -MP -MT $(OBJDIR)$*.o
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endif
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icc: neurofield
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# target: $(BINDIR)$(BIN) - Main target for the final build, linking objects into an executable.
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$(BINDIR)$(BIN): $(OBJ) | make_bin_dir
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$(CXX) $(CXXFLAGS) $(OBJ) -o $@
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@echo "====="
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@cat license.txt
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@$(CAT) license.txt
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@echo "====="
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@echo "USE OF NEUROFIELD CONSTITUTES ACCEPTANCE OF THE LICENSE CONDITIONS ABOVE"
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# target: make_bin_dir - Create the directory $BINDIR if it doesn't already exist.
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make_bin_dir:
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@test -d $(BINDIR) || { mkdir $(BINDIR) ; echo "mkdir $(BINDIR)"; }
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# target: make_obj_dir - Create the directory $OBJDIR if it doesn't already exist.
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make_obj_dir:
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@test -d $(OBJDIR) || { mkdir $(OBJDIR) ; echo "mkdir $(OBJDIR)"; }
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# target: make_dep_dir - Create the directory $DEPDIR if it doesn't already exist.
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make_dep_dir:
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@test -d $(DEPDIR) || { mkdir $(DEPDIR) ; echo "mkdir $(DEPDIR)"; }
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#Only create and include dependencies if the current target requires them.
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ifeq (, $(filter $(MAKECMDGOALS), $(NO_DEPS)))
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#Create obj/*.d header dependencies
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$(DEPDIR)%.d: $(SRCDIR)%.cpp | make_dep_dir
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$(CXX) $(DEPFLAGS) $< > $(DEPDIR)$*.d
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# Include any existing dependencies in the build
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-include $(OBJ:.o=.d)
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# Build object code and also create obj/*.d header dependencies
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obj/%.o: src/%.cpp
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@mkdir -p obj
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@$(CXX) $(CXXFLAGS) -c $< -o $@
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@$(CXX) -MM $(CXXFLAGS) $< > obj/$*.d
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@echo "CXX $<"
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@mv -f obj/$*.d obj/$*.d.tmp
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@sed -e 's|.*:|$@:|' < obj/$*.d.tmp > obj/$*.d
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@sed -e 's/.*://' -e 's/\\$$//' < obj/$*.d.tmp | fmt -1 | \
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sed -e 's/^ *//' -e 's/$$/:/' >> obj/$*.d
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@rm -f obj/$*.d.tmp
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# Build documentation: compile tex file and produce html docs from code
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build_docs:
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cd Documentation && pdflatex neurofield && pdflatex neurofield && cd ../ && doxygen Doxyfile
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.PHONY: clean doc help
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# target: help - Print this message
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help:
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@egrep "^# target:" Makefile
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-include $(DEP)
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endif
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# target: doc - compile Documentation/neurofield.pdf
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doc: Documentation/neurofield.pdf
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# Build object code
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$(OBJDIR)%.o: $(SRCDIR)%.cpp | make_obj_dir
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$(CXX) $(CXXFLAGS) -c $< -o $@
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# target: clean - Delete ./bin/, ./obj/, and LaTeX temporary files in ./Documentation/
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clean:
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@-rm -rf bin obj Documentation/{user,developer}.{aux,log,out,toc} Documentation/x.log
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# target: help - Print this message.
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help:
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@echo "Available Makefile targets, call as 'make target', eg. make all"
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@$(GREP) "^# target:" Makefile
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# target: help-dev - Print an extended list of targets.
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help-dev: help
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@echo "Additional targets, mainly useful for developers."
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@$(GREP) "^# target:" Makefile
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# target: info - A convenience target for debugging the Makefile.
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info:
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@echo " SHELL: $(SHELL)"
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@echo " MAKE_VERSION: $(MAKE_VERSION)"
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@echo " .VARIABLES: $(.VARIABLES)"
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@echo " .DEFAULT_GOAL: $(.DEFAULT_GOAL)"
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@echo " SRCDIR: $(SRCDIR)"
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@echo " OBJDIR: $(OBJDIR)"
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@echo " BINDIR: $(BINDIR)"
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@echo " DOCDIR: $(DOCDIR)"
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@echo " HEADER: $(HEADER)"
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@echo " CPP: $(CPP)"
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@echo " OBJ: $(OBJ)"
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@echo " DEP: $(DEP)"
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@echo " CXX: $(CXX)"
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@echo " CXXFLAGS: $(CXXFLAGS)"
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@echo " DEBUG: $(DEBUG)"
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@echo " NO_DEPS: $(NO_DEPS)"
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# target: docs - Build user and reference manuals.
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docs: user-manual reference-manual
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# target: user-manual - Build only the user-manual.
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user-manual: $(DOCDIR)$(USER_MANUAL)
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# target: $(DOCDIR)$(USER_MANUAL) - target that actually builds the user manual.
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$(DOCDIR)$(USER_MANUAL): $(DOCDIR)$(USER_MANUAL_SRC)
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cd $(DOCDIR) && \
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pdflatex $(USER_MANUAL_SRC) && \
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pdflatex $(USER_MANUAL_SRC)
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# target: reference-manual - Build only the reference-manual.
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reference-manual:
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doxygen Doxyfile
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# target: clean-docs - Delete temporary LaTeX files and Doxygen generated reference-manual.
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clean-docs: clean-user-manual clean-reference-manual
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# target: clean-user-manual - Delete temporary LaTeX files generated when building the user-manual.
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clean-user-manual:
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-$(RM) $(DOCDIR)$(USER_MANUAL_SRC:.tex=).{aux,log,out,toc}
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# target: clean-reference-manual - Delete Doxygen generated reference-manual.
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clean-reference-manual:
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-$(RMDIR) $(DOCDIR)html
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-$(RMDIR) $(DOCDIR)latex
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# target: clean-deps - Delete the dependencies created during build.
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clean-deps:
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-$(RM) $(DEP)
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# target: clean-objs - Delete the objects created during build.
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clean-objs:
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-$(RM) $(OBJ)
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# target: clean-bin - Delete the executable generated by the build.
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clean-bin:
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-$(RM) $(BINDIR)$(BIN)
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# target: clean - Delete dependency files, temporary build objects and temporary LaTeX files.
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clean: clean-deps clean-objs clean-user-manual
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# target: clean-all - Same as clean but also delete Doxygen generated docs, and the executable.
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clean-all: clean-deps clean-objs clean-bin clean-docs

‎README.md

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### Quick start
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make ./bin/neurofield -i configs/example.conf -o example.output
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doxygen Doxyfile
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The html files will be place under `doc/html`
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To build the executable on Linux or Mac, open a terminal in the neurofield directory and type:
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make
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this produces the executable (bin/neurofield). The user-manual is available as doc/NeurofieldManual.pdf.
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To build the reference manual, generated from the code, type:
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make reference-manual
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The html files for the reference-manual will be place under `doc/html`, point your browser at the index.html file in that directory.
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For a brief description of available Makefile targets, type:
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make help
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### Setup guide
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921
**Please check the [NeuroField wiki](https://github.com/BrainDynamicsUSYD/neurofield/wiki) for the setup walkthrough. The instructions below are a standalone summary if you do not have internet access. More detailed instructions are also included in the PDF documentation**
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1. Ensure you have a compiler that supports the `C++11` standard. We recommend GCC 4.8 or higher.
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2. Type `make` to build the binary `Release/NeuroField`. More information about [cross platform for non-Linux](https://github.com/BrainDynamicsUSYD/neurofield/wiki/Cross-platform-support) systems is also available.
25+
2. Type `make` to build the binary `bin/neurofield`. More information about [cross platform for non-Linux](https://github.com/BrainDynamicsUSYD/neurofield/wiki/Cross-platform-support) systems is also available.
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3. Example configurations including examples for published results are available in the `configs` folder.
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‎doc/NeurofieldManual.pdf

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‎doc/NeurofieldManual.tex

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\begin{tabular}{l p{13cm}}
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\type{src/}& \type{C++} source code.\\
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\type{(obj/)}& This folder is created during compilation and stores intermediate object code.\\
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\type{(dep/)}& This folder is created during compilation and stores dependency information.\\
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\type{(bin/)}& The compiled binary \type{neurofield} is created here.\\
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\type{configs/}& Stores example configuration files for \NF.\\
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\type{doc/}& Contains this manual.\\
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\type{doc/}& Contains this manual and the reference manual once it's built.\\
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\type{+nf/}& Matlab package folder containing \NF helper scripts.\\
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\type{test/}& Directory for development testing and is irrelevant for users.\\
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\end{tabular}
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128129
make
129130
\end{lstlisting}
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from the root directory. The compiler command is specified in \type{Makefile} and should be edited if you wish to use a different compiler, or if your compiler does not support some of the compiler flags. To run \NF on Windows, we suggest cross-compiling using MinGW on a Unix-like system. Example compiler flags for this are included in \type{Makefile}. Compiling with the Microsoft Visual \type{C++} compiler has not been tested.
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from the root directory. The compiler command is specified in \type{Makefile}. On Linux this defaults to \type{g++} and on Mac it defaults to \type{clang++}. To run \NF on Windows, we suggest cross-compiling using MinGW on a Unix-like system. Example compiler flags for this are included in \type{Makefile}. Compiling with the Microsoft Visual \type{C++} compiler has not been tested.
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The \type{Makefile} also provides two additional commands. This documentation can be generated by running
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The \type{Makefile} also provides a number of additional commands. This documentation along with the reference-manual can be generated by running
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\begin{lstlisting}
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make doc
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make docs
136137
\end{lstlisting}
137-
which will compile the \LaTeX\ files in the \type{doc/} directory. To delete the \NF binary files, object code, and temporary \LaTeX\ files (e.g., to perform a clean compile of the program), you can use
138+
which will recompile the \LaTeX\ files in the \type{doc/} directory if they've been updated since the last time this .pdf was generated, and run doxygen to generate the reference-manual from the source code. The reference manual can then be viewed by pointing your web-browser at
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\begin{lstlisting}
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doc/html/index.html
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\end{lstlisting}
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To delete the dependency files, object code, and temporary \LaTeX\ files (e.g., to perform a clean compile of the program), you can use
138145
\begin{lstlisting}
139146
make clean
140147
\end{lstlisting}
141-
which will delete the \type{bin} and \type{obj} folders, as well as the temporary files in \type{doc/}.
148+
which will delete the \type{dep/*.d} and \type{obj/*.o} files, as well as the temporary \LaTeX\ files in \type{doc/}. For a list of additional make targets, including brief descriptions of their function, run
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\begin{lstlisting}
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make help
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\end{lstlisting}
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143153
\section{Running NeuroField}
144154
\label{sec:running}
@@ -544,12 +554,14 @@ \subsubsection{Couple Classes}
544554
\begin{lstlisting}
545555
CaDP - nu: 13e-6 nu_max: 80e-6 Dth: .25e-6 Pth: .45e-6 xyth: 1e-4 x: 2.3e-2 y: 2e-2 B: 30e3 glu_0: 200e-6 gNMDA: 2e-3 t_BCM: 7
546556
\end{lstlisting}
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\item[DiffArctan]\ \\
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558+
\item[DiffArctan]\ \\
548559
This type of coupling allows the connection strength $\nu_{ab}$ to vary as a function of time, such that $\nu$ can be smoothly ramped up and down.
549560
\begin{lstlisting}
550561
DiffArctan - nu_min: 0.002 nu_max: 0.006 delta: 10 t_half_up:50 t_half_down:100
551562
\end{lstlisting}
552563
where \type{nu\_min} and \type{nu\_max} are the min and max $\nu$'s respectively. \type{delta} determines the slope of the ramp (1/\type{delta}) and is the time interval in which the connection strenght increases (decreases) from 0.25 to 0.75 of \type{nu\_max}. \type{t\_half\_up} and \type{t\_half\_down} are the half way times to maximum and minimum amplitude, respectively.
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553565
\end{description}
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\end{itemize}
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