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rheilandrheiland
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add Makefile
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‎user_projects/mech_voxel_size/Makefile‎

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VERSION := $(shell grep . VERSION.txt | cut -f1 -d:)
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PROGRAM_NAME := project
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CC := g++
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# CC := g++-mp-7 # typical macports compiler name
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# CC := g++-7 # typical homebrew compiler name
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# Check for environment definitions of compiler
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# e.g., on CC = g++-7 on OSX
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ifdef PHYSICELL_CPP
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CC := $(PHYSICELL_CPP)
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endif
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ifndef STATIC_OPENMP
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STATIC_OPENMP = -fopenmp
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endif
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ARCH := native # best auto-tuning
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# ARCH := core2 # a reasonably safe default for most CPUs since 2007
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# ARCH := corei7
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# ARCH := corei7-avx # earlier i7
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# ARCH := core-avx-i # i7 ivy bridge or newer
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# ARCH := core-avx2 # i7 with Haswell or newer
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# ARCH := nehalem
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# ARCH := westmere
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# ARCH := sandybridge # circa 2011
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# ARCH := ivybridge # circa 2012
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# ARCH := haswell # circa 2013
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# ARCH := broadwell # circa 2014
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# ARCH := skylake # circa 2015
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# ARCH := bonnell
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# ARCH := silvermont
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# ARCH := skylake-avx512
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# ARCH := nocona #64-bit pentium 4 or later
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# CFLAGS := -march=$(ARCH) -Ofast -s -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
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CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -mfpmath=both -fopenmp -m64 -std=c++11
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ifeq ($(OS),Windows_NT)
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else
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UNAME_S := $(shell uname -s)
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ifeq ($(UNAME_S),Darwin)
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UNAME_P := $(shell uname -p)
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var := $(shell which $(CC) | xargs file)
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ifeq ($(lastword $(var)),arm64)
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CFLAGS := -march=$(ARCH) -O3 -fomit-frame-pointer -fopenmp -m64 -std=c++11
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endif
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endif
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endif
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CFLAGS_LINK := $(shell echo $(CFLAGS) | sed -e "s/-fopenmp//g")
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COMPILE_COMMAND := $(CC) $(CFLAGS) $(EXTRA_FLAGS)
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LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
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BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
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BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o
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PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
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PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
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PhysiCell_signal_behavior.o PhysiCell_rules.o
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PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
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PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
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# put your custom objects here (they should be in the custom_modules directory)
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PhysiCell_custom_module_OBJECTS := custom.o
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pugixml_OBJECTS := pugixml.o
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PhysiCell_OBJECTS := $(BioFVM_OBJECTS) $(pugixml_OBJECTS) $(PhysiCell_core_OBJECTS) $(PhysiCell_module_OBJECTS)
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ALL_OBJECTS := $(PhysiCell_OBJECTS) $(PhysiCell_custom_module_OBJECTS)
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# compile the project
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all: main.cpp $(ALL_OBJECTS)
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$(COMPILE_COMMAND) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp
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make name
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static: main.cpp $(ALL_OBJECTS) $(MaBoSS)
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$(LINK_COMMAND) $(INC) -o $(PROGRAM_NAME) $(ALL_OBJECTS) main.cpp $(LIB) -static-libgcc -static-libstdc++ $(STATIC_OPENMP)
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name:
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@echo ""
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@echo "Executable name is" $(PROGRAM_NAME)
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@echo ""
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# PhysiCell core components
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PhysiCell_phenotype.o: ./core/PhysiCell_phenotype.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_phenotype.cpp
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PhysiCell_digital_cell_line.o: ./core/PhysiCell_digital_cell_line.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_digital_cell_line.cpp
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PhysiCell_cell.o: ./core/PhysiCell_cell.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_cell.cpp
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PhysiCell_cell_container.o: ./core/PhysiCell_cell_container.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_cell_container.cpp
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PhysiCell_standard_models.o: ./core/PhysiCell_standard_models.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_standard_models.cpp
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PhysiCell_utilities.o: ./core/PhysiCell_utilities.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_utilities.cpp
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PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_custom.cpp
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PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp
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PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp
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PhysiCell_rules.o: ./core/PhysiCell_rules.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_rules.cpp
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# BioFVM core components (needed by PhysiCell)
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BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_vector.cpp
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BioFVM_agent_container.o: ./BioFVM/BioFVM_agent_container.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_agent_container.cpp
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BioFVM_mesh.o: ./BioFVM/BioFVM_mesh.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_mesh.cpp
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BioFVM_microenvironment.o: ./BioFVM/BioFVM_microenvironment.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_microenvironment.cpp
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BioFVM_solvers.o: ./BioFVM/BioFVM_solvers.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_solvers.cpp
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BioFVM_utilities.o: ./BioFVM/BioFVM_utilities.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_utilities.cpp
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BioFVM_basic_agent.o: ./BioFVM/BioFVM_basic_agent.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_basic_agent.cpp
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BioFVM_matlab.o: ./BioFVM/BioFVM_matlab.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_matlab.cpp
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BioFVM_MultiCellDS.o: ./BioFVM/BioFVM_MultiCellDS.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/BioFVM_MultiCellDS.cpp
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pugixml.o: ./BioFVM/pugixml.cpp
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$(COMPILE_COMMAND) -c ./BioFVM/pugixml.cpp
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# standard PhysiCell modules
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PhysiCell_SVG.o: ./modules/PhysiCell_SVG.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_SVG.cpp
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PhysiCell_pathology.o: ./modules/PhysiCell_pathology.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_pathology.cpp
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PhysiCell_MultiCellDS.o: ./modules/PhysiCell_MultiCellDS.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_MultiCellDS.cpp
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PhysiCell_various_outputs.o: ./modules/PhysiCell_various_outputs.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_various_outputs.cpp
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PhysiCell_pugixml.o: ./modules/PhysiCell_pugixml.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_pugixml.cpp
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PhysiCell_settings.o: ./modules/PhysiCell_settings.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_settings.cpp
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PhysiCell_basic_signaling.o: ./core/PhysiCell_basic_signaling.cpp
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$(COMPILE_COMMAND) -c ./core/PhysiCell_basic_signaling.cpp
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PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
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$(COMPILE_COMMAND) -c ./modules/PhysiCell_geometry.cpp
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# user-defined PhysiCell modules
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custom.o: ./custom_modules/custom.cpp
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$(COMPILE_COMMAND) -c ./custom_modules/custom.cpp
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# cleanup
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reset:
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rm -f *.cpp
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cp ./sample_projects/Makefile-default Makefile
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rm -f ./custom_modules/*
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touch ./custom_modules/empty.txt
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touch ALL_CITATIONS.txt
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touch ./core/PhysiCell_cell.cpp
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rm ALL_CITATIONS.txt
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cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml
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touch ./config/empty.csv
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rm -f ./config/*.csv
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clean:
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rm -f *.o
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rm -f $(PROGRAM_NAME)*
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data-cleanup:
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rm -rf ./output
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mkdir ./output
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touch ./output/empty.txt
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# archival
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checkpoint:
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zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/*
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zip:
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zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
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cp latest.zip $$(date +%b_%d_%Y_%H%M).zip
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cp latest.zip VERSION_$(VERSION).zip
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mv *.zip archives/
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tar:
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tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/*
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cp latest.tar $$(date +%b_%d_%Y_%H%M).tar
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cp latest.tar VERSION_$(VERSION).tar
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mv *.tar archives/
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unzip:
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cp ./archives/latest.zip .
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unzip latest.zip
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untar:
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cp ./archives/latest.tar .
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tar -xzf latest.tar
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# easier animation
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FRAMERATE := 24
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OUTPUT := output
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jpeg:
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@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt
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@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt
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@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt
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@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt
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@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt
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@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
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rm -f __H*.txt __W*.txt __resize.txt
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gif:
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magick convert $(OUTPUT)/s*.svg $(OUTPUT)/out.gif
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movie:
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ffmpeg -r $(FRAMERATE) -f image2 -i $(OUTPUT)/snapshot%08d.jpg -vcodec libx264 -pix_fmt yuv420p -strict -2 -tune animation -crf 15 -acodec none $(OUTPUT)/out.mp4
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# upgrade rules
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SOURCE := PhysiCell_upgrade.zip
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get-upgrade:
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@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt
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@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt
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rm -f VER.txt
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$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
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rm -f DL_FILE.txt
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PhysiCell_upgrade.zip:
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make get-upgrade
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upgrade: $(SOURCE)
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unzip $(SOURCE) PhysiCell/VERSION.txt
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mv -f PhysiCell/VERSION.txt .
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unzip $(SOURCE) PhysiCell/core/*
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cp -r PhysiCell/core/* core
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unzip $(SOURCE) PhysiCell/modules/*
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cp -r PhysiCell/modules/* modules
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unzip $(SOURCE) PhysiCell/sample_projects/*
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cp -r PhysiCell/sample_projects/* sample_projects
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unzip $(SOURCE) PhysiCell/BioFVM/*
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cp -r PhysiCell/BioFVM/* BioFVM
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unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
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mv -f PhysiCell/documentation/User_Guide.pdf documentation
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rm -f -r PhysiCell
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rm -f $(SOURCE)
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# use: make save PROJ=your_project_name
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PROJ := my_project
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save:
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echo "Saving project as $(PROJ) ... "
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mkdir -p ./user_projects
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mkdir -p ./user_projects/$(PROJ)
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mkdir -p ./user_projects/$(PROJ)/custom_modules
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mkdir -p ./user_projects/$(PROJ)/config
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cp main.cpp ./user_projects/$(PROJ)
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cp Makefile ./user_projects/$(PROJ)
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cp VERSION.txt ./user_projects/$(PROJ)
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cp ./config/* ./user_projects/$(PROJ)/config
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cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
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load:
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echo "Loading project from $(PROJ) ... "
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cp ./user_projects/$(PROJ)/main.cpp .
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cp ./user_projects/$(PROJ)/Makefile .
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cp ./user_projects/$(PROJ)/config/* ./config/
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cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/
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pack:
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@echo " "
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@echo "Preparing project $(PROJ) for sharing ... "
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@echo " "
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cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
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@echo " "
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@echo "Share ./user_projects/$(PROJ).zip ... "
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@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
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@echo " "
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unpack:
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@echo " "
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@echo "Preparing shared project $(PROJ).zip for use ... "
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@echo " "
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cd ./user_projects && unzip $(PROJ).zip
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@echo " "
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@echo "Load this project via make load PROJ=$(PROJ) ... "
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@echo " "
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list-user-projects:
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@echo "user projects::"
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@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'

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