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#Makefile
# Supported platforms
# Unix / Linux LNX
# Mac MAC
# Compilation options
# 32-bit binary FORCE_32BIT
# dynamic compilation FORCE_DYNAMIC
# Set this variable to either LNX or MAC
SYS = LNX
# Leave blank after "=" to disable; put "= 1" to enable
SHOW_COMPILER_WARNINGS =
WITH_LAPACK = 1
WITH_OPENBLAS =
NO_INTEL_COMPAT =
FORCE_32BIT =
FORCE_DYNAMIC =
GCC_FLAGS = -O3 # extra flags -Wl,--allow-multiple-definition
DIST_NAME = gemma-0.97.1
TRAVIS_CI =
# --------------------------------------------------------------------
# Edit below this line with caution
# --------------------------------------------------------------------
EIGEN_INCLUDE_PATH=/usr/include/eigen3
BIN_DIR = ./bin
SRC_DIR = ./src
TEST_SRC_DIR = ./test/src
ifdef CXX
CPP = $(CXX)
CC = $(CXX)
else
CPP = g++
endif
ifdef DEBUG
CPPFLAGS = -g $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
else
# release mode
CPPFLAGS = -DNDEBUG $(GCC_FLAGS) -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
endif
ifdef SHOW_COMPILER_WARNINGS
CPPFLAGS += -Wall
endif
ifdef FORCE_DYNAMIC
LIBS = -lgsl -lgslcblas -pthread -lz
else
ifndef TRAVIS_CI # Travis static compile we cheat a little
CPPFLAGS += -static
endif
endif
OUTPUT = $(BIN_DIR)/gemma
SOURCES = $(SRC_DIR)/main.cpp
HDR =
# Detailed libary paths, D for dynamic and S for static
LIBS_LNX_D_LAPACK = -llapack
LIBS_LNX_D_BLAS = -lblas
LIBS_LNX_D_OPENBLAS = -lopenblas
LIBS_MAC_D_LAPACK = -framework Veclib
# LIBS_LNX_S_LAPACK = /usr/lib/libgsl.a /usr/lib/libgslcblas.a /usr/lib/lapack/liblapack.a -lz
LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition
SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp $(SRC_DIR)/ldr.cpp $(SRC_DIR)/bslmmdap.cpp $(SRC_DIR)/logistic.cpp $(SRC_DIR)/varcov.cpp $(SRC_DIR)/debug.cpp
HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
ifdef WITH_LAPACK
OBJS += $(SRC_DIR)/lapack.o
ifeq ($(SYS), MAC)
LIBS += $(LIBS_MAC_D_LAPACK)
else
ifdef FORCE_DYNAMIC
ifdef WITH_OPENBLAS
LIBS += $(LIBS_LNX_D_OPENBLAS)
else
LIBS += $(LIBS_LNX_D_BLAS)
endif
LIBS += $(LIBS_LNX_D_LAPACK)
else
LIBS += $(LIBS_LNX_S_LAPACK)
endif
endif
SOURCES += $(SRC_DIR)/lapack.cpp
HDR += $(SRC_DIR)/lapack.h
endif
ifdef NO_INTEL_COMPAT
else
ifdef FORCE_32BIT
CPPFLAGS += -m32
else
CPPFLAGS += -m64
endif
endif
# all
OBJS = $(SOURCES:.cpp=.o)
all: $(OUTPUT)
$(OUTPUT): $(OBJS)
$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
$(OBJS) : $(HDR)
.cpp.o:
$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
.SUFFIXES : .cpp .c .o $(SUFFIXES)
unittests: all contrib/catch-1.9.7/catch.hpp $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o
$(CPP) $(CPPFLAGS) $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(filter-out $(SRC_DIR)/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests
./bin/unittests
fast-check: all unittests
rm -vf test/output/*
cd test && ./dev_test_suite.sh | tee ../dev_test.log
grep -q 'success rate: 100%' dev_test.log
slow-check: all
rm -vf test/output/*
cd test && ./test_suite.sh | tee ../test.log
grep -q 'success rate: 100%' test.log
check: fast-check slow-check
clean:
rm -vf $(SRC_DIR)/*.o
rm -vf $(SRC_DIR)/*~
rm -vf $(TEST_SRC_DIR)/*.o
rm -vf $(OUTPUT)
rm -vf ./bin/unittests
DIST_COMMON = COPYING.txt README.txt Makefile
DIST_SUBDIRS = src doc example bin
tar:
mkdir -p ./$(DIST_NAME)
cp $(DIST_COMMON) ./$(DIST_NAME)/
cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/
tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/
rm -r ./$(DIST_NAME)
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