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Specifies a path that the linker will search before it searches the path specified in the LIB environment option. Use the /LIBPATH option to override the environment library path. The linker will first search in the path specified by this option, and then search in the path specified in the LIB environment variable. Check your PATH Setting. In the instructions below, $INSTALLDIR refers to the path to the new install directory, /path/to/dakota/install/directory/Dakota.
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| # Generic Makefile for GEMMA |
| # |
| # Supported platforms |
| # |
| # Unix / Linux LNX (default) |
| # Mac MAC |
| # |
| # Compilation options |
| # static compilation FORCE_STATIC |
| # |
| # Examples: |
| # |
| # Make GEMMA on Linux with OPENBLAS support: |
| # |
| # make WITH_OPENBLAS=1 |
| # |
| # Disable debug info and checks (slightly faster release mode) |
| # |
| # make WITH_OPENBLAS=1 DEBUG= |
| # |
| # Force static compilation |
| # |
| # make FORCE_STATIC=1 |
| # |
| # Run tests with |
| # |
| # make check |
| # |
| # See also the INSTALL.md document in the source tree at |
| # |
| # https://github.com/genetics-statistics/GEMMA/blob/master/INSTALL.md |
| GEMMA_VERSION = $(shell cat ./VERSION) |
| # Set this variable to either LNX or MAC |
| SYS = MAC # LNX|MAC (Linux is the default) |
| # Leave blank after '=' to disable; put '= 1' to enable |
| DIST_NAME = gemma-$(GEMMA_VERSION) |
| DEBUG = # DEBUG mode, set DEBUG= for a release |
| SHOW_COMPILER_WARNINGS = |
| WITH_LAPACK = 1 |
| WITH_OPENBLAS = # Defaults to LAPACK - OPENBLAS may be faster |
| FORCE_STATIC = # Static linking of libraries |
| GCC_FLAGS = -O3 -I/usr/local/Cellar/gsl/2.4/include -I./eigen |
| -I/System/Library/Frameworks/Accelerate.framework/Versions/Current/Frameworks/vecLib.framework/Headers |
| TRAVIS_CI = # used by TRAVIS for testing |
| EIGEN_INCLUDE_PATH= |
| CXX = g++ |
| # -------------------------------------------------------------------- |
| # Edit below this line with caution |
| # -------------------------------------------------------------------- |
| BIN_DIR = ./bin |
| SRC_DIR = ./src |
| TEST_SRC_DIR = ./test/src |
| ifdef CXX # CXX defined in environment |
| CPP = $(CXX) |
| CC = $(CXX) |
| else |
| CPP = g++ |
| endif |
| ifdef OPENBLAS |
| WITH_LAPACK = # OPENBLAS usually includes LAPACK |
| 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 |
| OUTPUT = $(BIN_DIR)/gemma |
| SOURCES = $(SRC_DIR)/main.cpp |
| HDR = |
| # Detailed libary paths, D for dynamic and S for static |
| LIBS += -framework Accelerate |
| /usr/local/opt/zlib/lib/libz.a |
| /usr/local/Cellar/gsl/2.4/lib/libgsl.a |
| /usr/local/Cellar/gsl/2.4/lib/libgslcblas.a |
| HDR = $(wildcard src/*.h) ./src/version.h |
| SOURCES = $(wildcard src/*.cpp) |
| # all |
| OBJS = $(SOURCES:.cpp=.o) |
| all: $(OUTPUT) |
| ./src/version.h: |
| ./scripts/gen_version_info.sh > src/version.h |
| <print-% : ; @echo $* = $($*) |
| $(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/main.o, $(OBJS)) $(LIBS) -o ./bin/unittests-gemma |
| ./bin/unittests-gemma |
| 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 |
| lengthy-check: all |
| rm -vf test/output/* |
| cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log |
| grep -q 'success rate: 100%' lengthy_test.log |
| check: fast-check slow-check |
| check-all: check lengthy-check |
| clean: |
| rm -vf $(SRC_DIR)/version.h |
| rm -vf $(SRC_DIR)/*.o |
| rm -vf $(SRC_DIR)/*~ |
| rm -vf $(TEST_SRC_DIR)/*.o |
| rm -vf $(OUTPUT) |
| rm -vf ./bin/unittests-gemma |
| DIST_COMMON = COPYING.txt README.txt Makefile |
| DIST_SUBDIRS = src doc example bin |
| tar: |
| mkdir -p ./$(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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