diff options
| -rw-r--r-- | Makefile.linux | 110 | ||||
| -rw-r--r-- | Makefile.macosx | 153 |
2 files changed, 0 insertions, 263 deletions
diff --git a/Makefile.linux b/Makefile.linux deleted file mode 100644 index ab6163d..0000000 --- a/Makefile.linux +++ /dev/null @@ -1,110 +0,0 @@ -#Makefile - -# Supported platforms -# Unix / Linux LNX -# Mac MAC -# Compilation options -# link to LAPACK WITH_LAPACK -# 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 -# Disable WITH_LAPACK option can slow computation speed significantly and is not recommended -# Disable WITH_ARPACK option only disable -apprx option in the software -WITH_LAPACK = 1 -FORCE_32BIT = -FORCE_DYNAMIC = -DIST_NAME = gemma-0.97.1 - -# -------------------------------------------------------------------- -# Edit below this line with caution -# -------------------------------------------------------------------- - -BIN_DIR = ./bin - -SRC_DIR = ./src - -CPP = g++ - -CPPFLAGS = -O3 -std=gnu++11 -I./eigen - -LIBS = /software/gsl-1.16-el7-x86_64/lib/libgslcblas.a \ - /software/gsl-1.16-el7-x86_64/lib/libgsl.a \ - -pthread -lz - -# ifdef FORCE_DYNAMIC -# LIBS = -lgsl -lgslcblas -lblas -pthread -lz -# else -# LIBS = -lgsl -lgslcblas -pthread -lz -# 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_MAC_D_LAPACK = -framework Veclib -LIBS_LNX_S_LAPACK = /software/atlas-3.10.3-el7-x86_64/lib/liblapack.a \ - /software/atlas-3.10.3-el7-x86_64/lib/libcblas.a \ - /software/atlas-3.10.3-el7-x86_64/lib/libf77blas.a \ - /software/atlas-3.10.3-el7-x86_64/lib/libatlas.a -lgfortran \ - -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 -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 += $(SRC_DIR)/lapack.o - CPPFLAGS += -DWITH_LAPACK -ifeq ($(SYS), MAC) - LIBS += $(LIBS_MAC_D_LAPACK) -else -ifdef FORCE_DYNAMIC - 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 FORCE_32BIT - CPPFLAGS += -m32 -else - CPPFLAGS += -m64 -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) - - -clean: - rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT) - -DIST_COMMON = COPYING.txt README.txt Makefile -DIST_SUBDIRS = src doc example bin - -tar: - mkdir -p ./$(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) - diff --git a/Makefile.macosx b/Makefile.macosx deleted file mode 100644 index fa7460e..0000000 --- a/Makefile.macosx +++ /dev/null @@ -1,153 +0,0 @@ -# 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) |