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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
#
# Run quick (development) tests with
#
# make fast-check
#
# Run full (lengthy) tests with
#
# make check-all
#
# See also the INSTALL.md document in the source tree at
#
# https://github.com/genetics-statistics/GEMMA/blob/master/INSTALL.md
# Set this variable to either LNX or MAC
SYS = LNX # LNX|MAC (Linux is the default)
# Leave blank after "=" to disable; put "= 1" to enable
DIST_NAME = gemma-0.97.3
DEBUG = 1 # DEBUG mode, set DEBUG=0 for a release
SHOW_COMPILER_WARNINGS =
WITH_LAPACK = 1
WITH_OPENBLAS = # Defaults to LAPACK - OPENBLAS may be faster
OPENBLAS_LEGACY = # Using older OpenBlas
FORCE_STATIC = # Static linking of libraries
GCC_FLAGS = -O3 -std=gnu++11 # extra flags -Wl,--allow-multiple-definition
TRAVIS_CI = # used by TRAVIS for testing
EIGEN_INCLUDE_PATH = /usr/include/eigen3
# --------------------------------------------------------------------
# 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 = $(CXX)
else
CPP = g++
endif
ifeq ($(CPP), clang++)
# macOS Homebrew settings (as used on Travis-CI)
GCC_FLAGS=-O3 -std=c++11 -stdlib=libc++ -isystem//usr/local/opt/openblas/include -isystem//usr/local/include/eigen3 -Wl,-L/usr/local/opt/openblas/lib
endif
ifdef WITH_OPENBLAS
OPENBLAS=1
# WITH_LAPACK = # OPENBLAS usually includes LAPACK
CPPFLAGS += -DOPENBLAS
ifdef OPENBLAS_LEGACY
CPPFLAGS += -DOPENBLAS_LEGACY
endif
endif
ifdef DEBUG
CPPFLAGS += -g $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
else
# release mode
CPPFLAGS += -DNDEBUG $(GCC_FLAGS) -isystem/$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
endif
ifdef SHOW_COMPILER_WARNINGS
CPPFLAGS += -Wall
endif
ifndef FORCE_STATIC
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 = $(SRC_DIR)/main.cpp
HDR =
# Detailed libary paths, D for dynamic and S for static
LIBS_LNX_D_LAPACK = -llapack
LIBS_LNX_D_BLAS = -lblas
LIBS_LNX_D_OPENBLAS = -lopenblas
LIBS_MAC_D_LAPACK = -framework Accelerate
# LIBS_LNX_S_LAPACK = /usr/lib/libgsl.a /usr/lib/libgslcblas.a /usr/lib/lapack/liblapack.a -lz
LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition
ifdef WITH_LAPACK
ifeq ($(SYS), MAC)
LIBS += $(LIBS_MAC_D_LAPACK)
else
ifndef FORCE_STATIC
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
endif
HDR = $(wildcard src/*.h)
SOURCES = $(wildcard src/*.cpp)
# 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/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)/*.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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