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|
# Generic Makefile for GEMMA
#
# Supported platforms
#
# Unix / Linux LNX (default)
# Mac OSX
# GNU Guix GUIX (set to profile)
#
# Compilation options
# static compilation FORCE_STATIC
#
# Examples:
#
# Make GEMMA on Linux without OPENBLAS support:
#
# make WITH_OPENBLAS=
#
# Disable debug info and checks (release mode is slightly faster)
#
# make debug
#
# Force static compilation
#
# make static
#
# Run tests with
#
# make check
#
# Run quick (development) tests with
#
# make fast-check
#
# Run full (lengthy) tests with
#
# make check-all
#
# To compile with CLANG
#
# make CXX=clang++
#
# See also the INSTALL.md document in the source tree at
#
# https://github.com/genetics-statistics/GEMMA/blob/master/INSTALL.md
GEMMA_VERSION = $(shell cat ./VERSION)
# Set this variable to either LNX or OSX
ifeq ($(OS),Windows_NT)
SYS = WIN
VGEN = scripts/gen_version_info.cmd
else
UNAME_S := $(shell uname -s)
ifeq ($(UNAME_S),Darwin)
SYS = OSX
else
SYS = LNX # default to linux
endif
VGEN = scripts/gen_version_info.sh
endif
# Leave blank after "=" to disable; put "= 1" to enable
DIST_NAME = gemma-$(GEMMA_VERSION)
DEBUG = 1 # DEBUG mode, set DEBUG=0 for a release
PROFILING = # Add profiling info
SHOW_COMPILER_WARNINGS =
WITH_OPENBLAS = 1 # Without OpenBlas uses LAPACK
WITH_ATLAS = # In place of OpenBlas(?)
WITH_LAPACK = # Force linking LAPACK (if OpenBlas lacks it)
WITH_GSLCBLAS = # Force linking gslcblas (if OpenBlas lacks it)
WITH_GFORTRAN = # Add -lgfortran (if OpenBlas does not pull it in)
OPENBLAS_LEGACY = # Using older OpenBlas
FORCE_STATIC = # Static linking of libraries
GCC_FLAGS = -DHAVE_INLINE -pthread -Wall -std=gnu++11 # extra flags -Wl,--allow-multiple-definition
GSL_INCLUDE_PATH =
ifeq ($(SYS), WIN)
GSL_INCLUDE_PATH = -isystemc:/MinGW/include -LC:/MinGW/lib
EIGEN_INCLUDE_PATH = ../eigen-git-mirror
OPENBLAS_INCLUDE_PATH = ../OpenBLAS-v0.2.19-Win64-int32/include -L../OpenBLAS-v0.2.19-Win64-int32/lib
else
OPENBLAS_INCLUDE_PATH = /usr/local/opt/openblas/include
ifeq ($(SYS), OSX)
EIGEN_INCLUDE_PATH = /usr/local/include/eigen3
else
EIGEN_INCLUDE_PATH = /usr/include/eigen3
endif
ifndef GUIX
ifdef GUIX_ENVIRONMENT
GUIX=$(GUIX_ENVIRONMENT)
endif
endif
ifdef GUIX
# Effectively disable paths for GNU Guix
OPENBLAS_INCLUDE_PATH = .
EIGEN_INCLUDE_PATH = $(GUIX)/include/eigen3
# RPATH = -Xlinker --rpath=$(GUIX)/lib
ifdef FORCE_STATIC
LIBS = -L$(GUIX)/lib
endif
GUIX_PROFILE =$(realpath $(GUIX))
endif
endif
# --------------------------------------------------------------------
# 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++)
GCC_FLAGS=-std=c++11 -isystem$(OPENBLAS_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH)
ifdef GUIX
CPPFLAGS += -I$(GUIX)/include/c++ -I$(GUIX)/include/c++/x86_64-unknown-linux-gnu
endif
endif
ifdef WITH_OPENBLAS
OPENBLAS=1
# WITH_LAPACK = # OPENBLAS usually includes LAPACK
CPPFLAGS += -DOPENBLAS -isystem$(OPENBLAS_INCLUDE_PATH)
ifdef OPENBLAS_LEGACY
# Legacy version (mostly for Travis-CI)
CPPFLAGS += -DOPENBLAS_LEGACY
endif
else
ifdef WITH_ATLAS
CPPFLAGS += -DUSE_BLAS=atlas
endif
endif
ifneq ($(CXX), clang++)
# Clang does not like this switch
debug check fast-check: CPPFLAGS += -Og
endif
debug check fast-check: CPPFLAGS += -g $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
profile: CPPFLAGS += -pg
release: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
static: CPPFLAGS += -DNDEBUG -O3 $(GCC_FLAGS) $(GSL_INCLUDE_PATH) -isystem$(EIGEN_INCLUDE_PATH) -Icontrib/catch-1.9.7 -Isrc
ifeq ($(SYS), WIN)
CPPFLAGS += -Duint="unsigned int" -D__CRT__NO_INLINE -D__STRING="__STRINGIFY" -DWINDOWS -DWITH_GSLCBLAS=1
endif
ifdef SHOW_COMPILER_WARNINGS
CPPFLAGS += -Wall
endif
static: CPPFLAGS += -static
LIBS += -lgsl -lz
ifdef WITH_OPENBLAS
LIBS += -lopenblas
else
LIBS += -latlas -lcblas -llapack -lblas
endif
ifdef WITH_GSLCBLAS
LIBS += -lgslcblas
endif
ifdef WITH_GFORTRAN
LIBS += -lgfortran
endif
.PHONY: all test
OUTPUT = $(BIN_DIR)/gemma
# Detailed libary paths, D for dynamic and S for static
ifdef WITH_LAPACK
LIBS += -llapack
endif
LIBS_OSX_D_LAPACK = -framework Accelerate
ifdef WITH_LAPACK
ifeq ($(SYS), OSX)
LIBS += $(LIBS_OSX_D_LAPACK)
ifdef WITH_OPENBLAS
LIBS += -Wl,-L/usr/local/opt/openblas/lib
endif
endif
endif
HDR = $(sort $(wildcard src/*.h)) ./src/version.h
SOURCES = $(sort $(wildcard src/*.cpp))
# all
OBJS = $(SOURCES:.cpp=.o)
all: release
release: $(OUTPUT)
static: $(OUTPUT)
debug: $(OUTPUT)
./src/version.h: ./VERSION
$(shell bash $(VGEN) $(GUIX_PROFILE) > src/version.h)
$(OUTPUT): $(OBJS)
$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
$(OBJS): $(HDR)
.SUFFIXES : .cpp .c .o $(SUFFIXES)
./bin/unittests-gemma: $(TEST_SRC_DIR)/unittests-main.o $(TEST_SRC_DIR)/unittests-math.o $(OBJS)
$(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
unittests: all ./bin/unittests-gemma
./bin/unittests-gemma
fast-check: all unittests
rm -vf test/output/*
cd test && ./dev_test_suite.sh | tee ../dev_test.log
tail -n 1 dev_test.log | grep -q 'OK'
slow-check: all
rm -vf test/output/*
cd test && ./test_suite.sh | tee ../test.log
tail -n 1 test.log | grep -q 'OK' 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 = *.md LICENSE VERSION Makefile
DIST_SUBDIRS = src doc example bin
tar: version all
@echo "Creating $(DIST_NAME)"
mkdir -p ./$(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)
|
