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Makefile
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Makefile
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# Makefile for Linux and Mac OSX systems for REGENIE
#
# * User needs to specify BGEN_PATH which is the directory
# where the BGEN library is installed
# * If the Boost Iostream library is installed on the system,
# user can specify to link to it during compilation by
# setting HAS_BOOST_IOSTREAM to 1
#
###############################################################
#
# Optional: To use external BLAS/LAPACK routines in Eigen
#
# For Intel MKL, add path of installed library to MKLROOT
# For OpenBLAS, add path of installed library to OPENBLAS_ROOT
# note: it also requires lapacke library
#
# For static compilation on Linux systems, set STATIC=1
# -> this excludes GLIBC
#
BGEN_PATH =
HAS_BOOST_IOSTREAM := 0
MKLROOT =
# directory containing libhts.a or libhts.so
HTSLIB_PATH =
OPENBLAS_ROOT =
STATIC := 0
############
# Use only if not set
CXX ?= g++
CXXFLAGS = -O3 -Wall -pedantic -ffast-math -std=c++11 -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-long-long -Wno-c11-extensions -fPIC
EFILE = regenie
CFLAGS ?=
# check BGEN_PATH is set
ifneq ($(MAKECMDGOALS),clean)
ifeq ($(strip $(BGEN_PATH)),)
$(warning You did not set the path to BGEN library, i.e. "BGEN_PATH")
endif
endif
# detect OS architecture and add flags
UNAME_S := $(shell uname -s)
ifeq ($(UNAME_S),Linux)
INC = -I${BGEN_PATH}/3rd_party/boost_1_55_0
CFLAGS += -fopenmp
ifeq ($(strip $(STATIC)),1)
LPATHS = -static-libgcc -static-libstdc++
DLIBS = -Wl,-Bdynamic
endif
else ifeq ($(UNAME_S),Darwin)
RGFLAGS += -stdlib=libc++
endif
RG_VERSION = $(shell cat VERSION)
## for docker
DFILE = ./Dockerfile
TEST_SCRIPT = ./test/test_docker.sh
ifeq ($(strip $(STATIC)),1)
ifneq ($(strip $(MKLROOT)),)
DFILE = ./Dockerfile_mkl # only for static linking
endif
endif
## for boost iostream
ifeq ($(HAS_BOOST_IOSTREAM),1)
RG_VERSION := $(RG_VERSION).gz
RGFLAGS += -DHAS_BOOST_IOSTREAM
ifeq ($(strip $(STATIC)),1)
SLIBS = -Wl,-Bstatic -lboost_iostreams
else
DLIBS += -lboost_iostreams
LIB_BIO2 = libboost-iostreams-dev ## for docker build
endif
LIB_BIO = libboost-iostreams-dev ## for docker build
endif
# Intel MKL or OpenBLAS
ifneq ($(strip $(MKLROOT)),)
ifeq ($(UNAME_S),Linux)
RGFLAGS += -DWITH_MKL -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
INC += -I${MKLROOT}/include/
# static linking
ifeq ($(strip $(STATIC)),1)
SLIBS += -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_gnu_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
DLIBS += -lgomp -lpthread
# dynamic linking
else
LIBMKL = -L${MKLROOT}/lib/intel64/
DLIBS += -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread
endif
endif
else ifneq ($(strip $(OPENBLAS_ROOT)),)
ifeq ($(UNAME_S),Linux)
RGFLAGS += -DWITH_OPENBLAS -DEIGEN_USE_BLAS -DEIGEN_USE_LAPACKE
INC += -I${OPENBLAS_ROOT}/include/
# static linking
ifeq ($(strip $(STATIC)),1)
SLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas
# dynamic linking
else
DLIBS += -Wl,-rpath=${OPENBLAS_ROOT}/lib/ -llapack -llapacke -lopenblas
endif
endif
endif
## for HTSlib
ifneq ($(strip $(HTSLIB_PATH)),)
ifeq ($(UNAME_S),Linux)
RGFLAGS += -DWITH_HTSLIB
ifeq ($(strip $(STATIC)),1)
SLIBS += ${HTSLIB_PATH}/libhts.a
else
SLIBS += ${HTSLIB_PATH}/libhts.so
endif
DLIBS += -lz -lbz2 -llzma -lcurl
endif
endif
# pass on version number to software
RGFLAGS += -DVERSION_NUMBER=\"$(RG_VERSION)\"
OBJECTS = $(patsubst %.cpp,%.o,$(wildcard ./src/*.cpp))
PGEN_PATH = ./external_libs/pgenlib/
INC += -I${PGEN_PATH} -I${PGEN_PATH}/simde/ -I${PGEN_PATH}/include/ -I./external_libs/cxxopts/include/ -I./external_libs/LBFGSpp/include/ -I${BGEN_PATH} -I./external_libs/eigen-3.4.0/ -I${BGEN_PATH}/genfile/include/ -I${BGEN_PATH}/3rd_party/boost_1_55_0/ -I${BGEN_PATH}/3rd_party/zstd-1.1.0/lib -I${BGEN_PATH}/db/include/ -I${BGEN_PATH}/3rd_party/sqlite3 -I./external_libs/remeta -I./external_libs/
LPATHS += ${LIBMKL} -L${BGEN_PATH}/build/ -L${BGEN_PATH}/build/3rd_party/zstd-1.1.0/ -L${BGEN_PATH}/build/db/ -L${BGEN_PATH}/build/3rd_party/sqlite3/ -L${BGEN_PATH}/build/3rd_party/boost_1_55_0 -L/usr/lib/
LIBS += ${SLIBS} -lbgen -lzstd -ldb -lsqlite3 -lboost
LIBS += -lz ${DLIBS} -lm -ldl -lgfortran
.PHONY: docker-build docker-test debug clean
all: ${EFILE}
${EFILE}: libMvtnorm libqf libquad pgenlib remeta ${OBJECTS}
${CXX} ${CXXFLAGS} ${RGFLAGS} ${CFLAGS} -o ${EFILE} ${OBJECTS} ./external_libs/mvtnorm/libMvtnorm.a ./external_libs/qf/qf.a ./external_libs/quadpack/libquad.a ./external_libs/pgenlib/pgenlib.a ./external_libs/remeta/remeta.a ${LPATHS} ${LIBS}
%.o: %.cpp
${CXX} ${CXXFLAGS} ${RGFLAGS} -o $@ -c $< ${INC} ${CFLAGS}
libMvtnorm:
(cd ./external_libs/mvtnorm/;$(MAKE))
libqf:
(cd ./external_libs/qf/;$(MAKE))
libquad:
(cd ./external_libs/quadpack/;$(MAKE))
pgenlib:
(cd ./external_libs/pgenlib/;$(MAKE))
remeta:
(cd ./external_libs/remeta/;$(MAKE) remeta.a HTSLIB_PATH=${HTSLIB_PATH})
#####
## For use with Docker
# create Docker image
docker-build:
@echo "Building docker image for REGENIE v${RG_VERSION}"
ifeq ($(HAS_BOOST_IOSTREAM),1)
@echo Compiling with Boost Iostream library
endif
ifeq ($(STATIC),1)
ifneq ($(strip $(MKLROOT)),)
@echo Compiling with Intel MKL library
endif
@echo Linking = static
else
@echo Linking = dynamic
endif
@docker build --rm -f ${DFILE} \
--no-cache --pull \
--build-arg BOOST_IO=${HAS_BOOST_IOSTREAM} \
--build-arg LIB_INSTALL=${LIB_BIO} \
--build-arg LIB_INSTALL2=${LIB_BIO2} \
--build-arg STATIC=${STATIC} \
-t regenie:v${RG_VERSION} .
docker-test:
@${TEST_SCRIPT} . "regenie:v${RG_VERSION}" ${HAS_BOOST_IOSTREAM}
####
debug: CXXFLAGS = -O0 -g -std=c++11 -fPIC
debug: ${EFILE}
clean:
rm -f ${EFILE} ./src/*.o
(cd ./external_libs/mvtnorm/;$(MAKE) clean)
(cd ./external_libs/qf/;$(MAKE) clean)
(cd ./external_libs/quadpack/;$(MAKE) clean)
(cd ./external_libs/pgenlib/;$(MAKE) clean)
(cd ./external_libs/remeta/;$(MAKE) clean)