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|
.PHONY: default
default: abpoa
#CC = gcc
OS := $(shell uname)
ARCH := $(shell arch)
EXTRA_FLAGS = -Wno-unused-function -Wno-misleading-indentation -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
CFLAGS += $(CPPFLAGS) -Wall -O3 $(EXTRA_FLAGS) $(LDFLAGS)
# for debug
ifneq ($(debug),)
DFLAGS = -D __DEBUG__
endif
# for gdb
ifneq ($(gdb),)
CFLAGS += -Wall -g ${DFLAGS} $(EXTRA_FLAGS)
else
CFLAGS += -Wall -O3 ${DFLAGS} $(EXTRA_FLAGS)
endif
# for gprof
ifneq ($(pg),)
PG_FLAG = -pg
CFLAGS += -pg
endif
LIB = -lm -lz -lpthread
ifneq ($(PREFIX),)
OUT_PRE_DIR = $(PREFIX)
else
OUT_PRE_DIR = .
endif
BIN_DIR = $(OUT_PRE_DIR)/bin
LIB_DIR = $(OUT_PRE_DIR)/lib
INC_DIR = ./include
SRC_DIR = ./src
# This is everything that gets bundled into our main library
OBJS = $(addprefix $(SRC_DIR)/, abpoa_align.o abpoa_graph.o abpoa_plot.o abpoa_seed.o abpoa_seq.o abpoa_output.o kalloc.o kstring.o simd_abpoa_align.o simd_check.o utils.o)
# auto-detect some appropriate defaults -- this helps users in the common case of macOS with arm
ifeq ($(ARCH), $(filter $(ARCH), aarch64 arm64))
ifeq ($(OS), Darwin)
# issues/44 suggests this doesn't work for some users
SIMD_FLAG = -march=armv8-a+simd -D__AVX2__
else
SIMD_FLAG = -march=armv8-a+simd -D__AVX2__
endif
endif
# some more possible overrides
FLAG_SSE2 = -msse2
FLAG_SSE41 = -msse4.1
FLAG_AVX2 = -mavx2
# FLAG_AVX512F = -mavx512f
# FLAG_AVX512BW = -mavx512bw
ifneq ($(sse2),)
SIMD_FLAG=$(FLAG_SSE2)
py_SIMD_FLAG = SSE2=1
else ifneq ($(sse41),)
SIMD_FLAG=$(FLAG_SSE41)
py_SIMD_FLAG = SSE41=1
else ifneq ($(avx2),)
SIMD_FLAG=$(FLAG_AVX2)
py_SIMD_FLAG = AVX2=1
#else ifneq ($(avx512f),)
# SIMD_FLAG=$(FLAG_AVX512F)
# py_SIMD_FLAG = AVX512f=1
#else ifneq ($(avx512bw),)
# SIMD_FLAG=$(FLAG_AVX512BW)
# py_SIMD_FLAG = AVX512BW=1
endif
# SIMD check -- unused
SIMD_CHECK_D = -D __CHECK_SIMD_MAIN__
$(SRC_DIR)/%.o: $(SRC_DIR)/%.c
$(CC) -c $(CFLAGS) $^ -I$(INC_DIR) -o $@
BIN = $(BIN_DIR)/abpoa
ifneq ($(gdb),)
BIN = $(BIN_DIR)/gdb_abpoa
endif
ABPOALIB = $(LIB_DIR)/libabpoa.a
# TODO add example
EXAMPLE = example
all: $(BIN)
abpoa: $(BIN)
libabpoa: $(ABPOALIB)
example: $(EXAMPLE)
$(BIN):$(SRC_DIR)/abpoa.o $(ABPOALIB)
if [ ! -d $(BIN_DIR) ]; then mkdir $(BIN_DIR); fi
$(CC) $(CFLAGS) $< -I$(INC_DIR) -L$(LIB_DIR) -labpoa $(LIB) -o $@ $(PG_FLAG)
$(EXAMPLE):example.c $(ABPOALIB)
$(CC) $(CFLAGS) $< -o $@ -I$(INC_DIR) -L$(LIB_DIR) -labpoa $(LIB)
$(ABPOALIB):$(OBJS)
if [ ! -d $(LIB_DIR) ]; then mkdir $(LIB_DIR); fi
$(AR) -csr $@ $(OBJS)
$(SRC_DIR)/abpoa.o:$(SRC_DIR)/abpoa.c $(SRC_DIR)/abpoa.h $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h \
$(SRC_DIR)/abpoa_seq.h $(SRC_DIR)/utils.h $(SRC_DIR)/simd_instruction.h
$(CC) -c $(CFLAGS) $(SIMD_FLAG) -I$(INC_DIR) $< -o $@
$(SRC_DIR)/simd_check.o:$(SRC_DIR)/simd_check.c $(SRC_DIR)/simd_instruction.h
$(CC) -c $(CFLAGS) $(SIMD_FLAG) -I$(INC_DIR) $< -o $@
$(SRC_DIR)/simd_abpoa_align.o:$(SRC_DIR)/simd_abpoa_align.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
$(CC) -c $(CFLAGS) $(SIMD_FLAG) -I$(INC_DIR) $< -o $@
install_py: setup.py python/cabpoa.pxd python/pyabpoa.pyx python/README.md
${py_SIMD_FLAG} python setup.py install
sdist: setup.py python/cabpoa.pxd python/pyabpoa.pyx python/README.md
${py_SIMD_FLAG} python setup.py sdist #bdist_wheel
publish_pypi: clean_py sdist
twine upload dist/*
clean:
rm -f $(SRC_DIR)/*.[oa] $(LIB_DIR)/*.[oa] $(BIN)
clean_py:
rm -rf build/ dist/ pyabpoa.egg-info/ python/pyabpoa.c pyabpoa.cpython-*.so
|
