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|
.PHONY: default
default: abpoa
#CC = gcc
OS := $(shell uname)
ARCH := $(shell uname -m)
# add -fno-tree-vectorize to avoid certain vectorization errors in O3 optimization
# right now, we are using -O3 for the best performance, and no vectorization errors were found
EXTRA_FLAGS = -Wall -Wno-unused-function -Wno-misleading-indentation# -fno-tree-vectorize
# SIMDE
EXTRA_FLAGS += -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
# for debug
ifneq ($(debug),)
EXTRA_FLAGS += -D __DEBUG__
endif
ifneq ($(sdebug),)
EXTRA_FLAGS += -D __SIMD_DEBUG__
endif
# for gdb
ifneq ($(gdb),)
OPT_FLAGS = -g
else
OPT_FLAGS = -O3
endif
CFLAGS += $(CPPFLAGS) $(OPT_FLAGS) $(EXTRA_FLAGS) $(LDFLAGS)
# for gprof
ifneq ($(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
BASIC_OBJS = $(addprefix $(SRC_DIR)/, abpoa_align.o abpoa_graph.o abpoa_plot.o abpoa_seed.o abpoa_seq.o abpoa_output.o abpoa_simd.o kalloc.o kstring.o utils.o)
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
# auto-detect some appropriate defaults -- this helps users in the common case of macOS with arm
# use ABPOA_DISPATCH_SIMD for x86_64
ifeq ($(ARCH), $(filter $(ARCH), x86_64 amd64))
# SIMD_FLAG = -march=native
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd_sse2.o abpoa_align_simd_sse41.o abpoa_align_simd_avx2.o abpoa_align_simd_avx512bw.o \
abpoa_dispatch_simd_sse2.o abpoa_dispatch_simd_sse41.o abpoa_dispatch_simd_avx2.o abpoa_dispatch_simd_avx512bw.o)
endif
ifeq ($(ARCH), $(filter $(ARCH), aarch64 arm64))
ifeq ($(OS), Darwin)
SIMD_FLAG = -mcpu=apple-m1 -D__AVX2__
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
else
SIMD_FLAG = -march=armv8-a+simd -D__AVX2__
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
endif
endif
# override if user specified
ifneq ($(armv7),) # for ARMv7
SIMD_FLAG = -march=armv7-a -mfpu=neon -D__AVX2__
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
else
ifneq ($(armv8),) # for ARMv8
ifneq ($(aarch64),) # for Aarch64
SIMD_FLAG = -march=armv8-a+simd -D__AVX2__
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
else # for Aarch32
SIMD_FLAG = -march=armv8-a+simd -mfpu=auto -D__AVX2__
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
endif
endif
endif
# some more possible overrides
FLAG_SSE2 = -msse2
FLAG_SSE41 = -msse4.1
FLAG_AVX2 = -mavx2
FLAG_AVX512BW = -mavx512bw
$(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 = $(LIB_DIR)/libabpoa.a
ifneq ($(sse2),)
SIMD_FLAG=$(FLAG_SSE2)
BIN = $(BIN_DIR)/abpoa_sse2
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
ifneq ($(gdb),)
BIN = $(BIN_DIR)/gdb_abpoa_sse2
endif
ABPOALIB = $(LIB_DIR)/libabpoa_sse2.a
py_SIMD_FLAG = SSE2=1
else ifneq ($(sse41),)
SIMD_FLAG=$(FLAG_SSE41)
BIN = $(BIN_DIR)/abpoa_sse41
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
ifneq ($(gdb),)
BIN = $(BIN_DIR)/gdb_abpoa_sse41
endif
ABPOALIB = $(LIB_DIR)/libabpoa_sse41.a
py_SIMD_FLAG = SSE41=1
else ifneq ($(avx2),)
SIMD_FLAG=$(FLAG_AVX2)
py_SIMD_FLAG = AVX2=1
BIN = $(BIN_DIR)/abpoa_avx2
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
ifneq ($(gdb),)
BIN = $(BIN_DIR)/gdb_abpoa_avx2
endif
ABPOALIB = $(LIB_DIR)/libabpoa_avx2.a
else ifneq ($(avx512bw),)
SIMD_FLAG=$(FLAG_AVX512BW)
BIN = $(BIN_DIR)/abpoa_avx512bw
OBJS = ${BASIC_OBJS} $(addprefix $(SRC_DIR)/, abpoa_align_simd.o)
ifneq ($(gdb),)
BIN = $(BIN_DIR)/gdb_abpoa_avx512bw
endif
ABPOALIB = $(LIB_DIR)/libabpoa_avx512bw.a
py_SIMD_FLAG = AVX512BW=1
endif
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
# nm -g $(ABPOALIB)
$(CC) $(CFLAGS) $< -I$(INC_DIR) $(ABPOALIB) $(LIB) -o $@ $(PG_FLAG)
# multiple SSE versions
multi:
make clean all sse2=1
make clean all sse41=1
make clean all avx2=1
make clean all avx512bw=1
$(EXAMPLE):example.c $(ABPOALIB)
$(CC) $(CFLAGS) $< -o $@ -I$(INC_DIR) $(ABPOALIB) $(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 $(CFLAGS) -I$(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 $@
$(SRC_DIR)/abpoa_align_simd.o:$(SRC_DIR)/abpoa_align_simd.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 $@
$(SRC_DIR)/abpoa_align_simd_sse2.o:$(SRC_DIR)/abpoa_align_simd.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -msse2 -U__SSE4_1__ -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_align_simd_sse41.o:$(SRC_DIR)/abpoa_align_simd.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -msse4.1 -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_align_simd_avx2.o:$(SRC_DIR)/abpoa_align_simd.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -mavx2 -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_align_simd_avx512bw.o:$(SRC_DIR)/abpoa_align_simd.c $(SRC_DIR)/abpoa_graph.h $(SRC_DIR)/abpoa_align.h $(SRC_DIR)/simd_instruction.h $(SRC_DIR)/utils.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -mavx512bw -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_dispatch_simd_sse2.o:$(SRC_DIR)/abpoa_dispatch_simd.c $(SRC_DIR)/abpoa.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -msse2 -U__SSE4_1__ -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_dispatch_simd_sse41.o:$(SRC_DIR)/abpoa_dispatch_simd.c $(SRC_DIR)/abpoa.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -msse4.1 -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_dispatch_simd_avx2.o:$(SRC_DIR)/abpoa_dispatch_simd.c $(SRC_DIR)/abpoa.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -mavx2 -I$(INC_DIR) $< -o $@
$(SRC_DIR)/abpoa_dispatch_simd_avx512bw.o:$(SRC_DIR)/abpoa_dispatch_simd.c $(SRC_DIR)/abpoa.h
$(CC) -c $(CFLAGS) -DABPOA_SIMD_DISPATCH -mavx512bw -I$(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
|
