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SIMDe made optional. Include paths changes for SIMDe.

This commit is contained in:
mbrcic 2020-04-21 01:08:32 +02:00
parent c172df7d2d
commit f47e8a525e
5 changed files with 57 additions and 24 deletions
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31
Makefile
View File

@ -1,11 +1,12 @@
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS= -DHAVE_KALLOC CPPFLAGS= -DHAVE_KALLOC
INCLUDES= -Ilib/simde/simde INCLUDES=
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o
PROG= minimap2 PROG= minimap2
PROG_EXTRA= sdust minimap2-lite PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread LIBS= -lm -lz -lpthread
ifeq ($(no_simd),) # if no_simd is not defined ifeq ($(no_simd),) # if no_simd is not defined
ifeq ($(arm_neon),) # if arm_neon is not defined ifeq ($(arm_neon),) # if arm_neon is not defined
OBJS+=ksw2_ll_sse.o OBJS+=ksw2_ll_sse.o
@ -16,6 +17,9 @@ else # if sse2only is defined
endif endif
else # if arm_neon is defined else # if arm_neon is defined
OBJS+=ksw2_ll_sse.o ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o OBJS+=ksw2_ll_sse.o ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
ifeq ($(simde),) # arm_neon without SIMDe -> use sse2neon
INCLUDES+=-Isse2neon
endif
ifeq ($(aarch64),) #if aarch64 is not defined ifeq ($(aarch64),) #if aarch64 is not defined
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
else #if aarch64 is defined else #if aarch64 is defined
@ -24,6 +28,12 @@ endif
endif endif
else else
OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o
simde=1 # no_simd can be used only with SIMDe
endif
ifneq ($(simde),) # if simde is defined
CFLAGS+=-DSIMDE_ENABLE_NATIVE_ALIASES -DUSE_SIMDE
INCLUDES+=-Ilib/simde
endif endif
ifneq ($(asan),) ifneq ($(asan),)
@ -85,31 +95,32 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
# NEON-specific targets on ARM # NEON-specific targets on ARM
ksw2_ll_neon.o:ksw2_ll_sse.c ksw2.h kalloc.h ksw2_ll_neon.o:ksw2_ll_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) -DSIMDE_ENABLE_NATIVE_ALIASES $(CPPFLAGS) $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
# no-SIMD version # no-SIMD version
ksw2_ll_nosimd.o:ksw2_ll_sse.c ksw2.h kalloc.h ksw2_ll_nosimd.o:ksw2_ll_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
ksw2_extz2_nosimd.o:ksw2_extz2_sse.c ksw2.h kalloc.h ksw2_extz2_nosimd.o:ksw2_extz2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
ksw2_extd2_nosimd.o:ksw2_extd2_sse.c ksw2.h kalloc.h ksw2_extd2_nosimd.o:ksw2_extd2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
ksw2_exts2_nosimd.o:ksw2_exts2_sse.c ksw2.h kalloc.h ksw2_exts2_nosimd.o:ksw2_exts2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_NO_NATIVE $(INCLUDES) $< -o $@
# other non-file targets # other non-file targets

14
ksw2_extd2_sse.c
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@ -4,16 +4,22 @@
#include "ksw2.h" #include "ksw2.h"
#ifdef __SSE2__ #ifdef __SSE2__
//#include <emmintrin.h> #ifndef USE_SIMDE
#include <x86/sse2.h> #include <emmintrin.h>
#else
#include <simde/x86/sse2.h>
#endif
#ifdef KSW_SSE2_ONLY #ifdef KSW_SSE2_ONLY
#undef __SSE4_1__ #undef __SSE4_1__
#endif #endif
#ifdef __SSE4_1__ #ifdef __SSE4_1__
//#include <smmintrin.h> #ifndef USE_SIMDE
#include <x86/sse4.1.h> #include <smmintrin.h>
#else
#include <simde/x86/sse4.1.h>
#endif
#endif #endif
#ifdef KSW_CPU_DISPATCH #ifdef KSW_CPU_DISPATCH

14
ksw2_exts2_sse.c
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@ -4,15 +4,21 @@
#include "ksw2.h" #include "ksw2.h"
#ifdef __SSE2__ #ifdef __SSE2__
//#include <emmintrin.h> #ifndef USE_SIMDE
#include <x86/sse2.h> #include <emmintrin.h>
#else
#include <simde/x86/sse2.h>
#endif
#ifdef KSW_SSE2_ONLY #ifdef KSW_SSE2_ONLY
#undef __SSE4_1__ #undef __SSE4_1__
#endif #endif
#ifdef __SSE4_1__ #ifdef __SSE4_1__
//#include <smmintrin.h> #ifndef USE_SIMDE
#include <x86/sse4.1.h> #include <smmintrin.h>
#else
#include <simde/x86/sse4.1.h>
#endif
#endif #endif
#ifdef KSW_CPU_DISPATCH #ifdef KSW_CPU_DISPATCH

14
ksw2_extz2_sse.c
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@ -3,16 +3,22 @@
#include "ksw2.h" #include "ksw2.h"
#ifdef __SSE2__ #ifdef __SSE2__
//#include <emmintrin.h> #ifndef USE_SIMDE
#include <x86/sse2.h> #include <emmintrin.h>
#else
#include <simde/x86/sse2.h>
#endif
#ifdef KSW_SSE2_ONLY #ifdef KSW_SSE2_ONLY
#undef __SSE4_1__ #undef __SSE4_1__
#endif #endif
#ifdef __SSE4_1__ #ifdef __SSE4_1__
//#include <smmintrin.h> #ifndef USE_SIMDE
#include <x86/sse4.1.h> #include <smmintrin.h>
#else
#include <simde/x86/sse4.1.h>
#endif
#endif #endif
#ifdef KSW_CPU_DISPATCH #ifdef KSW_CPU_DISPATCH

8
ksw2_ll_sse.c
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@ -1,10 +1,14 @@
#include <stdlib.h> #include <stdlib.h>
#include <stdint.h> #include <stdint.h>
#include <string.h> #include <string.h>
//#include <emmintrin.h>
#include <x86/sse2.h>
#include "ksw2.h" #include "ksw2.h"
#ifndef USE_SIMDE
#include <emmintrin.h>
#else
#include <simde/x86/sse2.h>
#endif
#ifdef __GNUC__ #ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x),1) #define LIKELY(x) __builtin_expect((x),1)
#define UNLIKELY(x) __builtin_expect((x),0) #define UNLIKELY(x) __builtin_expect((x),0)