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Changed sse2neon with SIMDe. Added building non-SIMD version.

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This commit is contained in:
mbrcic
2020-04-20 18:28:06 +02:00
parent 29f67a1666
commit 9e6fdd376b
7 changed files with 42 additions and 15 deletions
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3
.gitmodules vendored Normal file
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@@ -0,0 +1,3 @@
[submodule "lib/simde"]
path = lib/simde
url = https://github.com/nemequ/simde.git

31
Makefile
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@@ -1,11 +1,13 @@
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS= -DHAVE_KALLOC
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 ksw2_ll_sse.o
INCLUDES= -Ilib/simde/simde
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_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread
ifeq ($(no_simd),) # if no_simd is not defined
OBJS+=ksw2_ll_sse.o
ifeq ($(arm_neon),) # if arm_neon is not defined
ifeq ($(sse2only),) # if sse2only is not defined
OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
@@ -14,13 +16,15 @@ else # if sse2only is defined
endif
else # if arm_neon is defined
OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
INCLUDES+=-Isse2neon
ifeq ($(aarch64),) #if aarch64 is not defined
CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
else #if aarch64 is defined
CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char
endif
endif
else
OBJS+=ksw2_ll_nosimd.o ksw2_extz2_nosimd.o ksw2_extd2_nosimd.o ksw2_exts2_nosimd.o
endif
ifneq ($(asan),)
CFLAGS+=-fsanitize=address
@@ -83,15 +87,28 @@ ksw2_dispatch.o:ksw2_dispatch.c ksw2.h
$(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@
# NEON-specific targets on ARM
ksw2_extz2_neon.o:ksw2_extz2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
ksw2_extd2_neon.o:ksw2_extd2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@
$(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES $(INCLUDES) $< -o $@
# no-SIMD version
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 $@
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 $@
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 $@
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 $@
# other non-file targets

6
ksw2_extd2_sse.c
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@@ -4,14 +4,16 @@
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
//#include <emmintrin.h>
#include <x86/sse2.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
//#include <smmintrin.h>
#include <x86/sse4.1.h>
#endif
#ifdef KSW_CPU_DISPATCH

7
ksw2_exts2_sse.c
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@@ -4,14 +4,15 @@
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
//#include <emmintrin.h>
#include <x86/sse2.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
//#include <smmintrin.h>
#include <x86/sse4.1.h>
#endif
#ifdef KSW_CPU_DISPATCH

6
ksw2_extz2_sse.c
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@@ -3,14 +3,16 @@
#include "ksw2.h"
#ifdef __SSE2__
#include <emmintrin.h>
//#include <emmintrin.h>
#include <x86/sse2.h>
#ifdef KSW_SSE2_ONLY
#undef __SSE4_1__
#endif
#ifdef __SSE4_1__
#include <smmintrin.h>
//#include <smmintrin.h>
#include <x86/sse4.1.h>
#endif
#ifdef KSW_CPU_DISPATCH

3
ksw2_ll_sse.c
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@@ -1,7 +1,8 @@
#include <stdlib.h>
#include <stdint.h>
#include <string.h>
#include <emmintrin.h>
//#include <emmintrin.h>
#include <x86/sse2.h>
#include "ksw2.h"
#ifdef __GNUC__

1
lib/simde Submodule

Submodule lib/simde added at b30129b3b4