diff --git a/Makefile b/Makefile index b5fb136..164853a 100644 --- a/Makefile +++ b/Makefile @@ -3,6 +3,7 @@ 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 OBJS_SSE= ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o +DISPATCH_FLAG=-msse4.1 PROG= minimap2 PROG_EXTRA= sdust minimap2-lite LIBS= -lm -lz -lpthread @@ -14,9 +15,11 @@ ifeq ($(avx2),) OBJS+=$(OBJS_SSE) ksw2_dispatch.o else OBJS+=ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o + DISPATCH_FLAG=-mavx2 endif else OBJS+=ksw2_extd2_avx512.o ksw2_extd2_avx2.o $(OBJS_SSE) ksw2_dispatch.o + DISPATCH_FLAG=-mavx512bw endif else # if sse2only is defined OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o @@ -84,13 +87,8 @@ ksw2_exts2_sse41.o:ksw2_exts2_sse.c ksw2.h kalloc.h ksw2_exts2_sse2.o:ksw2_exts2_sse.c ksw2.h kalloc.h $(CC) -c $(CFLAGS) -msse2 -mno-sse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY $(INCLUDES) $< -o $@ -ifeq ($(avx2),) ksw2_dispatch.o:ksw2_dispatch.c ksw2.h - $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ -else -ksw2_dispatch.o:ksw2_dispatch.c ksw2.h - $(CC) -c $(CFLAGS) -mavx2 $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ -endif + $(CC) -c $(CFLAGS) $(DISPATCH_FLAG) $(CPPFLAGS) -DKSW_CPU_DISPATCH $(INCLUDES) $< -o $@ # NEON-specific targets on ARM diff --git a/ksw2_extd2_avx512.c b/ksw2_extd2_avx512.c index ed3bab3..05eae58 100644 --- a/ksw2_extd2_avx512.c +++ b/ksw2_extd2_avx512.c @@ -166,8 +166,8 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const __dp_code_block2; // save u[] and v[]; update a, b, a2 and b2 _mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_)); _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); - _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); - _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_)); + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_)); } } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment __m512i *pr = p + (size_t)r * n_col_ - st_; @@ -190,9 +190,9 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b, zero_), 0x10)); // d = b > 0? 1<<4 : 0 _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(a2, zero_), 0x20)); // d = a2 > 0? 1<<5 : 0 - _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_)); d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpgt_epi8_mask(b2, zero_), 0x40)); // d = b2 > 0? 1<<6 : 0 - _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_)); _mm512_store_si512(&pr[t], d); } } else { // gap right-alignment @@ -201,7 +201,7 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const for (t = st_; t <= en_; ++t) { __m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp; __dp_code_block1; - d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), _mm512_setzero(), _mm512_set1_epi8(1)); + d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), zero_, _mm512_set1_epi8(1)); z = _mm512_max_epi8(z, a); d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), d, _mm512_set1_epi8(2)); z = _mm512_max_epi8(z, b); @@ -216,9 +216,9 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b, zero_), 0x10)); // d = b >= 0? 1<<4 : 0 _mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_)); d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(a2, zero_), 0x20)); // d = a2 >= 0? 1<<5 : 0 - _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe_)); + _mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_)); d = _mm512_or_si512(d, _mm512_maskz_set1_epi8(_mm512_cmpge_epi8_mask(b2, zero_), 0x40)); // d = b2 >= 0? 1<<6 : 0 - _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe_)); + _mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_)); _mm512_store_si512(&pr[t], d); } }