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Pick the DP score width from bounds on the scores; check it, retry at 32 bits #14

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Merged
glennhickey merged 9 commits into from
Oct 12, 2026
+421 −29
Merged

Pick the DP score width from bounds on the scores; check it, retry at 32 bits #14

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f46f6c6
Pick the score width from bounds on the scores; check it, retry in 32…
glennhickey Oct 11, 2026
7312421
Test the score width choice, its checks and the 32-bit retry
glennhickey Oct 11, 2026
8eeb089
Scan for floor-zone scores after the DP, out of line
glennhickey Oct 11, 2026
0f6d155
Clamp row 0's gap scores at the floor, in 64 bits
glennhickey Oct 11, 2026
8d41b30
Print the match and mismatch scores the width rule used
glennhickey Oct 11, 2026
1a682ec
Align scores the 32-bit bounds cannot prove, checked, instead of refu…
glennhickey Oct 11, 2026
a41d204
Test row 0 on an input where its wrap gave a wrong result
glennhickey Oct 11, 2026
e2aa0f1
Align the DP's loops to 32 bytes on x86
glennhickey Oct 11, 2026
12f99c4
Say the scores are in range when a proven 32-bit alignment fails
glennhickey Oct 12, 2026
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17 changes: 12 additions & 5 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,13 @@ endif
endif
endif

# Loops of the DP aligned to 32 bytes on x86: on CPUs with Intel's JCC erratum (Skylake and its derivatives) the
# speed of the DP otherwise depends on where unrelated code changes happen to put its loops, by up to 15%.
# Used only if the compiler takes the flag.
ifeq ($(ARCH), $(filter $(ARCH), x86_64 amd64))
LOOP_ALIGN := $(shell $(CC) -falign-loops=32 -Werror -x c -c /dev/null -o /dev/null 2>/dev/null && echo -falign-loops=32)
endif

# some more possible overrides
FLAG_SSE2 = -msse2
FLAG_SSE41 = -msse4.1
Expand Down Expand Up @@ -182,16 +189,16 @@ $(SRC_DIR)/simd_check.o:$(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 $@
$(CC) -c $(CFLAGS) $(LOOP_ALIGN) $(SIMD_FLAG) -I$(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 $@
$(CC) -c $(CFLAGS) $(LOOP_ALIGN) -DABPOA_SIMD_DISPATCH -msse2 -U__SSE4_1__ -I$(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 $@
$(CC) -c $(CFLAGS) $(LOOP_ALIGN) -DABPOA_SIMD_DISPATCH -msse4.1 -I$(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 $@
$(CC) -c $(CFLAGS) $(LOOP_ALIGN) -DABPOA_SIMD_DISPATCH -mavx2 -I$(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 $@
$(CC) -c $(CFLAGS) $(LOOP_ALIGN) -DABPOA_SIMD_DISPATCH -mavx512bw -I$(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
Expand Down
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