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Fix ARM (Apple Silicon) build of the fast pair HMM #12

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Merged
glennhickey merged 1 commit into from
Oct 28, 2026
Merged

Fix ARM (Apple Silicon) build of the fast pair HMM #12

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19 changes: 16 additions & 3 deletions impl/pairwiseAligner.c
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Original file line number Diff line number Diff line change
Expand Up @@ -771,12 +771,18 @@ static void diagonalCalculationExpectations(StateMachine *sM, int64_t xay, DpMat
///////////////////////////////////
///////////////////////////////////

// The intrinsics below are x86 only. Checking the target as well as the feature macros matters
// on ARM, where cactus defines __AVX2__ itself (for abPOA's SIMDe) and the real headers do not exist.
#if defined(__x86_64__) || defined(__i386__)
#if defined(__SSE2__)
#define PAIR_HMM_X86_SSE2
#include <xmmintrin.h>
#endif
#if defined(__AVX2__)
#define PAIR_HMM_X86_AVX2
#include <immintrin.h>
#endif
#endif

#define PAIR_HMM_MAX_STATES 5

Expand Down Expand Up @@ -1221,7 +1227,7 @@ static void fastDiagonal_emissions(PairHmm *hmm, int64_t type, FastSymbols *symb
// is off its end. cX[i] is X[x0 - 1 + lo + i] and cY[i] is Y[y0 - 1 - lo - i].
const uint8_t *restrict cX = type != PAIR_HMM_GAP_Y ? symbols->x + (x0 - 1 + lo) : NULL;
const uint8_t *restrict cY = type != PAIR_HMM_GAP_X ? symbols->yReversed + (symbols->lY - y0 + lo) : NULL;
#if defined(__AVX2__)
#if defined(PAIR_HMM_X86_AVX2)
// Table lookups the compiler will not vectorise on its own
__m256d vScale = _mm256_set1_pd(scale);
__m128i vSymbols = _mm_set1_epi32(SYMBOL_NUMBER);
Expand Down Expand Up @@ -1422,10 +1428,15 @@ static bool getPosteriorProbsWithBandingFast(StateMachine *sM, stList *anchorPai
}
int64_t ns = hmm.stateNumber;

#if defined(__SSE2__)
#if defined(PAIR_HMM_X86_SSE2)
// Cells far off the alignment decay towards zero; flush them rather than crawl through denormals
unsigned int oldCsr = _mm_getcsr();
_mm_setcsr(oldCsr | 0x8040); // flush-to-zero and denormals-are-zero
#elif defined(__aarch64__)
// Same on ARM (FPCR.FZ covers inputs and outputs), which also keeps results the same as x86
uint64_t oldFpcr;
__asm__ __volatile__("mrs %0, fpcr" : "=r"(oldFpcr));
__asm__ __volatile__("msr fpcr, %0" : : "r"(oldFpcr | (UINT64_C(1) << 24)));
#endif

Band *band = p->dynamicAnchorExpansion ? band_constructDynamic(anchorPairs, sX.length, sY.length) :
Expand Down Expand Up @@ -1536,8 +1547,10 @@ static bool getPosteriorProbsWithBandingFast(StateMachine *sM, stList *anchorPai
free(backCells[i]);
}
band_destruct(band);
#if defined(__SSE2__)
#if defined(PAIR_HMM_X86_SSE2)
_mm_setcsr(oldCsr);
#elif defined(__aarch64__)
__asm__ __volatile__("msr fpcr, %0" : : "r"(oldFpcr));
#endif
return 1;
}
Expand Down