/// get the number of non-zero
size_t vec_i8_cnt_nonzero(const int8_t *p, size_t n)
{
size_t ans = 0;
#ifdef COREARRAY_SIMD_SSE2
const __m128i ZERO = { 0LL, 0LL };
const __m128i ONES = { 0x0101010101010101LL, 0x0101010101010101LL };
const __m128i ONE = { 1LL, 1LL };
// header 1, 16-byte aligned
size_t h = (16 - ((size_t)p & 0x0F)) & 0x0F;
for (; (n > 0) && (h > 0); n--, h--)
ans += (*p++) ? 1 : 0;
# ifdef COREARRAY_SIMD_AVX2
// header 2, 32-byte aligned
if ((n >= 16) && ((size_t)p & 0x10))
{
__m128i c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
__m128i bit = _mm_and_si128(c, ONES);
p += 16; n -= 16;
uint64_t array[2] __attribute__((aligned(16)));
*((__m128i*)array) = bit;
ans += 16 - POPCNT_U64(array[0]) - POPCNT_U64(array[1]);
}
const __m256i ZERO2 = { 0LL, 0LL, 0LL, 0LL };
const __m256i ONES2 = { 0x0101010101010101LL, 0x0101010101010101LL,
0x0101010101010101LL, 0x0101010101010101LL };
// body, AVX2
for (; n >= 256; n -= 256)
{
__m256i c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
__m256i bit = _mm256_and_si256(c, ONES2);
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
c = _mm256_cmpeq_epi8(_mm256_load_si256((__m256i const*)p), ZERO2);
bit = _mm256_or_si256(_mm256_sll_epi64(bit, ONE), _mm256_and_si256(c, ONES2));
p += 32;
uint64_t array[4] __attribute__((aligned(32)));
*((__m256i*)array) = bit;
ans += 256 - POPCNT_U64(array[0]) - POPCNT_U64(array[1]) -
POPCNT_U64(array[2]) - POPCNT_U64(array[3]);
}
# endif
// body, SSE2
for (; n >= 128; n -= 128)
{
__m128i c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
__m128i bit = _mm_and_si128(c, ONES);
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
bit = _mm_or_si128(_mm_sll_epi64(bit, ONE), _mm_and_si128(c, ONES));
p += 16;
uint64_t array[2] __attribute__((aligned(16)));
*((__m128i*)array) = bit;
ans += 128 - POPCNT_U64(array[0]) - POPCNT_U64(array[1]);
}
for (; n >= 16; n -= 16)
{
__m128i c = _mm_cmpeq_epi8(_mm_load_si128((__m128i const*)p), ZERO);
__m128i bit = _mm_and_si128(c, ONES);
p += 16;
uint64_t array[2] __attribute__((aligned(16)));
*((__m128i*)array) = bit;
ans += 16 - POPCNT_U64(array[0]) - POPCNT_U64(array[1]);
}
#else
// header, 8-byte aligned
size_t h = (8 - ((size_t)p & 0x07)) & 0x07;
for (; (n > 0) && (h > 0); n--, h--)
ans += (*p++) ? 1 : 0;
// body, unroll
for (; n >= 8; n -= 8)
{
ans += (p[0] ? 1 : 0) + (p[1] ? 1 : 0) +
(p[2] ? 1 : 0) + (p[3] ? 1 : 0) +
(p[4] ? 1 : 0) + (p[5] ? 1 : 0) +
(p[6] ? 1 : 0) + (p[7] ? 1 : 0);
p += 8;
}
#endif
// tail
for (; n > 0; n--) ans += (*p++) ? 1 : 0;
return ans;
}
void thread_ibs_num(size_t i, size_t n)
{
const size_t npack = nBlock >> 3;
const size_t npack2 = npack * 2;
C_UInt8 *Base = Geno1b.Get();
IdMatTri I = Array_Thread_MatIdx[i];
C_Int64 N = Array_Thread_MatCnt[i];
TS_KINGHomo *p = ptrKING + I.Offset();
for (; N > 0; N--, ++I, p++)
{
C_UInt8 *p1 = Base + I.Row() * npack2;
C_UInt8 *p2 = Base + I.Column() * npack2;
double *pAF = AF_1_AF.Get();
double *pAF2 = AF_1_AF_2.Get();
ssize_t m = npack;
#if defined(COREARRAY_SIMD_SSE2)
{
POPCNT_SSE2_HEAD
__m128i ibs0_sum, sumsq_sum;
ibs0_sum = sumsq_sum = _mm_setzero_si128();
__m128d sq_sum, sq_sum2;
sq_sum = sq_sum2 = _mm_setzero_pd();
for (; m > 0; m-=16)
{
__m128i g1_1 = _mm_load_si128((__m128i*)p1);
__m128i g1_2 = _mm_load_si128((__m128i*)(p1 + npack));
__m128i g2_1 = _mm_load_si128((__m128i*)p2);
__m128i g2_2 = _mm_load_si128((__m128i*)(p2 + npack));
p1 += 16; p2 += 16;
__m128i mask = (g1_1 | ~g1_2) & (g2_1 | ~g2_2);
__m128i ibs0 = (~((g1_1 ^ ~g2_1) | (g1_2 ^ ~g2_2))) & mask;
__m128i het = ((g1_1 ^ g1_2) ^ (g2_1 ^ g2_2)) & mask;
POPCNT_SSE2_RUN(ibs0)
ibs0_sum = _mm_add_epi32(ibs0_sum, ibs0);
POPCNT_SSE2_RUN(het)
sumsq_sum = _mm_add_epi32(_mm_add_epi32(sumsq_sum, het),
_mm_slli_epi32(ibs0, 2));
C_UInt64 m1 = _mm_cvtsi128_si64(mask);
C_UInt64 m2 = _mm_cvtsi128_si64(_mm_shuffle_epi32(mask,
_MM_SHUFFLE(1,0,3,2)));
for (size_t k=32; k > 0; k--)
{
switch (m1 & 0x03)
{
case 3:
sq_sum = _mm_add_pd(sq_sum, _mm_load_pd(pAF));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_load_pd(pAF2));
break;
case 1:
sq_sum = _mm_add_pd(sq_sum, _mm_set_pd(0, pAF[0]));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_set_pd(0, pAF2[0]));
break;
case 2:
sq_sum = _mm_add_pd(sq_sum, _mm_set_pd(pAF[1], 0));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_set_pd(pAF2[1], 0));
break;
}
pAF += 2; pAF2 += 2; m1 >>= 2;
}
for (size_t k=32; k > 0; k--)
{
switch (m2 & 0x03)
{
case 3:
sq_sum = _mm_add_pd(sq_sum, _mm_load_pd(pAF));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_load_pd(pAF2));
break;
case 1:
sq_sum = _mm_add_pd(sq_sum, _mm_set_pd(0, pAF[0]));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_set_pd(0, pAF2[0]));
break;
case 2:
sq_sum = _mm_add_pd(sq_sum, _mm_set_pd(pAF[1], 0));
sq_sum2 = _mm_add_pd(sq_sum2, _mm_set_pd(pAF2[1], 0));
break;
}
pAF += 2; pAF2 += 2; m2 >>= 2;
}
}
p->IBS0 += vec_sum_i32(ibs0_sum);
p->SumSq += vec_sum_i32(sumsq_sum);
p->SumAFreq += vec_sum_f64(sq_sum);
p->SumAFreq2 += vec_sum_f64(sq_sum2);
}
#else
for (; m > 0; m-=8)
{
C_UInt64 g1_1 = *((C_UInt64*)p1);
C_UInt64 g1_2 = *((C_UInt64*)(p1 + npack));
C_UInt64 g2_1 = *((C_UInt64*)p2);
C_UInt64 g2_2 = *((C_UInt64*)(p2 + npack));
p1 += 8; p2 += 8;
C_UInt64 mask = (g1_1 | ~g1_2) & (g2_1 | ~g2_2);
C_UInt64 ibs0 = (~((g1_1 ^ ~g2_1) | (g1_2 ^ ~g2_2))) & mask;
C_UInt64 het = ((g1_1 ^ g1_2) ^ (g2_1 ^ g2_2)) & mask;
p->IBS0 += POPCNT_U64(ibs0);
p->SumSq += POPCNT_U64(het) + POPCNT_U64(ibs0)*4;
double sum=0, sum2=0;
for (size_t k=64; k > 0; k--)
{
if (mask & 0x01)
{ sum += (*pAF); sum2 += (*pAF2); }
pAF ++; pAF2 ++;
mask >>= 1;
}
p->SumAFreq += sum;
p->SumAFreq2 += sum2;
}
#endif
}
}