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ksw2_extd2_avx.c
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ksw2_extd2_avx.c
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/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <[email protected]>;
Vasimuddin Md <[email protected]>; Sanchit Misra <[email protected]>;
Chirag Jain <[email protected]>; Heng Li <[email protected]>
*/
#include "ksw2_extd2_avx.h"
#ifdef __AVX512BW__
#define __dp_code_block1_pcl_512_mm2_fast \
/*__mmask64 mskc_ = mskc; */ \
/*if (t == st_) */ \
__mmask64 mskc_ = (t == st_) ? mskc_ar[(st0 - t*64)/16]:mskc; \
z = _mm512_load_si512(&s[t]); \
xt1 = _mm512_load_si512(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(xt1, 15); */ /* tmp <- x[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)x)[t*64 + 63]); \
/* xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_);*/ /* xt1 <- x[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(xt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
xt1 = _mm512_mask_blend_epi8(mskc_, slli512, x1_); \
x1_ = tmp; \
vt1 = _mm512_load_si512(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(vt1, 15); */ /* tmp <- v[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)v)[t*64 + 63]); \
/* vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); *//* vt1 <- v[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(vt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
vt1 = _mm512_mask_blend_epi8(mskc_, slli512, v1_); \
v1_ = tmp; \
a = _mm512_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
ut = _mm512_load_si512(&u[t]); /* ut <- u[t..t+15] */ \
b = _mm512_add_epi8(_mm512_load_si512(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */ \
x2t1= _mm512_load_si512(&x2[t]); \
/* tmp = _mm_srli_si128(x2t1, 15);*/ \
tmp = _mm512_set1_epi8(((int8_t*)x2)[t*64 + 63]); \
/* x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); */ \
shf512a = _mm512_shuffle_epi8(x2t1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
x2t1 = _mm512_mask_blend_epi8(mskc_, slli512, x21_); \
x21_= tmp; \
a2= _mm512_add_epi8(x2t1, vt1); \
b2= _mm512_add_epi8(_mm512_load_si512(&y2[t]), ut);
void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen,
const uint8_t *target, int8_t m, const int8_t *mat,
int8_t q, int8_t e, int8_t q2, int8_t e2, int w,
int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
{
// printf("AVX512 call\n");
__m512i ind512_srli = _mm512_set1_epi8(15);
__mmask8 msk_srli = 0x0003;
int8_t index[64] __attribute((aligned(64)));
for (int i=0; i<64; i++)
index[i] = i%16 - 1;
index[0] = 15;
index[16] = 31;
index[32] = 47;
index[48] = 63;
__m512i shf512a, shf512b, slli512;
__m512i ind512_slli = _mm512_load_si512((__m512i*) index);
__mmask8 mska = 0x90;
__mmask64 mskb = 0x0001000100010000;
__mmask64 mskc = 0x1;
__mmask64 mskc_ar[4] = {0x1, 0x10000, 0x100000000, 0x1000000000000};
__mmask64 msk_ar[5] = {0xFFFF, 0xFFFFFFFF, 0xFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF};
__mmask64 msk_ar2[5] = {0xFFFF, 0xFFFF, 0xFFFFFFFF, 0xFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF};
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc, min_sc, long_thres, long_diff;
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
int32_t *H = 0, H0 = 0, last_H0_t = 0;
uint8_t *qr, *sf, *mem, *mem2 = 0;
__m512i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_;
__m512i *u, *v, *x, *y, *x2, *y2, *s, *p = 0;
__m512i one_, two_, three_, four_, s1_, s2_, s3_, s4_;
ksw_reset_extz(ez);
if (m <= 1 || qlen <= 0 || tlen <= 0) return;
if (q2 + e2 < q + e) t = q, q = q2, q2 = t, t = e, e = e2, e2 = t; // make sure q+e no larger than q2+e2
s1_ = _mm512_set1_epi8(0x08);
s2_ = _mm512_set1_epi8(0x10);
s3_ = _mm512_set1_epi8(0x20);
s4_ = _mm512_set1_epi8(0x40);
one_ = _mm512_set1_epi8(1);
two_ = _mm512_set1_epi8(2);
three_ = _mm512_set1_epi8(3);
four_ = _mm512_set1_epi8(4);
__m512i four32_ = _mm512_set1_epi32(4);
__m512i bt32_ = _mm512_setr_epi32(0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12);
zero_ = _mm512_set1_epi8(0);
q_ = _mm512_set1_epi8(q);
q2_ = _mm512_set1_epi8(q2);
qe_ = _mm512_set1_epi8(q + e);
qe2_ = _mm512_set1_epi8(q2 + e2);
sc_mch_ = _mm512_set1_epi8(mat[0]);
sc_mis_ = _mm512_set1_epi8(mat[1]);
sc_N_ = mat[m*m-1] == 0? _mm512_set1_epi8(-e2) : _mm512_set1_epi8(mat[m*m-1]);
m1_ = _mm512_set1_epi8(m - 1); // wildcard
if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w;
tlen_ = (tlen + 63) / 64;
n_col_ = qlen < tlen? qlen : tlen;
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 63) / 64 + 1;
qlen_ = (qlen + 63) / 64;
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
max_sc = max_sc > mat[t]? max_sc : mat[t];
min_sc = min_sc < mat[t]? min_sc : mat[t];
}
if (-min_sc > 2 * (q + e)) return; // otherwise, we won't see any mismatches
long_thres = e != e2? (q2 - q) / (e - e2) - 1 : 0;
if (q2 + e2 + long_thres * e2 > q + e + long_thres * e)
++long_thres;
long_diff = long_thres * (e - e2) - (q2 - q) - e2;
mem = (uint8_t*)kcalloc(km, tlen_ * 8 + qlen_ + 1 + 63, 64); //TODO: saurabh - 63
u = (__m512i*)(((size_t)mem + 63) >> 6 << 6); // 16-byte aligned //TODO: saurabh mm_malloc
v = u + tlen_, x = v + tlen_, y = x + tlen_, x2 = y + tlen_, y2 = x2 + tlen_;
s = y2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 64;
memset(u, -q - e, tlen_ * 64);
memset(v, -q - e, tlen_ * 64);
memset(x, -q - e, tlen_ * 64);
memset(y, -q - e, tlen_ * 64);
memset(x2, -q2 - e2, tlen_ * 64);
memset(y2, -q2 - e2, tlen_ * 64);
if (!approx_max) {
H = (int32_t*)kmalloc(km, tlen_ * 64 * 4);
for (t = 0; t < tlen_ * 64; ++t) H[t] = KSW_NEG_INF;
}
if (with_cigar) {
// printf("qlen: %dm tlen: %dm ncol: %d\n", qlen, tlen, n_col_);
mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 64);
p = (__m512i*)(((size_t)mem2 + 63) >> 6 << 6);//TODO: saurabh
off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
off_end = off + qlen + tlen - 1;
}
#define ORIG 0 // for B1 block optimization
for (t = 0; t < qlen; ++t) {
#if ORIG
qr[t] = query[qlen - 1 - t];
#else
if (query[qlen - 1 - t] == 4)
qr[t] = 8;
else
qr[t] = query[qlen - 1 - t];
#endif
//assert(qr[t] < 5);
}
memcpy(sf, target, tlen);
#if TIMER_O
uint64_t tic = _rdtsc();
#endif
#if 1 // changes due to B1 modification
int8_t cN = mat[m*m-1] == 0? -e2 : mat[m*m-1];
int8_t pmat[64] __attribute((aligned(64))) = {0};
pmat[0] = mat[0];
pmat[1] = pmat[2] = pmat[3] = mat[1];
pmat[4] = pmat[5] = pmat[6] = pmat[7] = pmat[8] = pmat[9] = pmat[10] = pmat[11] = pmat[12] = cN;
__m512i vpmat = _mm512_load_si512(pmat);
vpmat = _mm512_shuffle_i32x4(vpmat, vpmat, 0x0000);
#endif
static int itr = 0;
itr++;
for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {
int st = 0, en = tlen - 1, st0, en0, st_, en_;
int8_t x1, x21, v1;
uint8_t *qrr = qr + (qlen - 1 - r);
int8_t *u8 = (int8_t*)u, *v8 = (int8_t*)v, *x8 = (int8_t*)x, *x28 = (int8_t*)x2;
__m512i x1_, x21_, v1_;
// find the boundaries
if (st < r - qlen + 1) st = r - qlen + 1;
if (en > r) en = r;
if (st < (r-wr+1)>>1) st = (r-wr+1)>>1; // take the ceil
if (en > (r+wl)>>1) en = (r+wl)>>1; // take the floor
if (st > en) {
ez->zdropped = 1;
break;
}
st0 = st, en0 = en;
{
// _mm_prefetch(sf + st0, _MM_HINT_T0);
// _mm_prefetch(qrr + st0, _MM_HINT_T0);
// _mm_prefetch(s + st0, _MM_HINT_T0);
// _mm_prefetch(sf + st0 + 64, _MM_HINT_T0);
// _mm_prefetch(qrr + st0 + 64, _MM_HINT_T0);
// _mm_prefetch(s + st0 + 64, _MM_HINT_T0);
}
int st_new = st / 16 * 16, en_new = (en + 16) / 16 * 16 - 1;//TODO: saurabh
// int st_new = st / 64 * 64, en_new = (en + 64) / 64 * 64 - 1;//TODO: saurabh
int stb = st, enb = en;
st = st / 64 * 64, en = (en + 64) / 64 * 64 - 1;//TODO: saurabh
int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;//TODO: saurabh
// set boundary conditions
//if(st_new != st)
{
//printf("st0 %d en0 %d st16 %d en16 %d st64 %d en64 %d\n", st0, en0, st_new, en_new, st, en);
//processed_vect64 += ceil(((double)(en - st) + 1)/64); possible_vect64 += ceil(((double)(en_new - st_new) + 1)/64);
//exit(0);
}
if (st_new > 0) {
if (st_new - 1 >= last_st && st_new - 1 <= last_en) {
x1 = x8[st_new - 1], x21 = x28[st_new - 1], v1 = v8[st_new - 1]; // (r-1,s-1) calculated in the last round
} else {
x1 = -q - e, x21 = -q2 - e2;
v1 = -q - e;
}
} else {
x1 = -q - e, x21 = -q2 - e2;
v1 = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2;
}
if (en_new >= r) {
((int8_t*)y)[r] = -q - e, ((int8_t*)y2)[r] = -q2 - e2;
u8[r] = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2;
}
#if TIMER_I
uint64_t tic = _rdtsc();
#endif
// loop fission: set scores first //TODO: saurabh: introducing mask64
if (!(flag & KSW_EZ_GENERIC_SC)) {
#if ORIG
for (t = st0; t <= en0; t += 64) {
__m512i sq, st, tmp_512, mask_512;
__mmask64 tmp, mask;
sq = _mm512_loadu_si512((__m512i*)&sf[t]);
st = _mm512_loadu_si512((__m512i*)&qrr[t]);
mask = (_mm512_cmpeq_epi8_mask(sq, m1_) | _mm512_cmpeq_epi8_mask(st, m1_));
tmp = _mm512_cmpeq_epi8_mask(sq, st);
#if 1
tmp_512 = _mm512_mask_blend_epi8(tmp, sc_mis_, sc_mch_);
tmp_512 = _mm512_mask_blend_epi8(mask, tmp_512, sc_N_);
#else
tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));//TODO: saurabh - left unchanged
tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp), _mm_and_si128(mask, sc_N_));
#endif
if (t + 64 > en0)
{
__mmask64 msk;
int ind = (en0 - t + 16) >> 4;
// assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8((__m512i*)((int8_t*)s + t), msk, tmp_512);
}
else
_mm512_storeu_si512((__m512i*)((int8_t*)s + t), tmp_512);
}
#else
for (t = 0; t <= (en0 - st0) - 64; t += 64) {
__m512i sq, st, tmp_512, mask_512;
__mmask64 tmp, mask;
// const int pdf = 4;
//_mm_prefetch(sf + t + 64*pdf, _MM_HINT_T0);
//_mm_prefetch(qrr + t + 64*pdf, _MM_HINT_T0);
//_mm_prefetch(s + t + 64*pdf, _MM_HINT_T0);
sq = _mm512_loadu_si512((__m512i*)&sf[st0 + t]);
st = _mm512_loadu_si512((__m512i*)&qrr[st0 + t]);
tmp_512 = _mm512_xor_si512(sq, st);
tmp_512 = _mm512_shuffle_epi8(vpmat, tmp_512);
_mm512_storeu_si512((__m512i*)((int8_t*)s + st0 + t), tmp_512);
}
{
__m512i sq, st, tmp_512, mask_512;
__mmask64 tmp, mask;
sq = _mm512_loadu_si512((__m512i*)&sf[st0 + t]);
st = _mm512_loadu_si512((__m512i*)&qrr[st0 + t]);
tmp_512 = _mm512_xor_si512(sq, st);
tmp_512 = _mm512_shuffle_epi8(vpmat, tmp_512);
if (t + 64 > en0 - st0)
{
__mmask64 msk;
int ind = ((en0 - st0) - t + 16) >> 4;
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8((__m512i*)((int8_t*)s + st0 + t), msk, tmp_512);
}
else
_mm512_storeu_si512((__m512i*)((int8_t*)s + st0 + t), tmp_512);
}
#endif
}
else
{
// printf("ELSE\n");
for (t = st0; t <= en0; ++t) {
#if ORIG
((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
#else
int8_t c = qrr[t];
if (qrr[t] == 8) {
c = 4;
}
((uint8_t*)s)[t] = mat[sf[t] * m + c];
#endif
}
}
#if TIMER_I
uint64_t toc = _rdtsc();
tprof[B1][0] += toc - tic;
#endif
//continue;
// core loop //TODO: saurabh - need more understanding of logic
// fprintf(stderr, "- r: %d, x1: %d, x21: %d, v1: %d, en_new: %d, e: %d, q: %d\n",
//r, x1, x21, v1, en_new, e, q);
x1_ = _mm512_set1_epi8((uint8_t)x1);
x21_ = _mm512_set1_epi8((uint8_t)x21);
v1_ = _mm512_set1_epi8((uint8_t)v1);
//st_ = st / 16, en_ = en / 16;
st_ = st / 64, en_ = en / 64;
//assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
#if TIMER_I
uint64_t tic = _rdtsc();
#endif
for (t = st_; t <= en_; ++t) {
__m512i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
//__dp_code_block1_pcl;
__dp_code_block1_pcl_512_mm2_fast;
z = _mm512_max_epi8(z, a);
z = _mm512_max_epi8(z, b);
z = _mm512_max_epi8(z, a2);
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl; // save u[] and v[]; update a, b, a2 and b2
#if 1
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
else {
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
#endif
#if 1
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
//assert(ind >= 0);
msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_));
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_));
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_));
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
}
else
#endif
{
_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_), qe2_));
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
}
// for (int l=0; l<64; l++)
// fprintf(stderr, "%d ", ((int8_t*)x)[l]);
}
#if TIMER_I
uint64_t toc = _rdtsc();
tprof[B2][0] += toc - tic;
#endif
} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
__m512i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
//_mm_prefetch(pr, _MM_HINT_T0);
for (t = st_; t < en_; ++t) {
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
//__dp_code_block1_pcl;
__dp_code_block1_pcl_512_mm2_fast;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a, z),zero_, one_); // d = a > z? 1 : 0
z = _mm512_max_epi8(z, a);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, two_); // d = b > z? 2 : d
z = _mm512_max_epi8(z, b);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, three_); // d = a2 > z? 3 : d
z = _mm512_max_epi8(z, a2);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, four_); // d = b2 > z? 4 : d
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s1_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s2_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s3_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s4_)); // d = b > 0? 1<<6 : 0
_mm512_store_si512(&pr[t], d);
//_mm_prefetch(&pr[t+1], _MM_HINT_T0);
}
#if TIMER_I
uint64_t tic = _rdtsc();
#endif
{
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
//__dp_code_block1_pcl;
__dp_code_block1_pcl_512_mm2_fast;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a, z),zero_, one_); // d = a > z? 1 : 0
z = _mm512_max_epi8(z, a);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, two_); // d = b > z? 2 : d
z = _mm512_max_epi8(z, b);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, three_); // d = a2 > z? 3 : d
z = _mm512_max_epi8(z, a2);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, four_); // d = b2 > z? 3 : d
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
#if 1
{
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
// assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
#endif
#if 1
{
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
off_end[r] -= (4-ind)*16;
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s1_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s2_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s3_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s4_)); // d = b > 0? 1<<6 : 0
//_mm512_store_si512(&pr[t], d);
_mm512_mask_storeu_epi8(&pr[t], msk, d);
}
#endif
}
#if TIMER_I
uint64_t toc = _rdtsc();
tprof[B3][0]+= toc - tic;
#endif
/*
for (t = st_; t <= en_; ++t) {
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
__dp_code_block1_pcl;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a, z), _mm512_set1_epi8(0), _mm512_set1_epi8(1)); // d = a > z? 1 : 0
z = _mm512_max_epi8(z, a);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, _mm512_set1_epi8(2)); // d = b > z? 2 : d
z = _mm512_max_epi8(z, b);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, _mm512_set1_epi8(3)); // d = a2 > z? 3 : d
z = _mm512_max_epi8(z, a2);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, _mm512_set1_epi8(4)); // d = b2 > z? 3 : d
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
#if 1
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
//assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
else {
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
#endif
#if 1
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16) >> 4;
msk = msk_ar2[ind];
off_end[r] -= (4-ind)*16;
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x40))); // d = b > 0? 1<<6 : 0
//_mm512_store_si512(&pr[t], d);
_mm512_mask_storeu_epi8(&pr[t], msk, d);
}
else
#endif
{
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x08))); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x10))); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, _mm512_set1_epi8(0x40))); // d = b > 0? 1<<6 : 0
// int64_t tic = _rdtsc();
_mm512_store_si512(&pr[t], d);
// int64_t toc = _rdtsc();
//fprintf(stderr, "store time: %d %ld\n", t, toc - tic);
}
}
*/
//continue;
} else { // gap right-alignment
// continue;
__m512i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
// off[r] = stn, off_end[r] = enn;
// fprintf(stderr, "t: %d, st0: %d\n", st_, st0);
#if TIMER_I
uint64_t tic = _rdtsc();
#endif
for (t = st_; t <= en_; ++t) {
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
//__dp_code_block1_pcl;
__dp_code_block1_pcl_512_mm2_fast;
//d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a),_mm512_set1_epi8(1), zero_);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), one_, zero_);
z = _mm512_max_epi8(z, a);
// d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), _mm512_set1_epi8(2), d); // d = z > b? d : 2
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), two_, d); // d = z > b? d : 2
z = _mm512_max_epi8(z, b);
// d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a2), _mm512_set1_epi8(3), d); // d = z > a2? d : 3
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a2), three_, d); // d = z > a2? d : 3
z = _mm512_max_epi8(z, a2);
// d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b2), _mm512_set1_epi8(4), d); // d = z > b2? d : 4
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b2), four_, d); // d = z > b2? d : 4
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
#if 1
__mmask64 msk;
if (t == en_) {
// __mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
off_end[r] -= (4-ind)*16;
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
else {
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
#endif
#if 1
if (t == en_) {
//__mmask64 msk;
//int ind = (en0 - t*64 + 16)/16;
//msk = msk_ar2[ind];
// off_end[r] -= (4-ind)*16;
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a, zero_), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x08), zero_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b);
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b, zero_), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x10), zero_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a2);
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a2, zero_), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x20), zero_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b2);
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b2, zero_), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x40), zero_)); // d = b > 0? 1<<6 : 0
// _mm512_store_si512(&pr[t], d);
_mm512_mask_storeu_epi8(&pr[t], msk, d);
}
else
#endif
{
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a);
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a, zero_), qe_));
// d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x08), zero_)); // d = a > 0? 1<<3 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s1_, zero_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b);
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b, zero_), qe_));
// d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x10), zero_)); // d = b > 0? 1<<4 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s2_, zero_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a2);
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a2, zero_), qe2_));
// d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x20), zero_)); // d = a > 0? 1<<5 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s3_, zero_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b2);
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b2, zero_), qe2_));
// d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, _mm512_set1_epi8(0x40), zero_)); // d = b > 0? 1<<6 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s4_, zero_)); // d = b > 0? 1<<6 : 0
_mm512_store_si512(&pr[t], d);
}
}
#if TIMER_I
uint64_t toc = _rdtsc();
tprof[B4][0] += toc - tic;
#endif
}
// continue;
#if TIMER_I
tic = _rdtsc();
#endif
if (!approx_max) { // find the exact max with a 32-bit score array
int32_t max_H, max_t;
// compute H[], max_H and max_t
if (r > 0) {
int32_t HH[16], tt[16], en1 = st0 + (en0 - st0) / 16 * 16, i; //TODO: saurabh HH[4] -> HH[16]. 4*4??
__m512i max_H_, max_t_;
max_H = H[en0] = en0 > 0? H[en0-1] + u8[en0] : H[en0] + v8[en0]; // special casing the last element
max_t = en0;
max_H_ = _mm512_set1_epi32(max_H);
max_t_ = _mm512_set1_epi32(max_t);
for (t = st0; t < en1; t += /*4*/16) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
__m512i H1, tmp, t_;
__mmask16 tmp_mask;
H1 = _mm512_loadu_si512((__m512i*)&H[t]);
__m128i t__ = _mm_load_si128((__m128i*) &v8[t]);
t_ = _mm512_cvtepi8_epi32(t__);
// t_ = _mm512_setr_epi32(v8[t], v8[t+1], v8[t+2], v8[t+3],v8[t+4], v8[t+5], v8[t+6], v8[t+7],v8[t+8], v8[t+9], v8[t+10], v8[t+11],v8[t+12], v8[t+13], v8[t+14], v8[t+15]); //TODO: need to understand well
H1 = _mm512_add_epi32(H1, t_);
_mm512_storeu_si512((__m512i*)&H[t], H1);
// new code by vasim: making it 4 lanes to match accuracy
{
#if 0
t_ = _mm512_set1_epi32(t);
__m512i shfH, shft, max1, max2;
for (int l=0; l<4; l++) {
//t_ = _mm512_set1_epi32(t + l*4);
// __m512i shfH = H1, shft = t_;
shfH = _mm512_shuffle_i32x4(H1, H1, l);
shft = _mm512_shuffle_i32x4(t_, t_, l);
tmp_mask = _mm512_cmpgt_epi32_mask(shfH, max_H_);
max_H_ = _mm512_mask_blend_epi32(tmp_mask, max_H_, shfH);
max_t_ = _mm512_mask_blend_epi32(tmp_mask, max_t_, shft);
t_ = _mm512_add_epi32(t_, four32_);
}
#else
__m512i shfH, shft, max1, max2;
t_ = _mm512_set1_epi32(t);
t_ = _mm512_add_epi32(t_, bt32_);
shfH = _mm512_shuffle_i32x4(H1, H1, 0x31);
shft = _mm512_shuffle_i32x4(t_, t_, 0x31);
tmp_mask = _mm512_cmpgt_epi32_mask(shfH, H1);
max1 = _mm512_mask_blend_epi32(tmp_mask, H1, shfH);
max2 = _mm512_mask_blend_epi32(tmp_mask, t_, shft);
shfH = _mm512_shuffle_i32x4(max1, max1, 0x2);
shft = _mm512_shuffle_i32x4(max2, max2, 0x2);
tmp_mask = _mm512_cmpgt_epi32_mask(shfH, max1);
max1 = _mm512_mask_blend_epi32(tmp_mask, max1, shfH);
max2 = _mm512_mask_blend_epi32(tmp_mask, max2, shft);
tmp_mask = _mm512_cmpgt_epi32_mask(max1, max_H_);
max_H_ = _mm512_mask_blend_epi32(tmp_mask, max_H_, max1);
max_t_ = _mm512_mask_blend_epi32(tmp_mask, max_t_, max2);
#endif
}
}
_mm512_storeu_si512((__m512i*)HH, max_H_);
_mm512_storeu_si512((__m512i*)tt, max_t_);
// fprintf(stderr, "max_H: %d, max_t: %d\n", max_H, max_t);
int rem = (en0 - t) / 4;
for (int l=0; l<rem; l++) {
int bt = t;
#pragma unroll
for (int j=0; j<4; j++) {
H[t] += (int32_t)v8[t];
if (H[t] > HH[j]) {
HH[j] = H[t];
tt[j] = bt;
}
t++;
}
}
#pragma unroll
for (i = 0; i < 4; ++i)
if (max_H < HH[i]) max_H = HH[i], max_t = tt[i] + i;
for (; t < en0; ++t) { // for the rest of values that haven't been computed with SSE
H[t] += (int32_t)v8[t];
if (H[t] > max_H) {
max_H = H[t], max_t = t;
}
}
} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
// update ez
if (en0 == tlen - 1 && H[en0] > ez->mte) {
// ez->mte = H[en0], ez->mte_q = r - en;
ez->mte = H[en0], ez->mte_q = r - en_new;
// fprintf(stderr, "r: %d, en: %d\n", r, en);
}
if (r - st0 == qlen - 1 && H[st0] > ez->mqe) {
ez->mqe = H[st0], ez->mqe_t = st0;
}
if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e2)) {
// fprintf(stderr, "Dropping out, r: %d\n", r);
break;
}
if (r == qlen + tlen - 2 && en0 == tlen - 1) {
ez->score = H[tlen - 1];
// fprintf(stderr, "ez->score: %d\n", ez->score);
}
} else { // find approximate max; Z-drop might be inaccurate, too.
if (r > 0) {
if (last_H0_t >= st0 && last_H0_t <= en0 && last_H0_t + 1 >= st0 && last_H0_t + 1 <= en0) {
int32_t d0 = v8[last_H0_t];
int32_t d1 = u8[last_H0_t + 1];
if (d0 > d1) H0 += d0;
else H0 += d1, ++last_H0_t;
// fprintf(stderr, "1. r: %d, d0: %d, d1: %d H0: %d, last_H0_t: %d\n", r, d0, d1, H0, last_H0_t);
} else if (last_H0_t >= st0 && last_H0_t <= en0) {
H0 += v8[last_H0_t];
// fprintf(stderr, "2. r: %d, H0: %d, last_H0_t: %d, v8: %d\n", r, H0, last_H0_t, v8[last_H0_t]);
} else {
++last_H0_t, H0 += u8[last_H0_t];
// fprintf(stderr, "3. r: %d, H0: %d, last_H0_t: %d, u8: %d\n", r, H0, last_H0_t, u8[last_H0_t]);
}
} else H0 = v8[0] - qe, last_H0_t = 0;
if ((flag & KSW_EZ_APPROX_DROP) && ksw_apply_zdrop(ez, 1, H0, r, last_H0_t, zdrop, e2)) {
// fprintf(stderr, "Dropping II\n");
break;
}
if (r == qlen + tlen - 2 && en0 == tlen - 1) {
ez->score = H0;
// fprintf(stderr, ">>r: %d, ez->score: %d\n", r, ez->score);
}
}
// last_st = st, last_en = en;
last_st = st_new, last_en = en_new;
#if TIMER_I
toc = _rdtsc();
tprof[B5][0] += toc - tic;
#endif
}
#if TIMER_O
uint64_t toc = _rdtsc();
tprof[OUTER][0] += toc - tic;
#endif
kfree(km, mem);
if (!approx_max) kfree(km, H);
#if 1
if (with_cigar) { // backtrack
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
ez->reach_end = 1;
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (ez->max_t >= 0 && ez->max_q >= 0) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
}
kfree(km, mem2); kfree(km, off);
}
#endif
//kfree_all();
}
void ksw_extd2_avx512_v1(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
{
__m512i bt32_ = _mm512_setr_epi32(0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12);
int8_t index[64] __attribute((aligned(64)));
for (int i=0; i<64; i++)
index[i] = i%16 - 1;
index[0] = 15;
index[16] = 31;
index[32] = 47;
index[48] = 63;
__m512i shf512a, shf512b, slli512;
__m512i ind512_slli = _mm512_load_si512((__m512i*) index);
__mmask8 mska = 0x90;
__mmask64 mskb = 0x0001000100010000;
__mmask64 mskc = 0x1;
__mmask64 mskc_ar[4] = {0x1, 0x10000, 0x100000000, 0x1000000000000};
#define __dp_code_block1_pcl \
/*__mmask64 mskc_ = mskc; */ \
/*if (t == st_) */ \
__mmask64 mskc_ = (t == st_) ? mskc_ar[(st0 - t*64)/16]:mskc; \
z = _mm512_load_si512(&s[t]); \
xt1 = _mm512_load_si512(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(xt1, 15); */ /* tmp <- x[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)x)[t*64 + 63]); \
/* xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_);*/ /* xt1 <- x[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(xt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
xt1 = _mm512_mask_blend_epi8(mskc_, slli512, x1_); \
x1_ = tmp; \
vt1 = _mm512_load_si512(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(vt1, 15); */ /* tmp <- v[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)v)[t*64 + 63]); \
/* vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); *//* vt1 <- v[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(vt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
vt1 = _mm512_mask_blend_epi8(mskc_, slli512, v1_); \
v1_ = tmp; \
a = _mm512_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
ut = _mm512_load_si512(&u[t]); /* ut <- u[t..t+15] */ \
b = _mm512_add_epi8(_mm512_load_si512(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */ \
x2t1= _mm512_load_si512(&x2[t]); \
/* tmp = _mm_srli_si128(x2t1, 15);*/ \
tmp = _mm512_set1_epi8(((int8_t*)x2)[t*64 + 63]); \
/* x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); */ \
shf512a = _mm512_shuffle_epi8(x2t1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
x2t1 = _mm512_mask_blend_epi8(mskc_, slli512, x21_); \
x21_= tmp; \
a2= _mm512_add_epi8(x2t1, vt1); \
b2= _mm512_add_epi8(_mm512_load_si512(&y2[t]), ut);
#define __dp_code_block2_pcl \
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1)); /* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
tmp = _mm512_sub_epi8(z, q_); \
a = _mm512_sub_epi8(a, tmp); \
b = _mm512_sub_epi8(b, tmp); \
tmp = _mm512_sub_epi8(z, q2_); \
a2= _mm512_sub_epi8(a2, tmp); \
b2= _mm512_sub_epi8(b2, tmp);
__mmask64 msk_ar2[5] = {0xFFFF, 0xFFFF, 0xFFFFFFFF, 0xFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF};
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc, min_sc, long_thres, long_diff;
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
int32_t *H = 0, H0 = 0, last_H0_t = 0;
uint8_t *qr, *sf, *mem, *mem2 = 0;
__m512i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_;
__m512i *u, *v, *x, *y, *x2, *y2, *s, *p = 0;