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Default compilation without AVX2

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This commit is contained in:
Saurabh
2021-07-20 12:32:34 -04:00
committed by Heng Li
parent f68b4b22df
commit 34e273c8ee
6 changed files with 70 additions and 42 deletions
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ksw2_extd2_avx.c
+25 -31
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@@ -33,8 +33,6 @@ Modified Copyright (C) 2021 Intel Corporation
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)
{
__m512i ind512_srli = _mm512_set1_epi8(15);
__mmask8 msk_srli = 0x0003;
__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)));
@@ -105,7 +103,6 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
a2= _mm512_sub_epi8(a2, tmp); \
b2= _mm512_sub_epi8(b2, tmp);
__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;
@@ -201,9 +198,9 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
st0 = st, en0 = en;
int st_new = st / 16 * 16, en_new = (en + 16) / 16 * 16 - 1;
// int st_new = st / 64 * 64, en_new = (en + 64) / 64 * 64 - 1;
int stb = st, enb = en;
//int stb = st, enb = en;
st = st / 64 * 64, en = (en + 64) / 64 * 64 - 1;
int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;
//int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;
// set boundary conditions
if (st_new > 0) {
if (st_new - 1 >= last_st && st_new - 1 <= last_en) {
@@ -224,7 +221,7 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
// loop fission: set scores first
if (!(flag & KSW_EZ_GENERIC_SC)) {
for (t = st0; t <= en0; t += 64) {
__m512i sq, st, tmp_512, mask_512;
__m512i sq, st, tmp_512;
__mmask64 tmp, mask;
sq = _mm512_loadu_si512((__m512i*)&sf[t]);
st = _mm512_loadu_si512((__m512i*)&qrr[t]);
@@ -446,7 +443,6 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
// __dp_code_block2_pcl;
__mmask64 msk;
{
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
@@ -551,7 +547,7 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
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_;
__m512i H1, t_;
__mmask16 tmp_mask;
H1 = _mm512_loadu_si512((__m512i*)&H[t]);
__m128i t__ = _mm_load_si128((__m128i*) &v8[t]);
@@ -659,6 +655,8 @@ void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const
}
kfree(km, mem2); kfree(km, off);
}
#undef __dp_code_block1_pcl
#undef __dp_code_block2_pcl
}
#endif
@@ -692,14 +690,14 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
__m256i shf256a, shf256b, slli256;
__m256i ind256_slli = _mm256_load_si256((__m256i*) index);
__mmask8 mska = 0x00;//0x90
__mmask32 mskb = 0x00010000;//0000 0000 0000 0001 0000 0000 0000 0000
__mmask32 mskc = 0x1;
//__mmask8 mska = 0x00;//0x90
//__mmask32 mskb = 0x00010000;//0000 0000 0000 0001 0000 0000 0000 0000
//__mmask32 mskc = 0x1;
__m256i mskb_v = _mm256_set_epi32(0,0,0,255,0,0,0,0);
__m256i mskc_v = _mm256_set_epi32(0,0,0,0,0,0,0,255);
__mmask32 mskc_ar[2] = {0x1, 0x10000};
//__mmask32 mskc_ar[2] = {0x1, 0x10000};
__m256i mskc_ar_v[2];// = {0x1, 0x10000};
mskc_ar_v[0] = _mm256_set_epi32(0,0,0,0,0,0,0,255);
mskc_ar_v[1] = _mm256_set_epi32(0,0,0,255,0,0,0,0);
@@ -760,7 +758,7 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
a2= _mm256_sub_epi8(a2, tmp); \
b2= _mm256_sub_epi8(b2, tmp);
__mmask32 msk_ar2[3] = {0xFFFF, 0xFFFF, 0xFFFFFFFF};
//__mmask32 msk_ar2[3] = {0xFFFF, 0xFFFF, 0xFFFFFFFF};
__m256i msk_ar2_v[3];
msk_ar2_v[0] = _mm256_set_epi32(0,0,0,0,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
msk_ar2_v[1] = _mm256_set_epi32(0,0,0,0,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF,0xFFFFFFFF);
@@ -861,9 +859,9 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
st0 = st, en0 = en;
int st_new = st / 16 * 16, en_new = (en + 16) / 16 * 16 - 1;
// int st_new = st / 64 * 64, en_new = (en + 64) / 64 * 64 - 1;
int stb = st, enb = en;
//int stb = st, enb = en;
st = st / 32 * 32, en = (en + 32) / 32 * 32 - 1;
int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;
//int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;
// set boundary conditions
if (st_new > 0) {
if (st_new - 1 >= last_st && st_new - 1 <= last_en) {
@@ -885,7 +883,6 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
if (!(flag & KSW_EZ_GENERIC_SC)) {
for (t = st0; t <= en0; t += 32) {
__m256i sq, st, tmp_256, mask_256;
__mmask32 tmp, mask;
sq = _mm256_loadu_si256((__m256i*)&sf[t]);
st = _mm256_loadu_si256((__m256i*)&qrr[t]);
// mask = (_mm256_cmpeq_epi8_mask(sq, m1_) | _mm256_cmpeq_epi8_mask(st, m1_));
@@ -897,10 +894,8 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
tmp_256 = _mm256_blendv_epi8(tmp_256, sc_N_, mask_256);
if (t + 32 > en0)
{
__mmask32 msk;
int ind = (en0 - t + 16)/16;
//assert(ind >= 0 && ind < 3);
msk = msk_ar2[ind];
__m256i msk_v = msk_ar2_v[ind];
__m256i str = (get_mask_store(msk_v, ((int8_t*)s + t), tmp_256));// msk_ar2_v[ind];
//__m256i str =_mm256_and_si256(get_mask_store(msk_v,(int8_t*)s + t), tmp_256);// msk_ar2_v[ind];
@@ -939,9 +934,7 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
z = _mm256_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl; // save u[] and v[]; update a, b, a2 and b2
if (t == en_) {
__mmask32 msk;
int ind = (en0 - t*32 + 16)/16;//doubt
msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm256_storeu_si256(&u[t], (get_mask_store(msk_ar2_v[ind], &u[t], _mm256_sub_epi8(z, vt1))));
_mm256_storeu_si256(&v[t], (get_mask_store(msk_ar2_v[ind], &v[t], _mm256_sub_epi8(z, ut))));
@@ -965,10 +958,10 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
}
if (t == en_) {
__mmask32 msk;
//__mmask32 msk;
int ind = (en0 - t*32 + 16)/16;//doubt
//assert(ind >= 0);
msk = msk_ar2[ind];
//msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm256_storeu_si256(&x[t], (get_mask_store(msk_ar2_v[ind], &x[t], _mm256_sub_epi8(_mm256_max_epi8(a, zero_), qe_))));
_mm256_storeu_si256(&y[t], (get_mask_store(msk_ar2_v[ind],&y[t], _mm256_sub_epi8(_mm256_max_epi8(b, zero_), qe_))));
@@ -1047,10 +1040,10 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
z = _mm256_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
{
__mmask32 msk;
//__mmask32 msk;
int ind = (en0 - t*32 + 16)/16;//doubt
// //assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
//msk = msk_ar2[ind];
_mm256_storeu_si256(&u[t], (get_mask_store(msk_ar2_v[ind], &u[t], _mm256_sub_epi8(z, vt1))));
_mm256_storeu_si256(&v[t], (get_mask_store(msk_ar2_v[ind],&v[t], _mm256_sub_epi8(z, ut))));
@@ -1063,9 +1056,9 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
}
{
__mmask32 msk;
//__mmask32 msk;
int ind = (en0 - t*32 + 16)/16;//doubt
msk = msk_ar2[ind];
//msk = msk_ar2[ind];
__m256i msk_v= msk_ar2_v[ind];
off_end[r] -= (2-ind)*16;//doubt
@@ -1116,7 +1109,7 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
// __dp_code_block2_pcl;
__mmask32 msk;
//__mmask32 msk;
{
_mm256_storeu_si256(&u[t], _mm256_sub_epi8(z, vt1));
_mm256_storeu_si256(&v[t], _mm256_sub_epi8(z, ut));
@@ -1172,11 +1165,11 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
// __dp_code_block2_pcl;
__mmask32 msk;
//__mmask32 msk;
// __mmask64 msk;
int ind = (en0 - t*32 + 16)/16;//doubt
msk = msk_ar2[ind];
//msk = msk_ar2[ind];
off_end[r] -= (2-ind)*16;//doubt
_mm256_storeu_si256(&u[t], (get_mask_store(msk_ar2_v[ind], &u[t], _mm256_sub_epi8(z, vt1))));
@@ -1222,7 +1215,7 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
max_H_ = _mm256_set1_epi32(max_H);
max_t_ = _mm256_set1_epi32(max_t);
for (t = st0; t < en1; t += /*4*/8) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
__m256i H1, tmp, t_;
__m256i H1, t_;
H1 = _mm256_loadu_si256((__m256i*)&H[t]);
//__m128i t__ = _mm_load_si128((__m128i*) &v8[t]);
//t_ = _mm256_cvtepi8_epi32(t__);
@@ -1232,7 +1225,6 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
// making it 4 lanes to match accuracy
__m256i shfH, shft, max1, max2;
__mmask8 tmp_mask;
__m256i tmp_mask_v;
t_ = _mm256_set1_epi32(t);
t_ = _mm256_add_epi32(t_, bt32_);
@@ -1340,6 +1332,8 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
}
kfree(km, mem2); kfree(km, off);
}
#undef __dp_code_block1_pcl
#undef __dp_code_block2_pcl
}
#endif