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avx2 implementation for mask_store

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Saurabh
2021-06-29 19:18:22 -04:00
committed by Heng Li
parent 6da640e551
commit 558be6b729
3 changed files with 79 additions and 26 deletions
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chain.c
+44 -1
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@@ -69,6 +69,10 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
v = (int32_t*)kmalloc(km, n * 4);
memset(t, 0, n * 4);
#if VECTORIZED_CHAINING && (__AVX512BW__ || __AVX2__)
/* Allocation for debugging
f_avx = (uint32_t*)kmalloc(km, n * 4);
p_avx = (int32_t*)kmalloc(km, n * 4);
*/
anchor_t* anchors = (anchor_t*)malloc(n* sizeof(anchor_t));
for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x;
@@ -79,8 +83,8 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
}
num_bits_t *anchor_r, *anchor_q, *anchor_l;
create_SoA_Anchors_32_bit(anchors, n, anchor_r, anchor_q, anchor_l);
dp_chain obj(max_dist_x, max_dist_y, bw, max_skip, max_iter, gap_scale, is_cdna, n_segs);
dp_chain obj(max_dist_x, max_dist_y, bw, max_skip, max_iter, gap_scale, is_cdna, n_segs);
obj.mm_dp_vectorized(n, &anchors[0], anchor_r, anchor_q, anchor_l, f, p, v, max_dist_x, max_dist_y, NULL, NULL);
// -16 is due to extra padding at the start of arrays
@@ -138,6 +142,45 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
f[i] = max_f, p[i] = max_j;
v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
}
#if 0
for (i = 0; i < n; ++i) {
assert(f[i] == f_avx[i] && p[i] == p_avx[i]);
//if(! (f[i] == f_avx[i] && p[i] == p_avx[i]))
{
#if 0
fprintf(stderr, "mm2-score:\n");
for (int itt = 0; itt < n; ++itt) {
fprintf(stderr, "%ld %ld \n", f[itt], p[itt]);
}
fprintf(stderr, "mm2-simd-score:\n");
for (int itt = 0; itt < n; ++itt) {
fprintf(stderr, "%ld %ld \n", f_avx[itt], p_avx[itt]);
}
fprintf(stderr, "anchors:\n");
fprintf(stderr, "%lld\n", n);
for (int itt = 0; itt < n; ++itt) {
uint64_t ri = a[itt].x;
int32_t qi = (int32_t)a[itt].y, q_span = a[itt].y>>32&0xff; // NB: only 8 bits of span is used!!!
fprintf(stderr, "%llu %ld %ld\n", ri, qi, q_span);
}
//exit(0);
#endif
}
}
#if 0
fprintf(stderr, "%llu\n", n);
for (int itt = 0; itt < n; ++itt) {
uint64_t ri = a[itt].x;
int32_t qi = (int32_t)a[itt].y, q_span = a[itt].y>>32&0xff; // NB: only 8 bits of span is used!!!
fprintf(stderr, "%llu %ld %ld\n", ri, qi, q_span);
}
#endif
kfree(km, f_avx); kfree(km, p_avx);
#endif
#endif
// find the ending positions of chains
memset(t, 0, n * 4);