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avx2 seg fault fixed

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Saurabh
2021-11-27 10:42:22 -05:00
committed by Heng Li
parent de90f2e655
commit 3b1deac0a5
2 changed files with 11 additions and 10 deletions
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ksw2_extd2_avx.c
+10 -10
View File
@@ -1759,11 +1759,11 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2); off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
off_end = off + qlen + tlen - 1; off_end = off + qlen + tlen - 1;
} }
for(uint64_t itr = 0; itr < ((qlen + tlen - 1) * n_col_ + 1) * 1; itr ++){ // for(uint64_t itr = 0; itr < ((qlen + tlen - 1) * n_col_ + 1) * 1; itr ++){
avg+= mem2[itr]; // avg+= mem2[itr];
} // }
#ifdef MANUAL_PROFILING #ifdef MANUAL_PROFILING
uint64_t align_start = __rdtsc(); // uint64_t align_start = __rdtsc();
#endif #endif
@@ -2174,15 +2174,15 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
max_H_ = _mm256_set1_epi32(max_H); max_H_ = _mm256_set1_epi32(max_H);
max_t_ = _mm256_set1_epi32(max_t); max_t_ = _mm256_set1_epi32(max_t);
#if 1 #if 1
//for (t = st0; t < en1; t +=1) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t; // for (t = st0; t < en1; t +=1) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
// H[t] += v8[t]; // H[t] += v8[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; 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, t_; __m256i H1, t_;
H1 = _mm256_loadu_si256((__m256i*)&H[t]); H1 = _mm256_loadu_si256((__m256i*)&H[t]);
__m128i t__ = _mm_load_si128((__m128i*) &v8[t]); __m128i t__ = _mm_loadu_si128((__m128i*) &v8[t]);
t_ = _mm256_cvtepi8_epi32(t__); t_ = _mm256_cvtepi8_epi32(t__);
// t_ = _mm256_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]); // t_ = _mm256_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]);
H1 = _mm256_add_epi32(H1, t_); H1 = _mm256_add_epi32(H1, t_);
_mm256_storeu_si256((__m256i*)&H[t], H1); _mm256_storeu_si256((__m256i*)&H[t], H1);
// making it 4 lanes to match accuracy // making it 4 lanes to match accuracy
@@ -2293,7 +2293,7 @@ void ksw_extd2_avx2(void *km, int qlen, const uint8_t *query, int tlen, const ui
} }
#ifdef MANUAL_PROFILING #ifdef MANUAL_PROFILING
alignment_time += (__rdtsc() - align_start); // alignment_time += (__rdtsc() - align_start);
#endif #endif
kfree(km, mem); kfree(km, mem);
lchain.c
+1
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@@ -5,6 +5,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "kalloc.h" #include "kalloc.h"
#include "krmq.h" #include "krmq.h"
#include <x86intrin.h>
//#include "simd_chain.h" //#include "simd_chain.h"
//#include "parallel_chaining_32_bit.h" //#include "parallel_chaining_32_bit.h"
#include "parallel_chaining_v2_22.h" #include "parallel_chaining_v2_22.h"