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From: Vasimuddin <wasim.mzr@gmail.com>
Date: Sun, 12 Dec 2021 21:56:48 -0800
Subject: fixed smem memory rellocation issue (issue167)
Origin: upstream, https://github.com/bwa-mem2/bwa-mem2/commit/edc703f883e8aaed83067100d8e54e0e9e810ef5
Forwarded: not-needed
---
src/bwamem.cpp | 8 ++++----
src/macro.h | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/src/bwamem.cpp b/src/bwamem.cpp
index 4a18aff..76d4148 100644
--- a/src/bwamem.cpp
+++ b/src/bwamem.cpp
@@ -924,13 +924,13 @@ int mem_kernel1_core(FMI_search *fmi,
for (i = 0; i < len; ++i)
seq[i] = seq[i] < 4? seq[i] : nst_nt4_table[(int)seq[i]]; //nst_nt4??
}
-
+ tot_len *= N_SMEM_KERNEL;
// This covers enc_qdb/SMEM reallocs
if (tot_len >= mmc->wsize_mem[tid])
{
fprintf(stderr, "[%0.4d] Re-allocating SMEM data structures due to enc_qdb\n", tid);
int64_t tmp = mmc->wsize_mem[tid];
- mmc->wsize_mem[tid] *= 2;
+ mmc->wsize_mem[tid] = tot_len;
mmc->matchArray[tid] = (SMEM *) _mm_realloc(mmc->matchArray[tid],
tmp, mmc->wsize_mem[tid], sizeof(SMEM));
//realloc(mmc->matchArray[tid], mmc->wsize_mem[tid] * sizeof(SMEM));
@@ -966,8 +966,8 @@ int mem_kernel1_core(FMI_search *fmi,
num_smem);
if (num_smem >= *wsize_mem){
- fprintf(stderr, "num_smem: %ld\n", num_smem);
- assert(num_smem < *wsize_mem);
+ fprintf(stderr, "Error [bug]: num_smem: %ld are more than allocated space.\n", num_smem);
+ exit(EXIT_FAILURE);
}
printf_(VER, "6. Done! mem_collect_smem, num_smem: %ld\n", num_smem);
tprof[MEM_COLLECT][tid] += __rdtsc() - tim;
diff --git a/src/macro.h b/src/macro.h
index d2da0cc..4adc980 100644
--- a/src/macro.h
+++ b/src/macro.h
@@ -48,7 +48,7 @@ Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@i
#define BATCH_SIZE 512 /* Block of reads alloacted to a thread for processing*/
#define BATCH_MUL 20
#define SEEDS_PER_CHAIN 1
-
+#define N_SMEM_KERNEL 3
#define READ_LEN 151
#define SEQ_LEN8 128 // redundant??
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