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r508: use two I/O threads for mapping

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-x sr applies this option by default
This commit is contained in:
Heng Li
2017-10-12 14:56:01 -04:00
parent 2801ed9b4b
commit 7c555f9b7e
4 changed files with 15 additions and 6 deletions
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map.c
+4 -3
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@@ -83,7 +83,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->best_n = 50;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND;
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND | MM_F_2_IO_THREADS;
mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->zdrop = 100;
@@ -500,7 +500,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads)
{
int i, j;
int i, j, pl_threads;
pipeline_t pl;
if (n_segs < 1) return -1;
memset(&pl, 0, sizeof(pipeline_t));
@@ -520,7 +520,8 @@ int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_
pl.opt = opt, pl.mi = idx;
pl.n_threads = n_threads > 1? n_threads : 1;
pl.mini_batch_size = opt->mini_batch_size;
kt_pipeline(n_threads == 1? 1 : 2, worker_pipeline, &pl, 3);
pl_threads = n_threads == 1? 1 : (opt->flag&MM_F_2_IO_THREADS)? 3 : 2;
kt_pipeline(pl_threads, worker_pipeline, &pl, 3);
free(pl.str.s);
for (i = 0; i < n_segs; ++i)
mm_bseq_close(pl.fp[i]);