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speed up multi-threading

This commit is contained in:
Heng Li 2011-04-07 17:26:08 -04:00
parent 87664941b0
commit 8d6b859bf8
2 changed files with 2 additions and 27 deletions
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15
bwtaln.c
View File

@ -13,9 +13,7 @@
#include "utils.h"
#ifdef HAVE_PTHREAD
#define THREAD_BLOCK_SIZE 1024
#include <pthread.h>
static pthread_mutex_t g_seq_lock = PTHREAD_MUTEX_INITIALIZER;
#endif
gap_opt_t *gap_init_opt()
@ -98,18 +96,7 @@ void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq_t *seq
for (i = 0; i != n_seqs; ++i) {
bwa_seq_t *p = seqs + i;
#ifdef HAVE_PTHREAD
if (opt->n_threads > 1) {
pthread_mutex_lock(&g_seq_lock);
if (p->tid < 0) { // unassigned
int j;
for (j = i; j < n_seqs && j < i + THREAD_BLOCK_SIZE; ++j)
seqs[j].tid = tid;
} else if (p->tid != tid) {
pthread_mutex_unlock(&g_seq_lock);
continue;
}
pthread_mutex_unlock(&g_seq_lock);
}
if (i % opt->n_threads != tid) continue;
#endif
p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
seq[0] = p->seq; seq[1] = p->rseq;

14
bwtsw2_aux.c
View File

@ -309,10 +309,6 @@ typedef struct {
bsw2seq1_t *seq;
} bsw2seq_t;
#ifdef HAVE_PTHREAD
static pthread_mutex_t g_dbwtsw_lock = PTHREAD_MUTEX_INITIALIZER;
#endif
static int fix_cigar(const char *qname, const bntseq_t *bns, bsw2hit_t *p, int n_cigar, uint32_t *cigar)
{
// FIXME: this routine does not work if the query bridge three reference sequences
@ -469,15 +465,7 @@ static void bsw2_aln_core(int tid, bsw2seq_t *_seq, const bsw2opt_t *_opt, const
l = p->l;
#ifdef HAVE_PTHREAD
if (_opt->n_threads > 1) {
pthread_mutex_lock(&g_dbwtsw_lock);
if (p->tid < 0) p->tid = tid;
else if (p->tid != tid) {
pthread_mutex_unlock(&g_dbwtsw_lock);
continue;
} // in pinciple else should not happen
pthread_mutex_unlock(&g_dbwtsw_lock);
}
if (x % _opt->n_threads != tid) continue;
#endif
// set opt->t