void
ri_timer_end(ri_timer_t *timer, const char *name)
{
timerinfo_t *p;
ri_log_and_return_if(name == NULL);
p = ri_hash_lookup(timer->entrylist, name);
if (p == NULL) {
printf("name = %s\n", name);
ri_log(LOG_WARN, "timer is not started");
return;
} else {
if (!p->starting) {
ri_log(LOG_WARN, "timer is not started");
return;
}
set_end_time(p);
p->count++;
p->elapsed += calc_elapsed_time(p);
}
}
int main(int argc, char **argv) {
init_needle(argc > 1 ? argv[1] : "GCAACGAGTGTCTTTG");
#ifdef DNA_DEBUG
printf("Looking for %s\n", needle);
#endif
struct timeval start_time;
print_current_time(&start_time);
printf(" START\n");
bufindex_t input_size = 3000000000L;
size_t page_size = sysconf(_SC_PAGESIZE);
ASSERT_NOT(page_size & (page_size - 1), "Page is not a power of 2");
size_t mask = page_size - 1;
size_t mem_size = (input_size | mask) + 1;
buflen_t buf_size = page_size << 14;
#ifdef DNA_DEBUG
printf("Buf size = %u\n", buf_size);;
#endif
init_threads();
ALGO_PREPARE
#ifdef DNA_DEBUG
long io_time, waiting_time;
struct timeval tx, ty, tz;
print_current_time(&tx);
printf(" Start reading data\n");
#endif
int fd = 0;
if (argc > 2 && (fd = open(argv[2], O_RDONLY)) == -1) ERROR_OCCURRED("open");
char *mapped_file = mmap(NULL, mem_size, PROT_READ, MAP_SHARED, fd, 0);
if (fd > 0 && close(fd) == -1) ERROR_OCCURRED("close");
char *buf;
bufindex_t start;
buflen_t bytes_read;
buflen_t len = buf_size + needle_len - 1;
for (start = 0, buf = mapped_file; start < input_size; start += buf_size, buf += buf_size) {
bytes_read = (start + len < input_size) ? len : input_size - start;
job_t *job = malloc(sizeof(job_t));
job->buf = buf;
job->len = bytes_read;
job->offset = start;
submit_job(job);
}
#ifdef DNA_DEBUG
print_current_time(&ty);
printf(" End submitting jobs\n");
io_time = calc_elapsed_time(&tx, &ty);
#endif
wait_jobs_completed();
munmap(mapped_file, mem_size);
#ifdef DNA_DEBUG
gettimeofday(&tz, NULL);
waiting_time = calc_elapsed_time(&ty, &tz);
#endif
destroy_threads();
ALGO_FREE
struct timeval end_time;
print_current_time(&end_time);
printf(" FINISH\n");
#ifdef DNA_DEBUG
print_elapsed_time(&start_time, &end_time);
printf("I/O: %ld\n", io_time);
printf("Waiting: %ld\n", waiting_time);
#endif
return 0;
}
