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#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <unistd.h>
#include <pthread.h>
#include <stdio.h>
#include <time.h>
#include "mrope.h"
/*******************************
*** Single-string insertion ***
*******************************/
mrope_t *mr_init(int max_nodes, int block_len, int sorting_order)
{
int a;
mrope_t *r;
assert(sorting_order >= 0 && sorting_order <= 2);
r = calloc(1, sizeof(mrope_t));
r->so = sorting_order;
r->thr_min = 1000;
for (a = 0; a != 6; ++a)
r->r[a] = rope_init(max_nodes, block_len);
return r;
}
void mr_destroy(mrope_t *r)
{
int a;
for (a = 0; a != 6; ++a)
if (r->r[a]) rope_destroy(r->r[a]);
free(r);
}
int mr_thr_min(mrope_t *r, int thr_min)
{
if (thr_min > 0)
r->thr_min = thr_min;
return r->thr_min;
}
int64_t mr_insert1(mrope_t *r, const uint8_t *str)
{
int64_t tl[6], tu[6], l, u;
const uint8_t *p;
int b, is_srt = (r->so != MR_SO_IO), is_comp = (r->so == MR_SO_RCLO);
for (u = 0, b = 0; b != 6; ++b) u += r->r[b]->c[0];
l = is_srt? 0 : u;
for (p = str, b = 0; *p; b = *p++) {
int a;
if (l != u) {
int64_t cnt = 0;
rope_rank2a(r->r[b], l, u, tl, tu);
if (is_comp && *p != 5) {
for (a = 4; a > *p; --a) l += tu[a] - tl[a];
l += tu[0] - tl[0];
} else for (a = 0; a < *p; ++a) l += tu[a] - tl[a];
rope_insert_run(r->r[b], l, *p, 1, 0);
while (--b >= 0) cnt += r->r[b]->c[*p];
l = cnt + tl[*p]; u = cnt + tu[*p];
} else {
l = rope_insert_run(r->r[b], l, *p, 1, 0);
while (--b >= 0) l += r->r[b]->c[*p];
u = l;
}
}
return rope_insert_run(r->r[b], l, 0, 1, 0);
}
void mr_rank2a(const mrope_t *mr, int64_t x, int64_t y, int64_t *cx, int64_t *cy)
{
int a, b;
int64_t z, c[6], l;
memset(c, 0, 48);
for (a = 0, z = 0; a < 6; ++a) {
const int64_t *ca = mr->r[a]->c;
l = ca[0] + ca[1] + ca[2] + ca[3] + ca[4] + ca[5];
if (z + l >= x) break;
for (b = 0; b < 6; ++b) c[b] += ca[b];
z += l;
}
assert(a != 6);
if (y >= 0 && z + l >= y) { // [x,y) is in the same bucket
rope_rank2a(mr->r[a], x - z, y - z, cx, cy);
for (b = 0; b < 6; ++b)
cx[b] += c[b], cy[b] += c[b];
return;
}
if (x != z) rope_rank1a(mr->r[a], x - z, cx);
else memset(cx, 0, 48);
for (b = 0; b < 6; ++b)
cx[b] += c[b], c[b] += mr->r[a]->c[b];
if (y < 0) return;
for (++a, z += l; a < 6; ++a) {
const int64_t *ca = mr->r[a]->c;
l = ca[0] + ca[1] + ca[2] + ca[3] + ca[4] + ca[5];
if (z + l >= y) break;
for (b = 0; b < 6; ++b) c[b] += ca[b];
z += l;
}
assert(a != 6);
if (y != z + l) rope_rank1a(mr->r[a], y - z, cy);
else for (b = 0; b < 6; ++b) cy[b] = mr->r[a]->c[b];
for (b = 0; b < 6; ++b) cy[b] += c[b];
}
/**********************
*** Mrope iterator ***
**********************/
void mr_itr_first(mrope_t *r, mritr_t *i, int to_free)
{
i->a = 0; i->r = r; i->to_free = to_free;
rope_itr_first(i->r->r[0], &i->i);
}
const uint8_t *mr_itr_next_block(mritr_t *i)
{
const uint8_t *s;
if (i->a >= 6) return 0;
while ((s = rope_itr_next_block(&i->i)) == 0) {
if (i->to_free) {
rope_destroy(i->r->r[i->a]);
i->r->r[i->a] = 0;
}
if (++i->a == 6) return 0;
rope_itr_first(i->r->r[i->a], &i->i);
}
return i->a == 6? 0 : s;
}
/*****************************************
*** Inserting multiple strings in RLO ***
*****************************************/
typedef struct {
uint64_t l;
uint64_t u:61, c:3;
const uint8_t *p;
} triple64_t;
typedef const uint8_t *cstr_t;
#define rope_comp6(c) ((c) >= 1 && (c) <= 4? 5 - (c) : (c))
static void mr_insert_multi_aux(rope_t *rope, int64_t m, triple64_t *a, int is_comp)
{
int64_t k, beg;
rpcache_t cache;
memset(&cache, 0, sizeof(rpcache_t));
for (k = 0; k != m; ++k) // set the base to insert
a[k].c = *a[k].p++;
for (k = 1, beg = 0; k <= m; ++k) {
if (k == m || a[k].u != a[k-1].u) {
int64_t x, i, l = a[beg].l, u = a[beg].u, tl[6], tu[6], c[6];
int start, end, step, b;
if (l == u && k == beg + 1) { // special case; still works without the following block
a[beg].l = a[beg].u = rope_insert_run(rope, l, a[beg].c, 1, &cache);
beg = k;
continue;
} else if (l == u) {
memset(tl, 0, 48);
memset(tu, 0, 48);
} else rope_rank2a(rope, l, u, tl, tu);
memset(c, 0, 48);
for (i = beg; i < k; ++i) ++c[a[i].c];
// insert sentinel
if (c[0]) rope_insert_run(rope, l, 0, c[0], &cache);
// insert A/C/G/T
x = l + c[0] + (tu[0] - tl[0]);
if (is_comp) start = 4, end = 0, step = -1;
else start = 1, end = 5, step = 1;
for (b = start; b != end; b += step) {
int64_t size = tu[b] - tl[b];
if (c[b]) {
tl[b] = rope_insert_run(rope, x, b, c[b], &cache);
tu[b] = tl[b] + size;
}
x += c[b] + size;
}
// insert N
if (c[5]) {
tu[5] -= tl[5];
tl[5] = rope_insert_run(rope, x, 5, c[5], &cache);
tu[5] += tl[5];
}
// update a[]
for (i = beg; i < k; ++i) {
triple64_t *p = &a[i];
p->l = tl[p->c], p->u = tu[p->c];
}
beg = k;
}
}
}
typedef struct {
volatile int *n_fin_workers;
volatile int to_run;
int to_exit;
mrope_t *mr;
int b, is_comp;
int64_t m;
triple64_t *a;
} worker_t;
static void *worker(void *data)
{
worker_t *w = (worker_t*)data;
struct timespec req, rem;
req.tv_sec = 0; req.tv_nsec = 1000000;
do {
while (!__sync_bool_compare_and_swap(&w->to_run, 1, 0)) nanosleep(&req, &rem); // wait for the signal from the master thread
if (w->m) mr_insert_multi_aux(w->mr->r[w->b], w->m, w->a, w->is_comp);
__sync_add_and_fetch(w->n_fin_workers, 1);
} while (!w->to_exit);
return 0;
}
void mr_insert_multi(mrope_t *mr, int64_t len, const uint8_t *s, int is_thr)
{
int64_t k, m, n0;
int b, is_srt = (mr->so != MR_SO_IO), is_comp = (mr->so == MR_SO_RCLO), stop_thr = 0;
volatile int n_fin_workers = 0;
triple64_t *a[2], *curr, *prev, *swap;
pthread_t *tid = 0;
worker_t *w = 0;
if (mr->thr_min < 0) mr->thr_min = 0;
assert(len > 0 && s[len-1] == 0);
{ // split into short strings
cstr_t p, q, end = s + len;
for (p = s, m = 0; p != end; ++p) // count #sentinels
if (*p == 0) ++m;
curr = a[0] = malloc(m * sizeof(triple64_t));
prev = a[1] = malloc(m * sizeof(triple64_t));
for (p = q = s, k = 0; p != end; ++p) // find the start of each string
if (*p == 0) prev[k++].p = q, q = p + 1;
}
for (k = n0 = 0; k < 6; ++k) n0 += mr->r[k]->c[0];
for (k = 0; k != m; ++k) {
if (is_srt) prev[k].l = 0, prev[k].u = n0;
else prev[k].l = prev[k].u = n0 + k;
prev[k].c = 0;
}
mr_insert_multi_aux(mr->r[0], m, prev, is_comp); // insert the first (actually the last) column
if (is_thr) {
tid = alloca(4 * sizeof(pthread_t));
w = alloca(4 * sizeof(worker_t));
memset(w, 0, 4 * sizeof(worker_t));
for (b = 0; b < 4; ++b) {
w[b].mr = mr, w[b].b = b + 1, w[b].is_comp = is_comp;
w[b].n_fin_workers = &n_fin_workers;
}
for (b = 0; b < 4; ++b) pthread_create(&tid[b], 0, worker, &w[b]);
}
n0 = 0; // the number of inserted strings
while (m) {
int64_t c[6], ac[6];
triple64_t *q[6];
memset(c, 0, 48);
for (k = n0; k != m; ++k) ++c[prev[k].c]; // counting
for (q[0] = curr + n0, b = 1; b < 6; ++b) q[b] = q[b-1] + c[b-1];
if (n0 + c[0] < m) {
for (k = n0; k != m; ++k) *q[prev[k].c]++ = prev[k]; // sort
for (b = 0; b < 6; ++b) q[b] -= c[b];
}
n0 += c[0];
if (is_thr && !stop_thr) {
struct timespec req, rem;
req.tv_sec = 0; req.tv_nsec = 1000000;
stop_thr = (m - n0 <= mr->thr_min);
for (b = 0; b < 4; ++b) {
w[b].a = q[b+1], w[b].m = c[b+1];
if (stop_thr) w[b].to_exit = 1; // signal the workers to exit
while (!__sync_bool_compare_and_swap(&w[b].to_run, 0, 1)); // signal the workers to start
}
if (c[5]) mr_insert_multi_aux(mr->r[5], c[5], q[5], is_comp); // the master thread processes the "N" bucket
while (!__sync_bool_compare_and_swap(&n_fin_workers, 4, 0)) // wait until all 4 workers finish
nanosleep(&req, &rem);
if (stop_thr && n0 < m)
fprintf(stderr, "[M::%s] Turn off parallelization for this batch as too few strings are left.\n", __func__);
} else {
for (b = 1; b < 6; ++b)
if (c[b]) mr_insert_multi_aux(mr->r[b], c[b], q[b], is_comp);
}
if (n0 == m) break;
memset(ac, 0, 48);
for (b = 1; b < 6; ++b) { // update the intervals to account for buckets ahead
int a;
for (a = 0; a < 6; ++a) ac[a] += mr->r[b-1]->c[a];
for (k = 0; k < c[b]; ++k) {
triple64_t *p = &q[b][k];
p->l += ac[p->c]; p->u += ac[p->c];
}
}
swap = curr, curr = prev, prev = swap;
}
if (is_thr) for (b = 0; b < 4; ++b) pthread_join(tid[b], 0);
free(a[0]); free(a[1]);
}
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