FastBQSR/ext/htslib/cram/pooled_alloc.c

/*
Copyright (c) 2009, 2013, 2015, 2018-2019 Genome Research Ltd.
Author: Rob Davies <rmd@sanger.ac.uk>

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.

   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#define HTS_BUILDING_LIBRARY // Enables HTSLIB_EXPORT, see htslib/hts_defs.h
#include <config.h>

#include <stdlib.h>
#include <stdio.h>
#include <stdint.h>

#include "pooled_alloc.h"
#include "misc.h"

//#define DISABLE_POOLED_ALLOC
//#define TEST_MAIN

#define PSIZE 1024*1024

// credit to http://graphics.stanford.edu/~seander/bithacks.html
static int next_power_2(unsigned int v) {
    v--;
    v |= v >> 1;
    v |= v >> 2;
    v |= v >> 4;
    v |= v >> 8;
    v |= v >> 16;
    v++;

    return v;
}

/*
 * Creates a pool.
 * Pool allocations are approx minimum of 1024*dsize or PSIZE.
 * (Assumes we're not trying to use pools for >= 2Gb or more)
 */
pool_alloc_t *pool_create(size_t dsize) {
    pool_alloc_t *p;

    if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p))))
        return NULL;

    /* Minimum size is a pointer, for free list */
    dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1);
    if (dsize < sizeof(void *))
        dsize = sizeof(void *);
    p->dsize = dsize;
    p->psize = MIN(PSIZE, next_power_2(p->dsize*1024));

    p->npools = 0;
    p->pools = NULL;
    p->free  = NULL;

    return p;
}

void pool_destroy(pool_alloc_t *p) {
    size_t i;

    for (i = 0; i < p->npools; i++) {
        free(p->pools[i].pool);
    }
    free(p->pools);
    free(p);
}

#ifndef DISABLE_POOLED_ALLOC

static pool_t *new_pool(pool_alloc_t *p) {
    size_t n = p->psize / p->dsize;
    pool_t *pool;

    pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools));
    if (NULL == pool) return NULL;
    p->pools = pool;
    pool = &p->pools[p->npools];

    pool->pool = malloc(n * p->dsize);
    if (NULL == pool->pool) return NULL;

    pool->used = 0;

    p->npools++;

    return pool;
}

void *pool_alloc(pool_alloc_t *p) {
    pool_t *pool;
    void *ret;

    /* Look on free list */
    if (NULL != p->free) {
        ret = p->free;
        p->free = *((void **)p->free);
        return ret;
    }

    /* Look for space in the last pool */
    if (p->npools) {
        pool = &p->pools[p->npools - 1];
        if (pool->used + p->dsize < p->psize) {
            ret = ((char *) pool->pool) + pool->used;
            pool->used += p->dsize;
            return ret;
        }
    }

    /* Need a new pool */
    pool = new_pool(p);
    if (NULL == pool) return NULL;

    pool->used = p->dsize;
    return pool->pool;
}

void pool_free(pool_alloc_t *p, void *ptr) {
    *(void **)ptr = p->free;
    p->free = ptr;
}

#else

void *pool_alloc(pool_alloc_t *p) {
    return malloc(p->dsize);
}

void pool_free(pool_alloc_t *p, void *ptr) {
    free(ptr);
}

#endif

#ifdef TEST_MAIN
typedef struct {
    int x, y, z;
} xyz;

#define NP 10000
int main(void) {
    int i;
    xyz *item;
    xyz **items;
    pool_alloc_t *p = pool_create(sizeof(xyz));

    items = (xyz **)malloc(NP * sizeof(*items));

    for (i = 0; i < NP; i++) {
        item = pool_alloc(p);
        item->x = i;
        item->y = i+1;
        item->z = i+2;
        items[i] = item;
    }

    for (i = 0; i < NP; i++) {
        item = items[i];
        if (i % 3)
            pool_free(p, item);
    }

    for (i = 0; i < NP; i++) {
        item = pool_alloc(p);
        item->x = 1000000+i;
        item->y = 1000000+i+1;
        item->z = 1000000+i+2;
    }

    for (i = 0; i < NP; i++) {
        item = items[i];
        printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z);
        pool_free(p, item);
    }

    free(items);
    return 0;
}
#endif