c_cpp/lib/htslib/cram/pooled_alloc.c

   1 /*
   2 Copyright (c) 2009 Genome Research Ltd.
   3 Author: Rob Davies <rmd@sanger.ac.uk>
   4
   5 Redistribution and use in source and binary forms, with or without
   6 modification, are permitted provided that the following conditions are met:
   7
   8    1. Redistributions of source code must retain the above copyright notice,
   9 this list of conditions and the following disclaimer.
  10
  11    2. Redistributions in binary form must reproduce the above copyright notice,
  12 this list of conditions and the following disclaimer in the documentation
  13 and/or other materials provided with the distribution.
  14
  15    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
  16 Institute nor the names of its contributors may be used to endorse or promote
  17 products derived from this software without specific prior written permission.
  18
  19 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
  20 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
  21 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
  22 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
  23 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
  24 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
  25 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
  26 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
  27 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  28 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  29 */
  30
  31 #include <config.h>
  32
  33 #include <stdlib.h>
  34 #include <stdio.h>
  35 #include <stdint.h>
  36
  37 #include "cram/pooled_alloc.h"
  38 #include "cram/misc.h"
  39
  40 //#define TEST_MAIN
  41
  42 #define PSIZE 1024*1024
  43
  44 // credit to http://graphics.stanford.edu/~seander/bithacks.html
  45 static int next_power_2(unsigned int v) {
  46     v--;
  47     v |= v >> 1;
  48     v |= v >> 2;
  49     v |= v >> 4;
  50     v |= v >> 8;
  51     v |= v >> 16;
  52     v++;
  53
  54     return v;
  55 }
  56
  57 /*
  58  * Creates a pool.
  59  * Pool allocations are approx minimum of 1024*dsize or PSIZE.
  60  * (Assumes we're not trying to use pools for >= 2Gb or more)
  61  */
  62 pool_alloc_t *pool_create(size_t dsize) {
  63     pool_alloc_t *p;
  64
  65     if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p))))
  66         return NULL;
  67
  68     /* Minimum size is a pointer, for free list */
  69     dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1);
  70     if (dsize < sizeof(void *))
  71         dsize = sizeof(void *);
  72     p->dsize = dsize;
  73     p->psize = MIN(PSIZE, next_power_2(p->dsize*1024));
  74
  75     p->npools = 0;
  76     p->pools = NULL;
  77     p->free  = NULL;
  78
  79     return p;
  80 }
  81
  82 static pool_t *new_pool(pool_alloc_t *p) {
  83     size_t n = p->psize / p->dsize;
  84     pool_t *pool;
  85
  86     pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools));
  87     if (NULL == pool) return NULL;
  88     p->pools = pool;
  89     pool = &p->pools[p->npools];
  90
  91     pool->pool = malloc(n * p->dsize);
  92     if (NULL == pool->pool) return NULL;
  93
  94     pool->used = 0;
  95
  96     p->npools++;
  97
  98     return pool;
  99 }
 100
 101 void pool_destroy(pool_alloc_t *p) {
 102     size_t i;
 103
 104     for (i = 0; i < p->npools; i++) {
 105         free(p->pools[i].pool);
 106     }
 107     free(p->pools);
 108     free(p);
 109 }
 110
 111 void *pool_alloc(pool_alloc_t *p) {
 112     pool_t *pool;
 113     void *ret;
 114
 115     /* Look on free list */
 116     if (NULL != p->free) {
 117         ret = p->free;
 118         p->free = *((void **)p->free);
 119         return ret;
 120     }
 121
 122     /* Look for space in the last pool */
 123     if (p->npools) {
 124         pool = &p->pools[p->npools - 1];
 125         if (pool->used + p->dsize < p->psize) {
 126             ret = ((char *) pool->pool) + pool->used;
 127             pool->used += p->dsize;
 128             return ret;
 129         }
 130     }
 131
 132     /* Need a new pool */
 133     pool = new_pool(p);
 134     if (NULL == pool) return NULL;
 135
 136     pool->used = p->dsize;
 137     return pool->pool;
 138 }
 139
 140 void pool_free(pool_alloc_t *p, void *ptr) {
 141     *(void **)ptr = p->free;
 142     p->free = ptr;
 143 }
 144
 145 #ifdef TEST_MAIN
 146 typedef struct {
 147     int x, y, z;
 148 } xyz;
 149
 150 #define NP 10000
 151 int main(void) {
 152     int i;
 153     xyz *item;
 154     xyz **items;
 155     pool_alloc_t *p = pool_create(sizeof(xyz));
 156
 157     items = (xyz **)malloc(NP * sizeof(*items));
 158
 159     for (i = 0; i < NP; i++) {
 160         item = pool_alloc(p);
 161         item->x = i;
 162         item->y = i+1;
 163         item->z = i+2;
 164         items[i] = item;
 165     }
 166
 167     for (i = 0; i < NP; i++) {
 168         item = items[i];
 169         if (i % 3)
 170             pool_free(p, item);
 171     }
 172
 173     for (i = 0; i < NP; i++) {
 174         item = pool_alloc(p);
 175         item->x = 1000000+i;
 176         item->y = 1000000+i+1;
 177         item->z = 1000000+i+2;
 178     }
 179
 180     for (i = 0; i < NP; i++) {
 181         item = items[i];
 182         printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z);
 183         pool_free(p, item);
 184     }
 185
 186     return 0;
 187 }
 188 #endif