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r411: refactored kalloc for clarity 

The new version is closer to K&R's original implementation.
This commit is contained in:
Heng Li 2017-09-18 19:49:15 -04:00
parent 60485790b4
commit 11081c6c27
5 changed files with 122 additions and 139 deletions
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1
align.c
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@ -1,5 +1,6 @@
#include <assert.h> #include <assert.h>
#include <string.h> #include <string.h>
#include <stdlib.h>
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#include "ksw2.h" #include "ksw2.h"

1
hit.c
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@ -1,4 +1,5 @@
#include <string.h> #include <string.h>
#include <stdlib.h>
#include <math.h> #include <math.h>
#include "mmpriv.h" #include "mmpriv.h"
#include "kalloc.h" #include "kalloc.h"

246
kalloc.c
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@ -1,175 +1,144 @@
#include <stdio.h> #include <stdio.h>
#include <stdlib.h> #include <stdlib.h>
#include <string.h> #include <string.h>
#include <limits.h>
#include "kalloc.h" #include "kalloc.h"
/* The whole thing is: ("@" for the kheader_t of the block, "-" for free /* In kalloc, a *core* is a large chunk of contiguous memory. Each core is
* memory, and "+" for allocated memory. One char for one unit.) * associated with a master header, which keeps the size of the current core
* * and the pointer to next core. Kalloc allocates small *blocks* of memory from
* This region is core 1. This region is core 2. * the cores and organizes free memory blocks in a circular single-linked list.
* *
* @-------@++++++@++++++++++++@------------ @----------@++++++++++++@+++++++@------------ * In the following diagram, "@" stands for the header of a free block (of type
* | | | | * header_t), "#" for the header of an allocated block (of type size_t), "-"
* p=p->ptr->ptr->ptr->ptr p->ptr p->ptr->ptr p->ptr->ptr->ptr * for free memory, and "+" for allocated memory.
*
* master This region is core 1. master This region is core 2.
* | |
* *@-------#++++++#++++++++++++@-------- *@----------#++++++++++++#+++++++@------------
* | | | |
* p=p->ptr->ptr->ptr->ptr p->ptr p->ptr->ptr p->ptr->ptr->ptr
*/ */
#define PTR(p) ((size_t*)((size_t*)p)[1]) #define MIN_CORE_SIZE 0x80000
typedef struct _allocated_t { typedef struct header_t {
struct _allocated_t *next; size_t size;
size_t *ptr; struct header_t *ptr;
} allocated_t; } header_t;
typedef struct { typedef struct {
size_t base[2], *loop_head; header_t base, *loop_head, *core_head; /* base is a zero-sized block always kept in the loop */
allocated_t list_head, *list_tail;
size_t total_allocated;
} kmem_t; } kmem_t;
void *km_init() static void panic(const char *s)
{
return calloc(1, sizeof(kmem_t));
}
static void kerror(const char *s)
{ {
fprintf(stderr, "%s\n", s); fprintf(stderr, "%s\n", s);
exit(1); abort();
} }
static size_t *morecore(kmem_t *km, size_t nu) void *km_init(void)
{ {
size_t rnu, *up; return calloc(1, sizeof(kmem_t));
rnu = (nu + 0xfffff) & (~(size_t)0xfffff);
up = (size_t*)malloc(rnu * sizeof(size_t));
if (!up) { /* fail to allocate memory */
km_stat(km);
fprintf(stderr, "[morecore] %lu bytes requested but not available.\n", (unsigned long)rnu * sizeof(size_t));
exit(1);
}
/* put the pointer in km->list_head */
if (km->list_tail == 0) km->list_tail = &km->list_head;
km->list_tail->ptr = up;
km->list_tail->next = (allocated_t*)calloc(1, sizeof(allocated_t));
km->list_tail = km->list_tail->next;
km->total_allocated += rnu * sizeof(size_t);
*up = rnu; /* the size of the current block, and in this case the block is the same as the new core */
kfree(km, up + 1); /* initialize the new "core" */
return km->loop_head;
} }
void km_destroy(void *_km) void km_destroy(void *_km)
{ {
kmem_t *km = (kmem_t*)_km; kmem_t *km = (kmem_t*)_km;
allocated_t *p, *q; header_t *p, *q;
if (km == 0) return; if (km == NULL) return;
p = &km->list_head; for (p = km->core_head; p != NULL;) {
do { q = p->ptr;
q = p->next; free(p);
free(p->ptr);
if (p != &km->list_head) free(p);
p = q; p = q;
} while (p && p->next); }
if (p != &km->list_head) free(p);
free(km); free(km);
} }
void kfree(void *_km, void *ap) static header_t *morecore(kmem_t *km, size_t nu)
{ {
size_t *p, *q; header_t *q;
size_t bytes, *p;
nu = (nu + 1 + (MIN_CORE_SIZE - 1)) / MIN_CORE_SIZE * MIN_CORE_SIZE; /* the first +1 for core header */
bytes = nu * sizeof(header_t);
q = (header_t*)malloc(bytes);
if (!q) panic("[morecore] insufficient memory");
q->ptr = km->core_head, q->size = nu, km->core_head = q;
p = (size_t*)(q + 1);
*p = nu - 1; /* the size of the free block; -1 because the first unit is used for the core header */
kfree(km, p + 1); /* initialize the new "core"; NB: the core header is not looped. */
return km->loop_head;
}
void kfree(void *_km, void *ap) /* kfree() also adds a new core to the circular list */
{
header_t *p, *q;
kmem_t *km = (kmem_t*)_km; kmem_t *km = (kmem_t*)_km;
if (!ap) return; if (!ap) return;
if (km == 0) { if (km == NULL) {
free(ap); free(ap);
return; return;
} }
p = (size_t*)ap - 1; /* *p is the size of the current block */ p = (header_t*)((size_t*)ap - 1);
p->size = *((size_t*)ap - 1);
/* Find the pointer that points to the block to be freed. The following loop can stop on two conditions: /* Find the pointer that points to the block to be freed. The following loop can stop on two conditions:
* *
* a) "p>q && p<q->ptr": @------@++++++++@+++++++@------- @---------------@+++++++@------- * a) "p>q && p<q->ptr": @------#++++++++#+++++++@------- @---------------#+++++++@-------
* (can also be in | | | -> | | * (can also be in | | | -> | |
* two cores) q p q->ptr q q->ptr * two cores) q p q->ptr q q->ptr
* *
* @-------- @+++++++++@-------- @-------- @------------------ * @-------- #+++++++++@-------- @-------- @------------------
* | | | -> | | * | | | -> | |
* q p q->ptr q q->ptr * q p q->ptr q q->ptr
* *
* b) "q>=q->ptr && (p>q || p<q->ptr)": @-------@+++++ @--------@+++++++ @-------@+++++ @---------------- * b) "q>=q->ptr && (p>q || p<q->ptr)": @-------#+++++ @--------#+++++++ @-------#+++++ @----------------
* | | | -> | | * | | | -> | |
* q->ptr q p q->ptr q * q->ptr q p q->ptr q
* *
* @+++++++@----- @++++++++@------- @------------- @++++++++@------- * #+++++++@----- #++++++++@------- @------------- #++++++++@-------
* | | | -> | | * | | | -> | |
* p q->ptr q q->ptr q * p q->ptr q q->ptr q
*/ */
for (q = km->loop_head; !(p > q && p < PTR(q)); q = PTR(q)) for (q = km->loop_head; !(p > q && p < q->ptr); q = q->ptr)
if (q >= PTR(q) && (p > q || p < PTR(q))) break; if (q >= q->ptr && (p > q || p < q->ptr)) break;
if (p + (*p) == PTR(q)) { /* two adjacent blocks, merge p and q->ptr (the 2nd and 4th cases) */ if (p + p->size == q->ptr) { /* two adjacent blocks, merge p and q->ptr (the 2nd and 4th cases) */
*p += *PTR(q); /* this is the new q->ptr size */ p->size += q->ptr->size;
p[1] = (size_t)PTR(PTR(q)); /* this is the new q->ptr->ptr */ p->ptr = q->ptr->ptr;
/* p is actually the new q->ptr. The actual change happens a few lines below. */ } else if (p + p->size > q->ptr && q->ptr >= p) {
} else if (p + (*p) > PTR(q) && PTR(q) >= p) { /* the end of the allocated block is in the next free block */ panic("[kfree] The end of the allocated block enters a free block.");
kerror("[kfree] The end of the allocated block enters a free block."); } else p->ptr = q->ptr; /* backup q->ptr */
} else p[1] = (size_t)PTR(q); /* backup q->ptr */
if (q + (*q) == p) { /* two adjacent blocks, merge q and p (the other two cases) */ if (q + q->size == p) { /* two adjacent blocks, merge q and p (the other two cases) */
*q += *p; q->size += p->size;
q[1] = (size_t)PTR(p); q->ptr = p->ptr;
km->loop_head = q; km->loop_head = q;
} else if (q + (*q) > p && p >= q) { /* the end of a free block in the allocated block */ } else if (q + q->size > p && p >= q) {
kerror("[kfree] The end of a free block enters the allocated block."); panic("[kfree] The end of a free block enters the allocated block.");
} else km->loop_head = p, q[1] = (size_t)p; /* in two cores, cannot be merged */ } else km->loop_head = p, q->ptr = p; /* in two cores, cannot be merged; create a new block in the list */
}
void *krealloc(void *_km, void *ap, size_t n_bytes)
{
kmem_t *km = (kmem_t*)_km;
size_t n_units, *p, *q;
if (n_bytes == 0) {
kfree(km, ap); return 0;
}
if (km == 0) return realloc(ap, n_bytes);
if (!ap) return kmalloc(km, n_bytes);
n_units = 1 + (n_bytes + sizeof(size_t) - 1) / sizeof(size_t);
p = (size_t*)ap - 1;
if (*p >= n_units) return ap; /* TODO: this prevents shrinking */
q = (size_t*)kmalloc(km, n_bytes);
memcpy(q, ap, (*p - 1) * sizeof(size_t));
kfree(km, ap);
return q;
} }
void *kmalloc(void *_km, size_t n_bytes) void *kmalloc(void *_km, size_t n_bytes)
{ {
kmem_t *km = (kmem_t*)_km; kmem_t *km = (kmem_t*)_km;
size_t n_units, *p, *q; size_t n_units;
header_t *p, *q;
if (n_bytes == 0) return 0; if (n_bytes == 0) return 0;
if (km == 0) return malloc(n_bytes); if (km == NULL) return malloc(n_bytes);
/* "n_units" means the number of units. The size of one unit equals to sizeof(kheader_t). n_units = (n_bytes + sizeof(size_t) + sizeof(header_t) - 1) / sizeof(header_t) + 1;
* "1" is the kheader_t of a block, which is always required. */
n_units = 1 + (n_bytes + sizeof(size_t) - 1) / sizeof(size_t);
if (n_units&1) ++n_units; /* make n_units an even number, or it will segfault if only one unit remains */
if (!(q = km->loop_head)) { /* the first time when kmalloc() is called, intialization */ if (!(q = km->loop_head)) /* the first time when kmalloc() is called, intialize it */
km->base[1] = (size_t)(km->loop_head = q = km->base); *q = 0; q = km->loop_head = km->base.ptr = &km->base;
} for (p = q->ptr;; q = p, p = p->ptr) { /* search for a suitable block */
for (p = PTR(q);; q = p, p = PTR(p)) { /* search for a suitable block */ if (p->size >= n_units) { /* p->size if the size of current block. This line means the current block is large enough. */
if (*p >= n_units) { /* p->size if the size of current block. This line means the current block is large enough. */ if (p->size == n_units) q->ptr = p->ptr; /* no need to split the block */
if (*p == n_units) q[1] = (size_t)PTR(p); /* no need to split the block */ else { /* split the block. NB: memory is allocated at the end of the block! */
else { /* split the block */ p->size -= n_units; /* reduce the size of the free block */
/* memory is allocated at the end of the block */ p += p->size; /* p points to the allocated block */
*p -= n_units; /* reduce the size of the free block */ *(size_t*)p = n_units; /* set the size */
p += *p; /* skip to the kheader_t of the allocated block */
*p = n_units; /* set the size */
} }
km->loop_head = q; /* set the end of chain */ km->loop_head = q; /* set the end of chain */
return p + 1; /* skip the kheader_t */ return (size_t*)p + 1;
} }
if (p == km->loop_head) { /* then ask for more "cores" */ if (p == km->loop_head) { /* then ask for more "cores" */
if ((p = morecore(km, n_units)) == 0) return 0; if ((p = morecore(km, n_units)) == 0) return 0;
@ -182,33 +151,44 @@ void *kcalloc(void *_km, size_t count, size_t size)
kmem_t *km = (kmem_t*)_km; kmem_t *km = (kmem_t*)_km;
void *p; void *p;
if (size == 0 || count == 0) return 0; if (size == 0 || count == 0) return 0;
if (km == 0) return calloc(count, size); if (km == NULL) return calloc(count, size);
p = kmalloc(km, count * size); p = kmalloc(km, count * size);
memset(p, 0, count * size); memset(p, 0, count * size);
return p; return p;
} }
void km_stat(const void *_km) void *krealloc(void *_km, void *ap, size_t n_bytes) // TODO: this can be made more efficient in principle
{ {
kmem_t *km = (kmem_t*)_km; kmem_t *km = (kmem_t*)_km;
unsigned n_blocks, n_units; size_t n_units, *p, *q;
size_t max_block = 0, *p, *q;
float frag;
if (km == 0 || !(p = km->loop_head)) return; if (n_bytes == 0) {
n_blocks = n_units = 0; kfree(km, ap); return 0;
do { }
q = PTR(p); if (km == NULL) return realloc(ap, n_bytes);
if (*p > max_block) max_block = *p; if (ap == NULL) return kmalloc(km, n_bytes);
n_units += *p; n_units = (n_bytes + sizeof(size_t) + sizeof(header_t) - 1) / sizeof(header_t);
if (p + (*p) > q && q > p) p = (size_t*)ap - 1;
kerror("[kr_stat] The end of a free block enters another free block."); if (*p >= n_units) return ap; /* TODO: this prevents shrinking */
p = q; q = (size_t*)kmalloc(km, n_bytes);
++n_blocks; memcpy(q, ap, (*p - 1) * sizeof(header_t));
} while (p != km->loop_head); kfree(km, ap);
return q;
--n_blocks; }
frag = 1.0/1024.0 * n_units * sizeof(size_t) / n_blocks;
fprintf(stderr, "[kr_stat] tot=%lu, free=%lu, n_block=%u, max_block=%lu, frag_len=%.3fK\n", void km_stat(const void *_km, km_stat_t *s)
(unsigned long)km->total_allocated, (unsigned long)n_units * sizeof(size_t), n_blocks, (unsigned long)max_block * sizeof(size_t), frag); {
kmem_t *km = (kmem_t*)_km;
header_t *p;
memset(s, 0, sizeof(km_stat_t));
if (km == NULL || km->loop_head == NULL) return;
for (p = km->loop_head;; p = p->ptr) {
s->available += p->size * sizeof(header_t);
if (p->size != 0) ++s->n_blocks; /* &kmem_t::base is always one of the cores. It is zero-sized. */
if (p->ptr > p && p + p->size > p->ptr)
panic("[km_stat] The end of a free block enters another free block.");
if (p->ptr == km->loop_head) break;
}
for (p = km->core_head; p != NULL; p = p->ptr)
++s->n_cores, s->capacity += p->size * sizeof(header_t);
} }

11
kalloc.h
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@ -1,14 +1,16 @@
#ifndef _KALLOC_H_ #ifndef _KALLOC_H_
#define _KALLOC_H_ #define _KALLOC_H_
#include <stdlib.h> #include <stddef.h> /* for size_t */
#define km_size(x) (*(((size_t*)(x))-1) * sizeof(size_t))
#ifdef __cplusplus #ifdef __cplusplus
extern "C" { extern "C" {
#endif #endif
typedef struct {
size_t capacity, available, n_blocks, n_cores;
} km_stat_t;
void *kmalloc(void *km, size_t size); void *kmalloc(void *km, size_t size);
void *krealloc(void *km, void *ptr, size_t size); void *krealloc(void *km, void *ptr, size_t size);
void *kcalloc(void *km, size_t count, size_t size); void *kcalloc(void *km, size_t count, size_t size);
@ -16,8 +18,7 @@ void kfree(void *km, void *ptr);
void *km_init(void); void *km_init(void);
void km_destroy(void *km); void km_destroy(void *km);
void km_stat(const void *_km, km_stat_t *s);
void km_stat(const void *km); // TODO: return numbers instead of print to stderr
#ifdef __cplusplus #ifdef __cplusplus
} }

2
main.c
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@ -6,7 +6,7 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "getopt.h" #include "getopt.h"
#define MM_VERSION "2.2-r409" #define MM_VERSION "2.2-r411-dirty"
#ifdef __linux__ #ifdef __linux__
#include <sys/resource.h> #include <sys/resource.h>