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Source code changes of the file "layer0/MemoryDebug.cpp" between
pymol-open-source-2.2.0.tar.gz and pymol-open-source-2.3.0.tar.gz

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

[ To the main PyMOL source changes report ]

MemoryDebug.cpp  (pymol-open-source-2.2.0):MemoryDebug.cpp  (pymol-open-source-2.3.0)
skipping to change at line 114 skipping to change at line 114
} }
if(vla->auto_zero) { if(vla->auto_zero) {
start = ((char *) vla) + soffset; start = ((char *) vla) + soffset;
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size); stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
MemoryZero(start, stop); MemoryZero(start, stop);
} }
} }
return ((void *) &(vla[1])); return ((void *) &(vla[1]));
} }
#ifdef _MemoryCache_ON
void *VLACacheExpand(PyMOLGlobals * G, void *ptr, unsigned int rec, int thread_i
ndex,
int block_id)
{
VLARec *vla;
char *start, *stop;
unsigned int soffset = 0;
vla = &(((VLARec *) ptr)[-1]);
if(rec >= vla->size) {
if(vla->auto_zero)
soffset = sizeof(VLARec) + (vla->unit_size * vla->size);
vla->size = ((unsigned int) (rec * vla->grow_factor)) + 1;
if(vla->size <= rec)
vla->size = rec + 1;
vla = (void *) _MemoryCacheRealloc(G, vla,
(vla->unit_size * vla->size) + sizeof(VLA
Rec),
thread_index, block_id MD_FILE_LINE_Call)
;
if(!vla) {
printf("VLAExpand-ERR: realloc failed.\n");
DieOutOfMemory();
}
if(vla->auto_zero) {
start = ((char *) vla) + soffset;
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
MemoryZero(start, stop);
}
}
return ((void *) &(vla[1]));
}
#endif
#ifndef _MemoryDebug_ON
void *VLAMalloc(ov_size init_size, ov_size unit_size, unsigned int grow_factor, void *VLAMalloc(ov_size init_size, ov_size unit_size, unsigned int grow_factor,
int auto_zero) int auto_zero)
#else
void *_VLAMalloc(const char *file, int line, ov_size init_size,
ov_size unit_size, unsigned int grow_factor, int auto_zero)
#endif
{ {
VLARec *vla; VLARec *vla;
char *start, *stop; char *start, *stop;
#ifndef _MemoryDebug_ON
vla = (VLARec*) mmalloc((init_size * unit_size) + sizeof(VLARec)); vla = (VLARec*) mmalloc((init_size * unit_size) + sizeof(VLARec));
#else
vla = (VLARec*)
MemoryDebugMalloc((init_size * unit_size) + sizeof(VLARec), file, line, _MDP
ointer);
#endif
if(!vla) { if(!vla) {
printf("VLAMalloc-ERR: malloc failed\n"); printf("VLAMalloc-ERR: malloc failed\n");
DieOutOfMemory(); DieOutOfMemory();
} }
vla->size = init_size; vla->size = init_size;
vla->unit_size = unit_size; vla->unit_size = unit_size;
vla->grow_factor = (1.0F + grow_factor * 0.1F); vla->grow_factor = (1.0F + grow_factor * 0.1F);
vla->auto_zero = auto_zero; vla->auto_zero = auto_zero;
if(vla->auto_zero) { if(vla->auto_zero) {
start = ((char *) vla) + sizeof(VLARec); start = ((char *) vla) + sizeof(VLARec);
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size); stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
MemoryZero(start, stop); MemoryZero(start, stop);
} }
return ((void *) &(vla[1])); return ((void *) &(vla[1]));
} }
#ifdef _MemoryCache_ON
#ifndef _MemoryDebug_ON
void *VLACacheMalloc(PyMOLGlobals * G, unsigned int init_size, unsigned int unit
_size,
unsigned int grow_factor, int auto_zero, int thread, int id
)
#else
void *_VLACacheMalloc(PyMOLGlobals * G, const char *file, int line,
unsigned int init_size, unsigned int unit_size,
unsigned int grow_factor, int auto_zero, int thread, int i
d)
#endif
{
VLARec *vla;
char *start, *stop;
vla = (void *) _MemoryCacheMalloc(G, (init_size * unit_size) + sizeof(VLARec),
thread, id MD_FILE_LINE_Nest);
if(!vla) {
printf("VLAMalloc-ERR: realloc failed\n");
DieOutOfMemory();
}
vla->size = init_size;
vla->unit_size = unit_size;
vla->grow_factor = (1.0F + grow_factor * 0.1F);
vla->auto_zero = auto_zero;
if(vla->auto_zero) {
start = ((char *) vla) + sizeof(VLARec);
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
MemoryZero(start, stop);
}
return ((void *) &(vla[1]));
}
#endif
void VLAFree(void *ptr) void VLAFree(void *ptr)
{ {
VLARec *vla; VLARec *vla;
if(!ptr) { if(!ptr) {
printf("VLAFree-ERR: tried to free NULL pointer!\n"); printf("VLAFree-ERR: tried to free NULL pointer!\n");
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} }
vla = &(((VLARec *) ptr)[-1]); vla = &(((VLARec *) ptr)[-1]);
mfree(vla); mfree(vla);
} }
#ifdef _MemoryCache_ON
void VLACacheFree(PyMOLGlobals * G, void *ptr, int thread, int id, int force)
{
VLARec *vla;
if(!ptr) {
printf("VLAFree-ERR: tried to free NULL pointer!\n");
exit(EXIT_FAILURE);
}
vla = &(((VLARec *) ptr)[-1]);
_MemoryCacheFree(G, vla, thread, id, force MD_FILE_LINE_Call);
}
#endif
unsigned int VLAGetSize(const void *ptr) unsigned int VLAGetSize(const void *ptr)
{ {
const VLARec *vla; const VLARec *vla;
vla = &((VLARec *) ptr)[-1]; vla = &((VLARec *) ptr)[-1];
return (vla->size); return (vla->size);
} }
void *VLANewCopy(const void *ptr) void *VLANewCopy(const void *ptr)
{ {
if(ptr) { /* NULL protected */ if(ptr) { /* NULL protected */
skipping to change at line 264 skipping to change at line 176
exit(EXIT_FAILURE); exit(EXIT_FAILURE);
} else { } else {
memcpy(new_vla, vla, size); memcpy(new_vla, vla, size);
} }
return ((void *) &(new_vla[1])); return ((void *) &(new_vla[1]));
} else { } else {
return NULL; return NULL;
} }
} }
#ifdef _MemoryCache_ON
void *VLACacheSetSize(PyMOLGlobals * G, void *ptr, unsigned int new_size, int gr
oup_id,
int block_id)
{
VLARec *vla;
char *start = NULL;
char *stop;
unsigned int soffset = 0;
vla = &((VLARec *) ptr)[-1];
if(vla->auto_zero) {
soffset = sizeof(VLARec) + (vla->unit_size * vla->size);
}
vla->size = new_size;
vla =
(void *) _MemoryCacheRealloc(G, vla, (vla->unit_size * vla->size) + sizeof(V
LARec),
group_id, block_id MD_FILE_LINE_Call);
if(!vla) {
printf("VLASetSize-ERR: realloc failed.\n");
DieOutOfMemory();
}
if(vla->auto_zero) {
start = ((char *) vla) + soffset;
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
if(start < stop)
MemoryZero(start, stop);
}
return ((void *) &(vla[1]));
}
void *VLACacheSetSizeForSure(PyMOLGlobals * G, void *ptr, unsigned int new_size,
int group_id, int block_id)
{
VLARec *vla;
char *start = NULL;
char *stop;
unsigned int soffset = 0;
vla = &((VLARec *) ptr)[-1];
if(vla->auto_zero) {
soffset = sizeof(VLARec) + (vla->unit_size * vla->size);
}
if(new_size < vla->size) {
vla->size = new_size;
vla =
(void *) _MemoryCacheShrinkForSure(G, vla,
(vla->unit_size * vla->size) + sizeof(V
LARec),
group_id, block_id MD_FILE_LINE_Call);
} else {
vla->size = new_size;
vla =
(void *) _MemoryCacheRealloc(G, vla, (vla->unit_size * vla->size) + sizeof
(VLARec),
group_id, block_id MD_FILE_LINE_Call);
}
if(!vla) {
printf("VLASetSize-ERR: realloc failed.\n");
DieOutOfMemory();
}
if(vla->auto_zero) {
start = ((char *) vla) + soffset;
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
if(start < stop)
MemoryZero(start, stop);
}
return ((void *) &(vla[1]));
}
#endif
void *VLASetSize(void *ptr, unsigned int new_size) void *VLASetSize(void *ptr, unsigned int new_size)
{ {
VLARec *vla; VLARec *vla;
char *start = NULL; char *start = NULL;
char *stop; char *stop;
unsigned int soffset = 0; unsigned int soffset = 0;
vla = &((VLARec *) ptr)[-1]; vla = &((VLARec *) ptr)[-1];
if(vla->auto_zero) { if(vla->auto_zero) {
soffset = sizeof(VLARec) + (vla->unit_size * vla->size); soffset = sizeof(VLARec) + (vla->unit_size * vla->size);
} }
skipping to change at line 455 skipping to change at line 301
DieOutOfMemory(); DieOutOfMemory();
} }
if(vla->auto_zero) { if(vla->auto_zero) {
start = ((char *) vla) + soffset; start = ((char *) vla) + soffset;
stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size); stop = ((char *) vla) + sizeof(VLARec) + (vla->unit_size * vla->size);
if(start < stop) if(start < stop)
MemoryZero(start, stop); MemoryZero(start, stop);
} }
return ((void *) &(vla[1])); return ((void *) &(vla[1]));
} }
#ifdef _MemoryDebug_ON
#ifndef NULL
#define NULL (void *)
#endif
#ifndef false
#define false 0
#endif
#ifndef true
#define true 1
#endif
#define _NO_GDB_ENTRY
#ifdef __cplusplus
extern "C" {
#endif
typedef struct DebugRec {
struct DebugRec *next;
char file[32], note[64];
int line;
size_t size;
int type;
} DebugRec;
#define HASH(x) ((x>>11)&0x3FF)
static DebugRec *HashTable[1024];
static int InitFlag = true;
static int Count;
static int MaxCount;
DebugRec *MemoryDebugRemove(void *ptr);
void MemoryDebugInit(void);
void MemoryDebugInit(void) {
int a;
for(a = 0; a < 1024; a++)
HashTable[a] = NULL;
InitFlag = false;
Count = 0;
MaxCount = 0;
}
int MemoryDebugUsage(void) {
int a;
unsigned int tot = 0;
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
for(a = 0; a < 1024; a++) {
rec = HashTable[a];
while(rec) {
rec = rec->next;
}
}
return (tot);
}
void MemoryDebugDump(void) {
int a;
int cnt = 0;
unsigned int tot = 0;
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
for(a = 0; a < 1024; a++) {
rec = HashTable[a];
while(rec) {
tot += rec->size;
printf("Memory: %12p %12p %8x %3.1f %s:%i\n",
(void *) (rec + 1),
((char *) (rec + 1) + rec->size), (unsigned int) rec->size,
rec->size / 1048576.0F, rec->file, rec->line);
rec = rec->next;
cnt++;
}
}
printf("Memory: %d blocks expected, %d found, %d maximum allocated.\n",
Count, cnt, MaxCount);
printf("Memory: current memory allocated %x bytes (%0.1f MB).\n", tot,
tot / (1024.0 * 1024));
}
void MemoryDebugHashAdd(DebugRec * rec);
DebugRec *MemoryDebugHashRemove(void *ptr);
void MemoryDebugHashAdd(DebugRec * rec) {
int hash;
hash = (size_t) rec;
hash = HASH(hash);
rec->next = HashTable[hash];
HashTable[hash] = rec;
}
DebugRec *MemoryDebugHashRemove(void *ptr) {
DebugRec *rec, *cur, *last;
int hash;
rec = (DebugRec *) ptr;
rec--;
hash = (size_t) rec;
hash = HASH(hash);
last = NULL;
cur = HashTable[hash];
while(cur) {
if(cur == rec) {
if(last)
last->next = cur->next;
else
HashTable[hash] = cur->next;
break;
}
last = cur;
cur = cur->next;
}
return (cur);
}
void *MemoryDebugMalloc(size_t size, const char *file, int line, int type) {
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
rec = (DebugRec *) malloc(sizeof(DebugRec) + size);
if(!rec) {
if(!size)
return (NULL);
else {
printf("MemoryDebugMalloc-ERR: alloc failed.\n");
DieOutOfMemory();
}
}
strcpy(rec->file, file);
rec->line = line;
rec->size = size;
rec->type = type;
MemoryDebugHashAdd(rec);
rec++;
Count++;
if(MaxCount < Count)
MaxCount = Count;
return ((void *) rec);
}
void *MemoryDebugCalloc(size_t num, size_t size, const char *file, int line, i
nt type) {
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
rec = (DebugRec *) calloc(1, sizeof(DebugRec) + size * num);
if(!rec)
return (NULL);
strcpy(rec->file, file);
rec->line = line;
rec->size = size;
rec->type = type;
MemoryDebugHashAdd(rec);
rec++;
Count++;
if(MaxCount < Count)
MaxCount = Count;
return ((void *) rec);
}
void *MemoryDebugRealloc(void *ptr, size_t size, const char *file, int line, i
nt type) {
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
if((!ptr) && (!size)) {
printf("MemoryDebug-ERR: realloc given (NULL,zero) (%s:%i)\n", file, line)
;
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
if(!ptr)
return (MemoryDebugMalloc(size, file, line, type));
else if(!size) {
MemoryDebugFree(ptr, file, line, type);
return (NULL);
} else {
rec = MemoryDebugHashRemove(ptr);
if(!rec) {
printf("MemoryDebug-ERR: realloc() corrupted tree or bad ptr! (%s:%i @%p
)\n",
file, line, ptr);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
} else {
if(rec->type != type) {
printf("MemoryDebug-ERR: ptr %p is of wrong type: %i!=%i (%s:%i)\n",
ptr, rec->type, type, file, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
rec = (DebugRec *) realloc(rec, size + sizeof(DebugRec));
if(!rec) {
printf("MemoryDebug-ERR: realloc() failed reallocation! (%s:%i)\n", fi
le, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
DieOutOfMemory();
} else {
MemoryDebugHashAdd(rec);
rec->size = size;
rec++;
return ((void *) rec);
}
}
}
return (ptr);
}
void *MemoryDebugReallocForSure(void *ptr, size_t size, const char *file,
int line, int type) {
DebugRec *rec, *new_rec;
if(InitFlag)
MemoryDebugInit();
if((!ptr) && (!size)) {
printf("MemoryDebug-ERR: realloc given (NULL,zero) (%s:%i)\n", file, line)
;
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
if(!ptr)
return (MemoryDebugMalloc(size, file, line, type));
else if(!size) {
MemoryDebugFree(ptr, file, line, type);
return (NULL);
} else {
rec = MemoryDebugHashRemove(ptr);
if(!rec) {
printf("MemoryDebug-ERR: realloc() corrupted tree or bad ptr! (%s:%i @%p
)\n",
file, line, ptr);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
} else {
if(rec->type != type) {
printf("MemoryDebug-ERR: ptr %p is of wrong type: %i!=%i (%s:%i)\n",
ptr, rec->type, type, file, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
new_rec = (DebugRec*) malloc(size + sizeof(DebugRec));
if(new_rec)
memcpy(new_rec, rec, size + sizeof(DebugRec));
free(rec);
rec = new_rec;
if(!rec) {
printf("MemoryDebug-ERR: realloc() failed reallocation! (%s:%i)\n", fi
le, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
DieOutOfMemory();
} else {
MemoryDebugHashAdd(rec);
rec->size = size;
rec++;
return ((void *) rec);
}
}
}
return (ptr);
}
void *MemoryDebugReallocForSureSafe(void *ptr, size_t size, size_t old_size,
const char *file, int line, int type) {
DebugRec *rec, *new_rec;
if(InitFlag)
MemoryDebugInit();
if((!ptr) && (!size)) {
printf("MemoryDebug-ERR: realloc given (NULL,zero) (%s:%i)\n", file, line)
;
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
if(!ptr)
return (MemoryDebugMalloc(size, file, line, type));
else if(!size) {
MemoryDebugFree(ptr, file, line, type);
return (NULL);
} else {
rec = MemoryDebugHashRemove(ptr);
if(!rec) {
printf("MemoryDebug-ERR: realloc() corrupted tree or bad ptr! (%s:%i @%p
)\n",
file, line, ptr);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
} else {
if(rec->type != type) {
printf("MemoryDebug-ERR: ptr %p is of wrong type: %i!=%i (%s:%i)\n",
ptr, rec->type, type, file, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
if(old_size > size) {
new_rec = (DebugRec*) malloc(size + sizeof(DebugRec));
if(new_rec)
memcpy(new_rec, rec, size + sizeof(DebugRec));
free(rec);
rec = new_rec;
} else {
rec = (DebugRec*) realloc(rec, size + sizeof(DebugRec));
}
if(!rec) {
printf("MemoryDebug-ERR: realloc() failed reallocation! (%s:%i)\n", fi
le, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
DieOutOfMemory();
} else {
MemoryDebugHashAdd(rec);
rec->size = size;
rec++;
return ((void *) rec);
}
}
}
return (ptr);
}
void MemoryDebugQuietFree(void *ptr, int type) {
DebugRec *rec;
if(InitFlag)
MemoryDebugInit();
if(!ptr) {
printf("MemoryDebug-ERR: MemoryDebugQuietFree() given NULL pointer\n");
}
rec = MemoryDebugHashRemove(ptr);
if(rec) {
if(rec->type != type) {
printf("MemoryDebug-ERR: ptr %p is of wrong type: %i!=%i (allocated %s:%
i)\n",
ptr, rec->type, type, rec->file, rec->line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
free(rec);
Count--;
} else
free(ptr);
}
void MemoryDebugFree(void *ptr, const char *file, int line, int type) {
DebugRec *rec;
if(!ptr)
return;
if(InitFlag)
MemoryDebugInit();
rec = MemoryDebugHashRemove(ptr);
if(rec) {
if(rec->type != type) {
printf("MemoryDebug-ERR: ptr %p is of wrong type: %i!=%i (%s:%i)\n",
ptr, rec->type, type, file, line);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
free(rec);
} else {
printf("MemoryDebug-ERR: free(): corrupted tree or bad ptr! (%s:%i @%p)\n"
,
file, line, ptr);
#ifdef GDB_ENTRY
MemoryDebugDump();
abort();
#endif
exit(EXIT_FAILURE);
}
Count--;
}
// strdup
char *MemoryDebugStrDup(const char *s, const char *file, int line, int type) {
size_t n = strlen(s) + 1;
void *ptr = MemoryDebugMalloc(n, file, line, type);
return (char*)memcpy(ptr, s, n);
}
#ifdef __cplusplus
}
#endif
#endif
 End of changes. 8 change blocks. 
165 lines changed or deleted 0 lines changed or added
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