struct dgNode *dgAddNode(struct diGraph *dg, char *name, void *val)
/* Create new node in graph. It's legal (but not efficient) to add
* a node with the same name and value twice. It's not legal to
* add a node with the same name and a different value.
* You can pass in NULL for the name in which case the
* hexadecimal representation of val will become the name. */
{
struct dgNode *node;
struct hashEl *hel;
struct hash *hash = dg->nodeHash;
char nbuf[17];
if (name == NULL)
{
sprintf(nbuf, "%p", val);
name = nbuf;
}
hel = hashLookup(hash, name);
if (hel != NULL)
{
node = hel->val;
if (node->val != val)
{
errAbort("Trying to add node %s with a new value (old 0x%"PRIxMAX" new 0x%"PRIxMAX")",
name, ptrToLL(node->val), ptrToLL(val));
}
return node;
}
AllocVar(node);
hel = hashAdd(hash, name, node);
node->name = hel->name;
node->val = val;
slAddHead(&dg->nodeList, node);
return node;
}
void carefulCheckHeap()
/* Walk through allocated memory and make sure that all cookies are
* in place. */
{
int maxPieces = 10000000; /* Assume no more than this many pieces allocated. */
struct carefulMemBlock *cmb;
char *pEndCookie;
size_t size;
if (carefulParent == NULL)
return;
for (cmb = (struct carefulMemBlock *)(cmbAllocedList->head); cmb->next != NULL; cmb = cmb->next)
{
size = cmb->size;
pEndCookie = (((char *)(cmb+1)) + size);
if (cmb->startCookie != cmbStartCookie)
errAbort("Bad start cookie %x checking %llx\n", cmb->startCookie,
ptrToLL(cmb+1));
if (memcmp(pEndCookie, cmbEndCookie, sizeof(cmbEndCookie)) != 0)
errAbort("Bad end cookie %x%x%x%x checking %llx\n",
pEndCookie[0], pEndCookie[1], pEndCookie[2], pEndCookie[3],
ptrToLL(cmb+1));
if (--maxPieces == 0)
errAbort("Loop or more than 10000000 pieces in memory list");
}
}
static struct perThreadAbortVars *getThreadVars()
/* Return a pointer to the perThreadAbortVars for the current pthread. */
{
pthread_t pid = pthread_self(); // can be a pointer or a number
// Don't safef, theoretically that could abort.
char pidStr[64];
snprintf(pidStr, sizeof(pidStr), "%lld", ptrToLL(pid));
pidStr[ArraySize(pidStr)-1] = '\0';
static char pidInUse[64] = ""; // use a string since there is no known unused value for pthread_t variable
if (sameString(pidStr, pidInUse)) // avoid deadlock on self
{ // this only happens when it has aborted already due to out of memory
// which should be a rare occurrence.
char *errMsg = "errAbort re-entered due to out-of-memory condition. Exiting.";
write(STDERR_FILENO, errMsg, strlen(errMsg));
exit(1);
}
static pthread_mutex_t ptavMutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_lock( &ptavMutex );
snprintf(pidInUse, sizeof(pidInUse), "%lld", ptrToLL(pid));
pidInUse[ArraySize(pidInUse)-1] = '\0';
static struct hash *perThreadVars = NULL;
if (perThreadVars == NULL)
perThreadVars = hashNew(0);
struct hashEl *hel = hashLookup(perThreadVars, pidStr);
if (hel == NULL)
{
// if it is the first time, initialization the perThreadAbortVars
struct perThreadAbortVars *ptav;
AllocVar(ptav);
ptav->debugPushPopErr = FALSE;
ptav->errAbortInProgress = FALSE;
ptav->warnIx = 0;
ptav->warnArray[0] = defaultVaWarn;
ptav->abortIx = 0;
ptav->abortArray[0] = defaultAbort;
hel = hashAdd(perThreadVars, pidStr, ptav);
}
pidInUse[0] = '\0';
pthread_mutex_unlock( &ptavMutex );
return (struct perThreadAbortVars *)(hel->val);
}
static void carefulFree(void *vpt)
/* Check cookies and free. */
{
struct carefulMemBlock *cmb = ((struct carefulMemBlock *)vpt)-1;
size_t size = cmb->size;
char *pEndCookie;
carefulAlloced -= size;
pEndCookie = (((char *)(cmb+1)) + size);
if (cmb->startCookie != cmbStartCookie)
errAbort("Bad start cookie %x freeing %llx\n", cmb->startCookie,
ptrToLL(vpt));
if (memcmp(pEndCookie, cmbEndCookie, sizeof(cmbEndCookie)) != 0)
errAbort("Bad end cookie %x%x%x%x freeing %llx\n",
pEndCookie[0], pEndCookie[1], pEndCookie[2], pEndCookie[3],
ptrToLL(vpt));
dlRemove((struct dlNode *)cmb);
carefulParent->free(cmb);
}