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oocsort.c
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#ifndef lint
static const char RCSid[] = "$Id: oocsort.c,v 2.4 2017/08/14 21:12:10 rschregle Exp $";
#endif
/*
=========================================================================
N-way out-of-core merge sort for records with 3D keys. Recursively
subdivides input into N blocks until these are of sufficiently small size
to be sorted in-core according to Z-order (Morton code), then N-way
merging them out-of-core using a priority queue as the stack unwinds.
Roland Schregle (roland.schregle@{hslu.ch, gmail.com})
(c) Lucerne University of Applied Sciences and Arts,
supported by the Swiss National Science Foundation (SNSF, #147053)
==========================================================================
$Id: oocsort.c,v 2.4 2017/08/14 21:12:10 rschregle Exp $
*/
#if !defined(_WIN32) && !defined(_WIN64) || defined(PMAP_OOC)
/* No Windoze support for now */
#include "oocsort.h"
#include "oocmorton.h"
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <fcntl.h>
#include <sys/wait.h>
/* Priority queue node */
typedef struct {
OOC_MortonIdx pri; /* Record's priority (sort key) */
unsigned blk; /* Block containing record */
} OOC_SortQueueNode;
/* Priority queue */
typedef struct {
OOC_SortQueueNode *node;
unsigned len, tail;
} OOC_SortQueue;
/* Additional data for qsort() compare function. We resort to instancing
* this as a global variable instead of passing it to the compare func via
* qsort_r(), since the latter is a non-portable GNU extension. */
typedef struct {
RREAL *(*key)(const void*); /* Callback to access 3D key in record */
FVECT bbOrg; /* Origin of bbox containing keys */
RREAL mortonScale; /* Scale for generating Morton code */
} OOC_KeyData;
static OOC_KeyData keyData;
static int OOC_KeyCompare (const void *rec1, const void *rec2)
/* Comparison function for in-core quicksort */
{
OOC_MortonIdx pri1, pri2;
if (!rec1 || !rec2)
return 0;
pri1 = OOC_Key2Morton(keyData.key(rec1), keyData.bbOrg,
keyData.mortonScale);
pri2 = OOC_Key2Morton(keyData.key(rec2), keyData.bbOrg,
keyData.mortonScale);
if (pri1 < pri2)
return -1;
else if (pri1 > pri2)
return 1;
else
return 0;
}
static int OOC_SortRead (FILE *file, unsigned recSize, char *rec)
/* Read next record from file; return 0 and record in rec on success,
* else -1 */
{
if (!rec || feof(file) || !fread(rec, recSize, 1, file))
return -1;
return 0;
}
static int OOC_SortPeek (FILE *file, unsigned recSize, char *rec)
/* Return next record from file WITHOUT advancing file position;
* return 0 and record in rec on success, else -1 */
{
const unsigned long filePos = ftell(file);
if (OOC_SortRead(file, recSize, rec))
return -1;
/* Workaround; fseek(file, -recSize, SEEK_CUR) causes subsequent
* fread()'s to fail until rewind() */
rewind(file);
if (fseek(file, filePos, SEEK_SET) < 0)
return -1;
return 0;
}
static int OOC_SortWrite (FILE *file, unsigned recSize, const char *rec)
/* Output record to file; return 0 on success, else -1 */
{
if (!rec || !fwrite(rec, recSize, 1, file))
return -1;
return 0;
}
#ifdef DEBUG_OOC_SORT
static int OOC_SortQueueCheck (OOC_SortQueue *pq, unsigned root)
/* Priority queue sanity check */
{
unsigned kid;
if (root < pq -> tail) {
if ((kid = (root << 1) + 1) < pq -> tail) {
if (pq -> node [kid].pri < pq -> node [root].pri)
return -1;
else return OOC_SortQueueCheck(pq, kid);
}
if ((kid = kid + 1) < pq -> tail) {
if (pq -> node [kid].pri < pq -> node [root].pri)
return -1;
else return OOC_SortQueueCheck(pq, kid);
}
}
return 0;
}
#endif
static int OOC_SortPush (OOC_SortQueue *pq, OOC_MortonIdx pri, unsigned blk)
/* Insert specified block index into priority queue; return block index
* or -1 if queue is full */
{
OOC_SortQueueNode *pqn = pq -> node;
unsigned kid, root;
if (pq -> tail >= pq -> len)
/* Queue full */
return -1;
/* Append node at tail and re-sort */
kid = pq -> tail++;
while (kid) {
root = (kid - 1) >> 1;
/* Compare with parent node and swap if necessary, else terminate */
if (pri < pqn [root].pri) {
pqn [kid].pri = pqn [root].pri;
pqn [kid].blk = pqn [root].blk;
kid = root;
}
else break;
}
pqn [kid].pri = pri;
pqn [kid].blk = blk;
#ifdef DEBUG_OOC_SORT
if (OOC_SortQueueCheck(pq, 0) < 0) {
fprintf(stderr, "OOC_Sort: priority queue inconsistency\n");
return -1;
}
#endif
return blk;
}
static int OOC_SortPop (OOC_SortQueue *pq)
/* Remove head of priority queue and return its block index
or -1 if queue empty */
{
OOC_SortQueueNode *pqn = pq -> node;
OOC_MortonIdx pri;
unsigned kid, kid2, root = 0, blk, res;
if (!pq -> tail)
/* Queue empty */
return -1;
res = pqn -> blk;
pri = pqn [--pq -> tail].pri;
blk = pqn [pq -> tail].blk;
/* Replace head with tail node and re-sort */
while ((kid = (root << 1) + 1) < pq -> tail) {
/* Compare with smaller kid and swap if necessary, else terminate */
if ((kid2 = (kid + 1)) < pq -> tail && pqn [kid2].pri < pqn [kid].pri)
kid = kid2;
if (pri > pqn [kid].pri) {
pqn [root].pri = pqn [kid].pri;
pqn [root].blk = pqn [kid].blk;
}
else break;
root = kid;
}
pqn [root].pri = pri;
pqn [root].blk = blk;
#ifdef DEBUG_OOC_SORT
if (OOC_SortQueueCheck(pq, 0) < 0) {
fprintf(stderr, "OOC_Sort: priority queue inconsistency\n");
return -1;
}
#endif
return res;
}
/* Active subprocess counter updated by parent process; must persist when
* recursing into OOC_SortRecurse(), hence global */
static unsigned procCnt = 0;
static int OOC_SortRecurse (FILE *in, unsigned long blkLo,
unsigned long blkHi, FILE *out,
unsigned numBlk, unsigned long maxBlkSize,
unsigned numProc, unsigned recSize,
char *sortBuf, OOC_SortQueue *pqueue,
const OOC_KeyData *keyData)
/* Recursive part of OOC_Sort(). Reads block of records from input file
* within the interval [blkLo, blkHi] and divides it into numBlk blocks
* until the size (in bytes) does not exceed maxBlkSize, then quicksorts
* each block into a temporary file. These files are then mergesorted via a
* priority queue to the output file as the stack unwinds. NOTE: Critical
* sections are prepended with '!!!'
*
* Parameters are as follows:
* in Input file containing unsorted records (assumed to be open)
* blkLo Start of current block in input file, in number of records
* blkHi End of current block in input file, in number of records
* out Output file containing sorted records (assumed to be open)
* numBlk Number of blocks to divide into / merge from
* maxBlkSize Max block size and size of in-core sort buffer, in bytes
* numProc Number of parallel processes for in-core sort
* recSize Size of input records in bytes
* sortBuf Preallocated in-core sort buffer of size maxBlkSize
* pqueue Preallocated priority queue of length numBlk for block merge
* keyData Aggregate data for Morton code generation and comparison
*/
{
const unsigned long blkLen = blkHi - blkLo + 1,
blkSize = blkLen * recSize;
int stat;
if (!blkLen || blkHi < blkLo)
return 0;
if (blkSize > maxBlkSize) {
unsigned long blkLo2 = blkLo, blkHi2 = blkLo, blkSize2;
const double blkLen2 = (double)blkLen / numBlk;
FILE *blkFile [numBlk]; /* Violates C89! */
char rec [recSize]; /* Ditto */
OOC_MortonIdx pri;
int b, pid;
#ifdef DEBUG_OOC_SORT
unsigned long pqCnt = 0;
#endif
/* ======================================================
* Block too large for in-core sort -> divide into numBlk
* subblocks and recurse
* ====================================================== */
#ifdef DEBUG_OOC_SORT
fprintf(stderr, "OOC_Sort: splitting block [%lu - %lu]\n",
blkLo, blkHi);
#endif
for (b = 0; b < numBlk; b++) {
/* Open temporary file as output for subblock */
if (!(blkFile [b] = tmpfile())) {
perror("OOC_Sort: failed opening temporary block file");
return -1;
}
/* Subblock interval [blkLo2, blkHi2] of size blkSize2 */
blkHi2 = blkLo + (b + 1) * blkLen2 - 1;
blkSize2 = (blkHi2 - blkLo2 + 1) * recSize;
if (blkSize2 <= maxBlkSize) {
/* !!! Will be in-core sorted on recursion -> fork kid process,
* !!! but don't fork more than numProc kids; wait if necessary */
while (procCnt >= numProc && wait(&stat) >= 0) {
if (!WIFEXITED(stat) || WEXITSTATUS(stat))
return -1;
procCnt--;
}
/* Now fork kid process */
if (!(pid = fork())) {
/* Recurse on subblocks with new input filehandle; */
if (OOC_SortRecurse(in, blkLo2, blkHi2, blkFile [b], numBlk,
maxBlkSize, numProc, recSize, sortBuf,
pqueue, keyData))
exit(-1);
/* !!! Apparently the parent's tmpfile isn't deleted when the
* !!! child exits (which is what we want), though some
* !!! sources suggest using _Exit() instead; is this
* !!! implementation specific? */
exit(0);
}
else if (pid < 0) {
fprintf(stderr, "OOC_Sort: failed to fork subprocess\n");
return -1;
}
#ifdef DEBUG_OOC_FORK
fprintf(stderr, "OOC_Sort: forking kid %d for block %d\n",
procCnt, b);
#endif
/* Parent continues here */
procCnt++;
}
else {
/* Recurse on subblock; without forking */
if (OOC_SortRecurse(in, blkLo2, blkHi2, blkFile [b], numBlk,
maxBlkSize, numProc, recSize, sortBuf,
pqueue, keyData))
return -1;
}
/* Prepare for next block */
blkLo2 = blkHi2 + 1;
}
/* !!! Wait for any forked processes to terminate */
while (procCnt && wait(&stat) >= 0) {
if (!WIFEXITED(stat) || WEXITSTATUS(stat))
return -1;
procCnt--;
}
/* ===============================================================
* Subblocks are now sorted; prepare priority queue by peeking and
* enqueueing first record from corresponding temporary file
* =============================================================== */
#ifdef DEBUG_OOC_SORT
fprintf(stderr, "OOC_Sort: merging block [%lu - %lu]\n", blkLo, blkHi);
#endif
for (b = 0; b < numBlk; b++) {
#ifdef DEBUG_OOC_SORT
fseek(blkFile [b], 0, SEEK_END);
if (ftell(blkFile [b]) % recSize) {
fprintf(stderr, "OOC_Sort: truncated record in tmp block "
"file %d\n", b);
return -1;
}
fprintf(stderr, "OOC_Sort: tmp block file %d contains %ld rec\n",
b, ftell(blkFile [b]) / recSize);
#endif
rewind(blkFile [b]);
if (OOC_SortPeek(blkFile [b], recSize, rec)) {
fprintf(stderr, "OOC_Sort: error reading from block file\n");
return -1;
}
/* Enqueue record along with its Morton code as priority */
pri = OOC_Key2Morton(keyData -> key(rec), keyData -> bbOrg,
keyData -> mortonScale);
if (OOC_SortPush(pqueue, pri, b) < 0) {
fprintf(stderr, "OOC_Sort: failed priority queue insertion\n");
return -1;
}
}
/* ==========================================================
* Subblocks now sorted and priority queue filled; merge from
* temporary files
* ========================================================== */
do {
/* Get next node in priority queue, read next record in corresponding
* block, and send to output */
b = OOC_SortPop(pqueue);
if (b >= 0) {
/* Priority queue non-empty */
if (OOC_SortRead(blkFile [b], recSize, rec)) {
/* Corresponding record should still be in the input block */
fprintf(stderr, "OOC_Sort: unexpected end reading block file\n");
return -1;
}
if (OOC_SortWrite(out, recSize, rec)) {
fprintf(stderr, "OOC_Sort; error writing output file\n");
return -1;
}
#ifdef DEBUG_OOC_SORT
pqCnt++;
#endif
/* Peek next record from same block and insert in priority queue */
if (!OOC_SortPeek(blkFile [b], recSize, rec)) {
/* Block not exhausted */
pri = OOC_Key2Morton(keyData -> key(rec), keyData -> bbOrg,
keyData -> mortonScale);
if (OOC_SortPush(pqueue, pri, b) < 0) {
fprintf(stderr, "OOC_Sort: failed priority queue insert\n");
return -1;
}
}
}
} while (b >= 0);
#ifdef DEBUG_OOC_SORT
fprintf(stderr, "OOC_Sort: dequeued %lu rec\n", pqCnt);
fprintf(stderr, "OOC_Sort: merged file contains %lu rec\n",
ftell(out) / recSize);
#endif
/* Priority queue now empty -> done; close temporary subblock files,
* causing them to be automatically deleted. */
for (b = 0; b < numBlk; b++) {
fclose(blkFile [b]);
}
/* !!! Commit output file to disk before caller reads it; omitting
* !!! this apparently leads to corrupted files (race condition?) when
* !!! the caller tries to read them! */
fflush(out);
fsync(fileno(out));
}
else {
/* ======================================
* Block is small enough for in-core sort
* ====================================== */
int ifd = fileno(in), ofd = fileno(out);
#ifdef DEBUG_OOC_SORT
fprintf(stderr, "OOC_Sort: Proc %d (%d/%d) sorting block [%lu - %lu]\n",
getpid(), procCnt, numProc - 1, blkLo, blkHi);
#endif
/* Atomically seek and read block into in-core sort buffer */
/* !!! Unbuffered I/O via pread() avoids potential race conditions
* !!! and buffer corruption which can occur with lseek()/fseek()
* !!! followed by read()/fread(). */
if (pread(ifd, sortBuf, blkSize, blkLo * recSize) != blkSize) {
perror("OOC_Sort: error reading from input file");
return -1;
}
/* Quicksort block in-core and write to output file */
qsort(sortBuf, blkLen, recSize, OOC_KeyCompare);
if (write(ofd, sortBuf, blkSize) != blkSize) {
perror("OOC_Sort: error writing to block file");
return -1;
}
fsync(ofd);
#ifdef DEBUG_OOC_SORT
fprintf(stderr, "OOC_Sort: proc %d wrote %ld records\n",
getpid(), lseek(ofd, 0, SEEK_END) / recSize);
#endif
}
return 0;
}
int OOC_Sort (FILE *in, FILE *out, unsigned numBlk,
unsigned long blkSize, unsigned numProc, unsigned recSize,
FVECT bbOrg, RREAL bbSize, RREAL *(*key)(const void*))
/* Sort records in inFile and append to outFile by subdividing inFile into
* small blocks, sorting these in-core, and merging them out-of-core via a
* priority queue.
*
* This is implemented as a recursive (numBlk)-way sort; the input is
* successively split into numBlk smaller blocks until these are of size <=
* blkSize, i.e. small enough for in-core sorting, then merging the sorted
* blocks as the stack unwinds. The in-core sort is parallelised over
* numProx processes.
*
* Parameters are as follows:
* inFile Opened input file containing unsorted records
* outFile Opened output file containing sorted records
* numBlk Number of blocks to divide into / merge from
* blkSize Max block size and size of in-core sort buffer, in bytes
* numProc Number of parallel processes for in-core sort
* recSize Size of input records in bytes
* bbOrg Origin of bounding box containing record keys for Morton code
* bbSize Extent of bounding box containing record keys for Morton code
* key Callback to access 3D coords from records for Morton code
*/
{
unsigned long numRec;
OOC_SortQueue pqueue;
char *sortBuf = NULL;
int stat;
if (numBlk < 1)
numBlk = 1;
/* Open input file & get size in number of records */
if (fseek(in, 0, SEEK_END) < 0) {
fputs("OOC_Sort: failed seek in input file\n", stderr);
return -1;
}
if (!(numRec = ftell(in) / recSize)) {
fputs("OOC_Sort: empty input file\n", stderr);
return -1;
}
/* Allocate & init priority queue */
if (!(pqueue.node = calloc(numBlk, sizeof(OOC_SortQueueNode)))) {
fputs("OOC_Sort: failure allocating priority queue\n", stderr);
return -1;
}
pqueue.tail = 0;
pqueue.len = numBlk;
/* Allocate in-core sort buffa */
if (!(sortBuf = malloc(blkSize))) {
fprintf(stderr, "OOC_Sort: failure allocating in-core sort buffer");
return -1;
}
/* Set up key data to pass to qsort()'s comparison func */
keyData.key = key;
keyData.mortonScale = OOC_MORTON_MAX / bbSize;
VCOPY(keyData.bbOrg, bbOrg);
stat = OOC_SortRecurse(in, 0, numRec - 1, out, numBlk, blkSize, numProc,
recSize, sortBuf, &pqueue, &keyData);
/* Cleanup */
free(pqueue.node);
free(sortBuf);
return stat;
}
#endif /* NIX / PMAP_OOC */
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