/usr/lib/grass70/include/grass/iostream/empq_impl.h is in grass-dev 7.0.3-1build1.
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*
* MODULE: iostream
*
* COPYRIGHT (C) 2007 Laura Toma
*
*
* Iostream is a library that implements streams, external memory
* sorting on streams, and an external memory priority queue on
* streams. These are the fundamental components used in external
* memory algorithms.
* Credits: The library was developed by Laura Toma. The kernel of
* class STREAM is based on the similar class existent in the GPL TPIE
* project developed at Duke University. The sorting and priority
* queue have been developed by Laura Toma based on communications
* with Rajiv Wickremesinghe. The library was developed as part of
* porting Terraflow to GRASS in 2001. PEARL upgrades in 2003 by
* Rajiv Wickremesinghe as part of the Terracost project.
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* General Public License for more details. *
* **************************************************************************/
#ifndef __EMPQ_IMPL_H
#define __EMPQ_IMPL_H
#include <ostream>
#include <vector>
#include "empq.h"
#if(0)
#include "option.H"
#define MY_LOG_DEBUG_ID(x) \
if(GETOPT("debug")) cerr << __FILE__ << ":" << __LINE__<< " " << x << endl;
#endif
#undef XXX
#define XXX if(0)
#define MY_LOG_DEBUG_ID(x)
/*****************************************************************/
/* encapsulation of the element=<key/prio, data> together with <buffer_id>
and <stream_id>; used during stream merging to remember where each
key comes from;
assumes that class T implements: Key getPriority()
implements operators {<, <=, ...} such that a< b iff a.x.prio < b.x.prio
*/
template<class T,class Key>
class ExtendedEltMergeType {
private:
T x;
unsigned short buf_id;
unsigned int str_id;
public:
ExtendedEltMergeType() {}
ExtendedEltMergeType(T &e, unsigned short bid, unsigned int sid):
x(e), buf_id(bid), str_id(sid) {}
~ExtendedEltMergeType() {}
void set (T &e, unsigned short bid, unsigned int sid) {
x = e;
buf_id = bid;
str_id = sid;
}
T elt() const {
return x;
}
unsigned short buffer_id() const {
return buf_id;
}
unsigned int stream_id() const {
return str_id;
}
Key getPriority() const {
return x.getPriority();
}
//print
friend ostream& operator<<(ostream& s,
const ExtendedEltMergeType<T,Key> &elt) {
return s << "<buf_id=" << elt.buf_id
<< ",str_id=" << elt.str_id << "> "
<< elt.x << " ";
}
friend int operator < (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() < e2.getPriority());
}
friend int operator <= (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() <= e2.getPriority());
}
friend int operator > (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() > e2.getPriority());
}
friend int operator >= (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() >= e2.getPriority());
}
friend int operator != (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() != e2.getPriority());
}
friend int operator == (const ExtendedEltMergeType<T,Key> &e1,
const ExtendedEltMergeType<T,Key> &e2) {
return (e1.getPriority() == e2.getPriority());
}
};
//************************************************************/
//create an em_pqueue
template<class T, class Key>
em_pqueue<T,Key>::em_pqueue(long pq_sz, long buf_sz ,
unsigned short nb_buf,
unsigned int buf_ar):
pqsize(pq_sz), bufsize(buf_sz), max_nbuf(nb_buf),
crt_buf(0), buf_arity(buf_ar) {
//____________________________________________________________
//ESTIMATE AVAILABLE MEMORY BEFORE ALLOCATION
AMI_err ae;
size_t mm_avail = getAvailableMemory();
printf("EM_PQUEUE:available memory before allocation: %.2fMB\n",
mm_avail/(float)(1<<20));
printf("EM_PQUEUE:available memory before allocation: %ldB\n",
mm_avail);
//____________________________________________________________
//ALLOCATE STRUCTURE
//some dummy checks..
assert(pqsize > 0 && bufsize > 0);
MEMORY_LOG("em_pqueue: allocating int pqueue\n");
//initialize in memory pqueue
pq = new MinMaxHeap<T>(pqsize);
assert(pq);
MEMORY_LOG("em_pqueue: allocating buff_0\n");
//initialize in memory buffer
buff_0 = new im_buffer<T>(bufsize);
assert(buff_0);
char str[200];
sprintf(str, "em_pqueue: allocating array of %ld buff pointers\n",
(long)max_nbuf);
MEMORY_LOG(str);
//allocate ext memory buffers array
buff = new em_buffer<T,Key>* [max_nbuf];
assert(buff);
for (unsigned short i=0; i<max_nbuf; i++) {
buff[i] = NULL;
}
//____________________________________________________________
//some memory checks- make sure the empq fits in memory !!
//estimate available memory after allocation
mm_avail = getAvailableMemory();
printf("EM_PQUEUE: available memory after allocation: %.2fMB\n",
mm_avail/(float)(1<<20));
//estimate AMI_STREAM memory usage
size_t sz_stream;
AMI_STREAM<T> dummy;
if ((ae = dummy.main_memory_usage(&sz_stream,
MM_STREAM_USAGE_MAXIMUM)) !=
AMI_ERROR_NO_ERROR) {
cout << "em_pqueue constructor: failing to get stream_usage\n";
exit(1);
}
cout << "EM_PQUEUE:AMI_stream memory usage: " << sz_stream << endl;
cout << "EM_PQUEUE: item size=" << sizeof(T) << endl;
//estimate memory overhead
long mm_overhead = buf_arity*sizeof(merge_key<Key>) +
max_nbuf * sizeof(em_buffer<T,Key>) +
2*sz_stream + max_nbuf*sz_stream;
mm_overhead *= 8; //overestimate
cout << "EM_PQUEUE: mm_overhead estimated as " << mm_overhead << endl;
if (mm_overhead > mm_avail) {
cout << "overhead bigger than available memory"
<< "increase -m and try again\n";
exit(1);
}
mm_avail -= mm_overhead;
//arity*sizeof(AMI_STREAM) < memory
cout << "pqsize=" << pqsize
<< ", bufsize=" << bufsize
<< ", maximum allowed arity=" << mm_avail/sz_stream << endl;
if (buf_arity * sz_stream > mm_avail) {
cout << "sorry - empq excedes memory limits\n";
cout << "try again decreasing arity or pqsize/bufsize\n";
cout.flush();
}
}
//************************************************************/
//create an em_pqueue capable to store <= N elements
template<class T, class Key>
em_pqueue<T,Key>::em_pqueue() {
MY_LOG_DEBUG_ID("em_pqueue constructor");
/************************************************************/
//available memory
AMI_err ae;
//available memory
size_t mm_avail = getAvailableMemory();
printf("EM_PQUEUE:available memory before allocation: %.2fMB\n",
mm_avail/(float)(1<<20));
cout.flush();
//AMI_STREAM memory usage
size_t sz_stream;
AMI_STREAM<T> dummy;
if ((ae = dummy.main_memory_usage(&sz_stream,
MM_STREAM_USAGE_MAXIMUM)) !=
AMI_ERROR_NO_ERROR) {
cout << "em_pqueue constructor: failing to get main_memory_usage\n";
exit(1);
}
cout << "EM_PQUEUE:AMI_stream memory usage: " << sz_stream << endl;
cout << "EM_PQUEUE: item size=" << sizeof(T) << endl;
cout.flush();
//assume max_nbuf=2 suffices; check after arity is computed
max_nbuf = 2;
//account for temporary memory usage (set up a preliminary arity)
buf_arity = mm_avail/(2 * sz_stream);
long mm_overhead = buf_arity*sizeof(merge_key<Key>) +
max_nbuf * sizeof(em_buffer<T,Key>) +
2*sz_stream + max_nbuf*sz_stream;
mm_overhead *= 8; //overestimate
cout << "EM_PQUEUE: mm_overhead estimated as " << mm_overhead << endl;
if (mm_overhead > mm_avail) {
cout << "overhead bigger than available memory"
<< "increase -m and try again\n";
exit(1);
}
mm_avail -= mm_overhead;
#ifdef SAVE_MEMORY
//assign M/2 to pq
pqsize = mm_avail/(2*sizeof(T));
//assign M/2 to buff_0
bufsize = mm_avail/(2*sizeof(T));
#else
//assign M/4 to pq
pqsize = mm_avail/(4*sizeof(T));
//assign M/4 to buff_0
bufsize = mm_avail/(4*sizeof(T));
#endif
cout << "EM_PQUEUE: pqsize set to " << pqsize << endl;
cout << "EM_PQUEUE: bufsize set to " << bufsize << endl;
cout << "EM_PQUEUE: nb buffers set to " << max_nbuf << endl;
//assign M/2 to AMI_STREAMS and compute arity
/* arity is mainly constrained by the size of an AMI_STREAM; the
rest of the memory must accomodate for arity * max_nbuf
*sizeof(AMI_STREAM); there are some temporary stuff like arity *
sizeof(long) (the deleted array), arity * sizeof(T) (the array of
keys for merging) and so on, but the main factor is the
AMI_STREAM size which is roughly B * LBS * 2 (each AMI_STREAM
allocates 2 logical blocks) */
#ifdef SAVE_MEMORY
buf_arity = mm_avail/(2 * sz_stream);
#else
buf_arity = mm_avail/(2 * max_nbuf * sz_stream);
#endif
//overestimate usage
if (buf_arity > 3) {
buf_arity -= 3;
} else {
buf_arity = 1;
}
cout << "EM_PQUEUE: arity set to " << buf_arity << endl;
crt_buf = 0;
//initialize in memory pqueue
MEMORY_LOG("em_pqueue: allocating int pqueue\n");
pq = new MinMaxHeap<T>(pqsize);
assert(pq);
//initialize in memory buffer
MEMORY_LOG("em_pqueue: allocating buff_0\n");
buff_0 = new im_buffer<T>(bufsize);
assert(buff_0);
//allocate ext memory buffers array
char str[200];
sprintf(str,"em_pqueue: allocating array of %ld buff pointers\n",
(long)max_nbuf);
MEMORY_LOG(str);
//allocate ext memory buffers array
buff = new em_buffer<T,Key>* [max_nbuf];
assert(buff);
for (unsigned short i=0; i<max_nbuf; i++) {
buff[i] = NULL;
}
//max nb of items the structure can accomodate (constrained by max_nbuf)
cout << "EM_PQUEUE: maximum length is " << maxlen() << "\n";
cout.flush();
//check that structure can accomodate N elements
// assert(N < buf_arity * (buf_arity + 1) * bufsize);
//assert(N < maxlen());
mm_avail = getAvailableMemory();
printf("EM_PQUEUE: available memory after allocation: %.2fMB\n",
mm_avail/(float)(1<<20));
}
#ifdef SAVE_MEMORY
//************************************************************/
// create an empq, initialize its pq with im and insert amis in
// buff[0]; im should not be used/deleted after that outside empq;
//
// assumption: im was allocated such that maxsize = mm_avail/T;
// when this constructor is called im is only half full, so we must
// free half of its space and give to buff_0
template<class T, class Key>
em_pqueue<T,Key>::em_pqueue(MinMaxHeap<T> *im, AMI_STREAM<T> *amis) {
AMI_err ae;
int pqcapacity; /* amount of memory we can use for each of new
minmaxheap, and em-buffer */
unsigned int pqcurrentsize; /* number of elements currently in im */
assert(im && amis);
pqcapacity = im->get_maxsize()/2; // we think this memory is now available
pqsize = pqcapacity + 1; //truncate errors
pqcurrentsize = im->size();
//assert( pqcurrentsize <= pqsize);
if(!(pqcurrentsize <= pqsize)) {
cout << "EMPQ: pq maxsize=" << pqsize <<", pq crtsize=" << pqcurrentsize
<< "\n";
assert(0);
exit(1);
}
LOG_avail_memo();
/* at this point im is allocated all memory, but it is only at most
half full; we need to relocate im to half space and to allocate
buff_0 the other half; since we use new, there is no realloc, so
we will copy to a file...*/
{
//copy im to a stream and free its memory
T x;
AMI_STREAM<T> tmpstr;
for (unsigned int i=0; i<pqcurrentsize; i++) {
im->extract_min(x);
ae = tmpstr.write_item(x);
assert(ae == AMI_ERROR_NO_ERROR);
}
delete im; im = NULL;
LOG_avail_memo();
//allocate pq and buff_0 half size
bufsize = pqcapacity;
cout << "EM_PQUEUE: allocating im_buffer size=" << bufsize
<< " total " << (float)bufsize*sizeof(T)/(1<<20) << "MB\n";
cout.flush();
buff_0 = new im_buffer<T>(bufsize);
assert(buff_0);
cout << "EM_PQUEUE: allocating pq size=" << pqsize
<< " total " << (float)pqcapacity*sizeof(T)/(1<<20) << "MB\n";
cout.flush();
pq = new MinMaxHeap<T>(pqsize);
assert(pq);
//fill pq from tmp stream
ae = tmpstr.seek(0);
assert(ae == AMI_ERROR_NO_ERROR);
T *elt;
for (unsigned int i=0; i<pqcurrentsize; i++) {
ae = tmpstr.read_item(&elt);
assert(ae == AMI_ERROR_NO_ERROR);
pq->insert(*elt);
}
assert(pq->size() == pqcurrentsize);
}
//estimate buf_arity
//AMI_STREAM memory usage
size_t sz_stream;
AMI_STREAM<T> dummy;
if ((ae = dummy.main_memory_usage(&sz_stream,
MM_STREAM_USAGE_MAXIMUM)) !=
AMI_ERROR_NO_ERROR) {
cout << "em_pqueue constructor: failing to get main_memory_usage\n";
exit(1);
}
cout << "EM_PQUEUE: AMI_stream memory usage: " << sz_stream << endl;
cout << "EM_PQUEUE: item size=" << sizeof(T) << endl;
//assume max_nbuf=2 suffices; check after arity is computed
max_nbuf = 2;
buf_arity = pqcapacity * sizeof(T) / sz_stream;
//should account for some overhead
if (buf_arity == 0) {
cout << "EM_PQUEUE: arity=0 (not enough memory..)\n";
exit(1);
}
if (buf_arity > 3) {
buf_arity -= 3;
} else {
buf_arity = 1;
}
//added on 05/16/2005 by Laura
if (buf_arity > MAX_STREAMS_OPEN) {
buf_arity = MAX_STREAMS_OPEN;
}
//allocate ext memory buffer array
char str[200];
sprintf(str,"em_pqueue: allocating array of %ld buff pointers\n",
(long)max_nbuf);
MEMORY_LOG(str);
buff = new em_buffer<T,Key>* [max_nbuf];
assert(buff);
for (unsigned short i=0; i<max_nbuf; i++) {
buff[i] = NULL;
}
crt_buf = 0;
cout << "EM_PQUEUE: new pqsize set to " << pqcapacity << endl;
cout << "EM_PQUEUE: bufsize set to " << bufsize << endl;
cout << "EM_PQUEUE: buf arity set to " << buf_arity << endl;
cout << "EM_PQUEUE: nb buffers set to " << max_nbuf << endl;
cout << "EM_PQUEUE: maximum length is " << maxlen() << "\n";
cout.flush();
//estimate available remaining memory
size_t mm_avail = getAvailableMemory();
printf("EM_PQUEUE: available memory after allocation: %.2fMB\n",
mm_avail/(float)(1<<20));
//last thing: insert the input stream in external buffers
//allocate buffer if necessary
//assert(crt_buf==0 && !buff[0]);// given
if(amis->stream_len()) {
//create buff[0] as a level1 buffer
MEMORY_LOG("em_pqueue::empty_buff_0: create new em_buffer\n");
buff[0] = new em_buffer<T,Key>(1, bufsize, buf_arity);
buff[0]->insert(amis);
crt_buf = 1;
}
}
#endif
//************************************************************/
//free space
template<class T, class Key>
em_pqueue<T,Key>::~em_pqueue() {
//delete in memory pqueue
if (pq) {
delete pq; pq = NULL;
}
//delete in memory buffer
if (buff_0) {
delete buff_0; buff_0 = NULL;
}
//delete ext memory buffers
for (unsigned short i=0; i< crt_buf; i++) {
if (buff[i]) delete buff[i];
}
delete [] buff;
}
//************************************************************/
//return maximum capacity of i-th external buffer
template<class T, class Key>
long em_pqueue<T,Key>::maxlen(unsigned short i) {
if (i >= max_nbuf) {
printf("em_pqueue::max_len: level=%d exceeds capacity=%d\n",
i, max_nbuf);
return 0;
}
if (i < crt_buf) {
return buff[i]->get_buf_maxlen();
}
//try allocating buffer
em_buffer<T,Key> * tmp = new em_buffer<T,Key>(i+1, bufsize, buf_arity);
if (!tmp) {
cout << "em_pqueue::max_len: cannot allocate\n";
return 0;
}
long len = tmp->get_buf_maxlen();
delete tmp;
return len;
}
//************************************************************/
//return maximum capacity of em_pqueue
template<class T, class Key>
long em_pqueue<T,Key>::maxlen() {
long len = 0;
for (unsigned short i=0; i< max_nbuf; i++) {
len += maxlen(i);
}
return len + buff_0->get_buf_maxlen();
}
//************************************************************/
//return the total nb of elements in the structure
template<class T, class Key>
unsigned long em_pqueue<T,Key>::size() {
//sum up the lengths(nb of elements) of the external buffers
unsigned long elen = 0;
for (unsigned short i=0; i < crt_buf; i++) {
elen += buff[i]->get_buf_len();
}
return elen + pq->size() + buff_0->get_buf_len();
}
//************************************************************/
//return true if empty
template<class T, class Key>
bool em_pqueue<T,Key>::is_empty() {
//return (size() == 0);
//more efficient?
return ((pq->size() == 0) && (buff_0->get_buf_len() == 0) &&
(size() == 0));
}
//************************************************************/
//called when pq must be filled from external buffers
template<class T, class Key>
bool em_pqueue<T,Key>::fillpq() {
#ifndef NDEBUG
{
int k=0;
for (unsigned short i=0; i<crt_buf; i++) {
k |= buff[i]->get_buf_len();
}
if(!k) {
cerr << "fillpq called with empty external buff!" << endl;
}
assert(k);
}
#endif
#ifdef EMPQ_PQ_FILL_PRINT
cout << "filling pq\n"; cout .flush();
#endif
XXX cerr << "filling pq" << endl;
MY_LOG_DEBUG_ID("fillpq");
AMI_err ae;
{
char str[200];
sprintf(str, "em_pqueue::fillpq: allocate array of %hd AMI_STREAMs\n",
crt_buf);
MEMORY_LOG(str);
}
//merge pqsize smallest elements from each buffer into a new stream
ExtendedMergeStream** outstreams;
outstreams = new ExtendedMergeStream* [crt_buf];
/* gets stream of smallest pqsize elts from each level */
for (unsigned short i=0; i< crt_buf; i++) {
MY_LOG_DEBUG_ID(crt_buf);
outstreams[i] = new ExtendedMergeStream();
assert(buff[i]->get_buf_len());
ae = merge_buffer(buff[i], outstreams[i], pqsize);
assert(ae == AMI_ERROR_NO_ERROR);
assert(outstreams[i]->stream_len());
//print_stream(outstreams[i]); cout.flush();
}
/* merge above streams into pqsize elts in minstream */
if (crt_buf == 1) {
//just one level; make common case faster :)
merge_bufs2pq(outstreams[0]);
delete outstreams[0];
delete [] outstreams;
} else {
//merge the outstreams to get the global mins and delete them afterwards
ExtendedMergeStream *minstream = new ExtendedMergeStream();
//cout << "merging streams\n";
ae = merge_streams(outstreams, crt_buf, minstream, pqsize);
assert(ae == AMI_ERROR_NO_ERROR);
for (int i=0; i< crt_buf; i++) {
delete outstreams[i];
}
delete [] outstreams;
//copy the minstream in the internal pqueue while merging with buff_0;
//the smallest <pqsize> elements between minstream and buff_0 will be
//inserted in internal pqueue;
//also, the elements from minstram which are inserted in pqueue must be
//marked as deleted in the source streams;
merge_bufs2pq(minstream);
delete minstream; minstream = NULL;
//cout << "after merge_bufs2pq: \n" << *this << "\n";
}
XXX assert(pq->size());
XXX cerr << "fillpq done" << endl;
return true;
}
//************************************************************/
//return the element with minimum priority in the structure
template<class T, class Key>
bool
em_pqueue<T,Key>::min(T& elt){
bool ok;
MY_LOG_DEBUG_ID("em_pqueue::min");
//try first the internal pqueue
if (!pq->empty()) {
ok = pq->min(elt);
assert(ok);
return ok;
}
MY_LOG_DEBUG_ID("extract_min: reset pq");
pq->reset();
//if external buffers are empty
if (crt_buf == 0) {
//if internal buffer is empty too, then nothing to extract
if (buff_0->is_empty()) {
//cerr << "min called on empty empq" << endl;
return false;
} else {
#ifdef EMPQ_PRINT_FILLPQ_FROM_BUFF0
cout << "filling pq from B0\n"; cout.flush();
#endif
//ext. buffs empty; fill int pqueue from buff_0
long n = pq->fill(buff_0->get_array(), buff_0->get_buf_len());
buff_0->reset(pqsize, n);
ok = pq->min(elt);
assert(ok);
return true;
}
} else {
//external buffers are not empty;
//called when pq must be filled from external buffers
XXX print_size();
fillpq();
XXX cerr << "fillpq done; about to take min" << endl;
ok = pq->min(elt);
XXX cerr << "after taking min" << endl;
assert(ok);
return ok;
} //end of else (if ext buffers are not empty)
assert(0); //not reached
}
//************************************************************/
template<class T,class Key>
static void print_ExtendedMergeStream(ExtendedMergeStream &str) {
ExtendedEltMergeType<T,Key> *x;
str.seek(0);
while (str.read_item(&x) == AMI_ERROR_NO_ERROR) {
cout << *x << ", ";
}
cout << "\n";
}
//************************************************************/
//delete the element with minimum priority in the structure;
//return false if pq is empty
template<class T, class Key>
bool em_pqueue<T,Key>::extract_min(T& elt) {
bool ok;
MY_LOG_DEBUG_ID("\n\nEM_PQUEUE::EXTRACT_MIN");
//try first the internal pqueue
if (!pq->empty()) {
//cout << "extract from internal pq\n";
MY_LOG_DEBUG_ID("extract from internal pq");
ok = pq->extract_min(elt);
assert(ok);
return ok;
}
//if internal pqueue is empty, fill it up
MY_LOG_DEBUG_ID("internal pq empty: filling it up from external buffers");
MY_LOG_DEBUG_ID("extract_min: reset pq");
pq->reset();
//if external buffers are empty
if (crt_buf == 0) {
//if internal buffer is empty too, then nothing to extract
if (buff_0->is_empty()) {
return false;
} else {
#ifdef EMPQ_PRINT_FILLPQ_FROM_BUFF0
cout << "filling pq from B0\n"; cout.flush();
#endif
MY_LOG_DEBUG_ID("filling pq from buff_0");
//ext. buffs empty; fill int pqueue from buff_0
long n = pq->fill(buff_0->get_array(), buff_0->get_buf_len());
buff_0->reset(pqsize, n);
ok = pq->extract_min(elt);
assert(ok);
return true;
}
} else {
//external buffers are not empty;
//called when pq must be filled from external buffers
MY_LOG_DEBUG_ID("filling pq from buffers");
#ifdef EMPQ_PRINT_SIZE
long x = size(), y;
y = x*sizeof(T) >> 20;
cout << "pqsize:[" << active_streams() << " streams: ";
print_stream_sizes();
cout << " total " << x << "(" << y << "MB)]" << endl;
cout.flush();
#endif
fillpq();
MY_LOG_DEBUG_ID("pq filled");
XXX cerr << "about to get the min" << endl;
assert(pq);
ok = pq->extract_min(elt);
if (!ok) {
cout << "failing assertion: pq->extract_min == true\n";
this->print();
assert(ok);
}
return ok;
} //end of else (if ext buffers are not empty)
assert(0); //not reached
}
//************************************************************/
//extract all elts with min key, add them and return their sum
//delete the element with minimum priority in the structure;
//return false if pq is empty
template<class T, class Key>
bool em_pqueue<T,Key>::extract_all_min(T& elt) {
//cout << "em_pqueue::extract_min_all(T): sorry not implemented\n";
//exit(1);
T next_elt;
bool done = false;
MY_LOG_DEBUG_ID("\n\nEM_PQUEUE::EXTRACT_ALL_MIN");
//extract first elt
if (!extract_min(elt)) {
return false;
} else {
while (!done) {
//peek at the next min elt to see if matches
if ((!min(next_elt)) ||
!(next_elt.getPriority() == elt.getPriority())) {
done = true;
} else {
extract_min(next_elt);
elt = elt + next_elt;
MY_LOG_DEBUG_ID("EXTRACT_ALL_MIN: adding " );
MY_LOG_DEBUG_ID(elt);
}
}
}
#ifdef EMPQ_PRINT_EXTRACTALL
cout << "EXTRACTED: " << elt << endl; cout.flush();
#endif
#ifdef EMPQ_PRINT_EMPQ
this->print();
cout << endl;
#endif
return true;
}
//************************************************************/
//copy the minstream in the internal pqueue while merging with buff_0;
//the smallest <pqsize> elements between minstream and buff_0 will be
//inserted in internal pqueue;
//also, the elements from minstram which are inserted in pqueue must be
//marked as deleted in the source streams;
template<class T, class Key>
void em_pqueue<T,Key>::merge_bufs2pq(ExtendedMergeStream *minstream) {
//cout << "bufs2pq: \nminstream: "; print_stream(minstream);
MY_LOG_DEBUG_ID("merge_bufs2pq: enter");
AMI_err ae;
//sort the internal buffer
buff_0->sort();
//cout << "bufs2pq: \nbuff0: " << *buff_0 << endl;
ae = minstream->seek(0); //rewind minstream
assert(ae == AMI_ERROR_NO_ERROR);
bool strEmpty= false, bufEmpty=false;
unsigned int bufPos = 0;
ExtendedEltMergeType<T,Key> *strItem;
T bufElt, strElt;
ae = minstream->read_item(&strItem);
if (ae == AMI_ERROR_END_OF_STREAM) {
strEmpty = true;
} else {
assert(ae == AMI_ERROR_NO_ERROR);
}
if (bufPos < buff_0->get_buf_len()) {
bufElt = buff_0->get_item(bufPos);
} else {
//cout << "buff0 empty\n";
bufEmpty = true;
}
XXX cerr << "pqsize=" << pqsize << endl;
XXX if(strEmpty) cerr << "stream is empty!!" << endl;
for (unsigned int i=0; i< pqsize; i++) {
if (!bufEmpty) {
if ((!strEmpty) && (strElt = strItem->elt(),
bufElt.getPriority() > strElt.getPriority())) {
delete_str_elt(strItem->buffer_id(), strItem->stream_id());
pq->insert(strElt);
ae = minstream->read_item(&strItem);
if (ae == AMI_ERROR_END_OF_STREAM) {
strEmpty = true;
} else {
assert(ae == AMI_ERROR_NO_ERROR);
}
} else {
bufPos++;
pq->insert(bufElt);
if (bufPos < buff_0->get_buf_len()) {
bufElt = buff_0->get_item(bufPos);
} else {
bufEmpty = true;
}
}
} else {
if (!strEmpty) { //stream not empty
strElt = strItem->elt();
//cout << "i=" << i << "str & buff empty\n";
delete_str_elt(strItem->buffer_id(), strItem->stream_id());
pq->insert(strElt);
//cout << "insert " << strElt << "\n";
ae = minstream->read_item(&strItem);
if (ae == AMI_ERROR_END_OF_STREAM) {
strEmpty = true;
} else {
assert(ae == AMI_ERROR_NO_ERROR);
}
} else { //both empty: < pqsize items
break;
}
}
}
//shift left buff_0 in case elements were deleted from the beginning
buff_0->shift_left(bufPos);
MY_LOG_DEBUG_ID("pq filled");
#ifdef EMPQ_PQ_FILL_PRINT
cout << "merge_bufs2pq: pq filled; now cleaning\n"; cout .flush();
#endif
//this->print();
//clean buffers in case some streams have been emptied
cleanup();
MY_LOG_DEBUG_ID("merge_bufs2pq: done");
}
//************************************************************/
//deletes one element from <buffer, stream>
template<class T, class Key>
void em_pqueue<T,Key>::delete_str_elt(unsigned short buf_id,
unsigned int stream_id) {
//check them
assert(buf_id < crt_buf);
assert(stream_id < buff[buf_id]->get_nbstreams());
//update;
buff[buf_id]->incr_deleted(stream_id);
}
//************************************************************/
//clean buffers in case some streams have been emptied
template<class T, class Key>
void em_pqueue<T,Key>::cleanup() {
MY_LOG_DEBUG_ID("em_pqueue::cleanup()");
#ifdef EMPQ_PQ_FILL_PRINT
cout << "em_pqueue: cleanup enter\n"; cout .flush();
#endif
//adjust buffers in case whole streams got deleted
for (unsigned short i=0; i< crt_buf; i++) {
//cout << "clean buffer " << i << ": "; cout.flush();
buff[i]->cleanup();
}
if (crt_buf) {
short i = crt_buf-1;
while ((i>=0) && buff[i]->is_empty()) {
crt_buf--;
i--;
}
}
#ifdef EMPQ_PQ_FILL_PRINT
cout << "em_pqueue: cleanup done\n"; cout .flush();
#endif
//if a stream becomes too short move it on previous level
//to be added..
//cout <<"done cleaning up\n";
}
//************************************************************/
//insert an element; return false if insertion fails
template<class T, class Key>
bool em_pqueue<T,Key>::insert(const T& x) {
bool ok;
#ifdef EMPQ_ASSERT_EXPENSIVE
long init_size = size();
#endif
T val = x;
MY_LOG_DEBUG_ID("\nEM_PQUEUE::INSERT");
//if structure is empty insert x in pq; not worth the trouble..
if ((crt_buf == 0) && (buff_0->is_empty())) {
if (!pq->full()) {
MY_LOG_DEBUG_ID("insert in pq");
pq->insert(x);
return true;
}
}
if (!pq->empty()) {
T pqmax;
bool ok;
ok = pq->max(pqmax);
assert(ok);
// cout << "insert " << x << " max: " << pqmax << "\n";
if (x <= pqmax) {
//if x is smaller then pq_max and pq not full, insert x in pq
if (!pq->full()) {
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
pq->insert(x);
return true;
} else {
//if x is smaller then pq_max and pq full, exchange x with pq_max
pq->extract_max(val);
pq->insert(x);
//cout << "max is: " << val << endl;
}
}
}
/* at this point, x >= pqmax.
we need to insert val==x or val==old max.
*/
//if buff_0 full, empty it
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
if (buff_0->is_full()) {
#ifdef EMPQ_PRINT_SIZE
long x = size(), y;
y = x*sizeof(T) >> 20;
cout << "pqsize:[" << active_streams() << " streams: ";
print_stream_sizes();
cout << " total " << x << "(" << y << "MB)]" << endl;
cout.flush();
#endif
empty_buff_0();
}
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
//insert x in buff_0
assert(!buff_0->is_full());
MY_LOG_DEBUG_ID("insert in buff_0");
ok = buff_0->insert(val);
assert(ok);
#ifdef EMPQ_PRINT_INSERT
cout << "INSERTED: " << x << endl; cout.flush();
#endif
#ifdef EMPQ_PRINT_EMPQ
this->print();
cout << endl;
#endif
MY_LOG_DEBUG_ID("EM_PQUEUE: INSERTED");
return true;
}
//************************************************************/
/* called when buff_0 is full to empty it on external level_1 buffer;
can produce cascading emptying
*/
template<class T, class Key> bool
em_pqueue<T,Key>::empty_buff_0() {
#ifdef EMPQ_ASSERT_EXPENSIVE
long init_size = size();
#endif
#ifdef EMPQ_EMPTY_BUF_PRINT
cout << "emptying buff_0\n"; cout.flush();
print_size();
#endif
MY_LOG_DEBUG_ID("empty buff 0");
assert(buff_0->is_full());
//sort the buffer
buff_0->sort();
//cout << "sorted buff_0: \n" << *buff_0 << "\n";
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
//allocate buffer if necessary
if (!buff[0]) { // XXX should check crt_buf
//create buff[0] as a level1 buffer
MEMORY_LOG("em_pqueue::empty_buff_0: create new em_buffer\n");
buff[0] = new em_buffer<T,Key>(1, bufsize, buf_arity);
}
//check that buff_0 fills exactly a stream of buff[0]
assert(buff_0->get_buf_len() == buff[0]->get_stream_maxlen());
//save buff_0 to stream
MY_LOG_DEBUG_ID("empty buff_0 to stream");
AMI_STREAM<T>* buff_0_str = buff_0->save2str();
assert(buff_0_str);
//MY_LOG_DEBUG_ID("buff_0 emptied");
//reset buff_0
buff_0->reset();
MY_LOG_DEBUG_ID("buf_0 now reset");
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() + buff_0->maxlen() == init_size);
#endif
//copy data from buff_0 to buff[0]
if (buff[0]->is_full()) {
//if buff[0] full, empty it recursively
empty_buff(0);
}
buff[0]->insert(buff_0_str);
MY_LOG_DEBUG_ID("stream inserted in buff[0]");
//update the crt_buf pointer if necessary
if (crt_buf == 0) crt_buf = 1;
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
return true;
}
//************************************************************/
/* sort and empty buff[i] into buffer[i+1] recursively; called
by empty_buff_0() to empty subsequent buffers; i must
be a valid (i<crt_buf) full buffer;
*/
template<class T, class Key>
void
em_pqueue<T,Key>::empty_buff(unsigned short i) {
#ifdef EMPQ_ASSERT_EXPENSIVE
long init_size = size();
#endif
#ifdef EMPQ_EMPTY_BUF_PRINT
cout << "emptying buffer_" << i << "\n"; cout.flush();
print_size();
#endif
MY_LOG_DEBUG_ID("empty buff ");
MY_LOG_DEBUG_ID(i);
//i must be a valid, full buffer
assert(i<crt_buf);
assert(buff[i]->is_full());
//check there is space to empty to
if (i == max_nbuf-1) {
cerr << "empty_buff:: cannot empty further - structure is full..\n";
print_size();
cerr << "ext buff array should reallocate in a future version..\n";
exit(1);
}
//create next buffer if necessary
if (!buff[i+1]) {
//create buff[i+1] as a level-(i+2) buffer
char str[200];
sprintf(str, "em_pqueue::empty_buff( %hd ) allocate new em_buffer\n", i);
MEMORY_LOG(str);
buff[i+1] = new em_buffer<T,Key>(i+2, bufsize, buf_arity);
}
assert(buff[i+1]);
//check that buff[i] fills exactly a stream of buff[i+1];
//extraneous (its checked in insert)
//assert(buff[i]->len() == buff[i+1]->streamlen());
//sort the buffer into a new stream
MY_LOG_DEBUG_ID("sort buffer ");
AMI_STREAM<T>* sorted_buf = buff[i]->sort();
//assert(sorted_buf->stream_len() == buff[i]->len());
//this is just for debugging
if (sorted_buf->stream_len() != buff[i]->get_buf_len()) {
cout << "sorted_stream_len: " << sorted_buf->stream_len()
<< " , bufflen: " << buff[i]->get_buf_len() << endl; cout.flush();
AMI_err ae;
ae = sorted_buf->seek(0);
assert(ae == AMI_ERROR_NO_ERROR);
T *x;
while (sorted_buf->read_item(&x) == AMI_ERROR_NO_ERROR) {
cout << *x << ", "; cout.flush();
}
cout << "\n";
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(sorted_buf->stream_len() == buff[i]->len());
#endif
}
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
//reset buff[i] (delete all its streams )
buff[i]->reset();
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size - sorted_buf->stream_len());
#endif
//link sorted buff[i] as a substream into buff[i+1];
//sorted_buf is a new stream, so it starts out with 0 deleted elements;
//of ocurse, its length might be smaller than nominal;
if (buff[i+1]->is_full()) {
empty_buff(i+1);
}
buff[i+1]->insert(sorted_buf, 0);
//update the crt_buf pointer if necessary
if (crt_buf < i+2) crt_buf = i+2;
#ifdef EMPQ_ASSERT_EXPENSIVE
assert(size() == init_size);
#endif
}
//************************************************************/
/* merge the first <K> elements of the streams of input buffer,
starting at position <buf.deleted[i]> in each stream; there are
<buf.arity> streams in total; write output in <outstream>; the
items written in outstream are of type <merge_output_type> which
extends T with the stream nb and buffer nb the item comes from;
this information is needed later to distribute items back; do not
delete the K merged elements from the input streams; <bufid> is the
id of the buffer whose streams are being merged;
the input streams are assumed sorted in increasing order of keys;
*/
template<class T, class Key>
AMI_err
em_pqueue<T,Key>::merge_buffer(em_buffer<T,Key> *buf,
ExtendedMergeStream *outstream, long K) {
long* bos = buf->get_bos();
/* buff[0] is a level-1 buffer and so on */
unsigned short bufid = buf->get_level() - 1;
/* Pointers to current leading elements of streams */
unsigned int arity = buf->get_nbstreams();
AMI_STREAM<T>** instreams = buf->get_streams();
std::vector<T*> in_objects(arity);
AMI_err ami_err;
unsigned int i, j;
MY_LOG_DEBUG_ID("merge_buffer ");
MY_LOG_DEBUG_ID(buf->get_level());
assert(outstream);
assert(instreams);
assert(buf->get_buf_len());
assert(K>0);
//array initialized with first key from each stream (only non-null keys
//must be included)
MEMORY_LOG("em_pqueue::merge_buffer: allocate keys array\n");
merge_key<Key>* keys = new merge_key<Key> [arity];
/* count number of non-empty runs */
j = 0;
/* rewind and read the first item from every stream */
for (i = 0; i < arity ; i++ ) {
assert(instreams[i]);
//rewind stream
if ((ami_err = instreams[i]->seek(bos[i])) != AMI_ERROR_NO_ERROR) {
cerr << "WARNING!!! EARLY EXIT!!!" << endl;
return ami_err;
}
/* read first item */
ami_err = instreams[i]->read_item(&(in_objects[i]));
switch(ami_err) {
case AMI_ERROR_END_OF_STREAM:
in_objects[i] = NULL;
break;
case AMI_ERROR_NO_ERROR:
//cout << "stream " << i << " read " << *in_objects[i] << "\n";
//cout.flush();
// include this key in the array of keys
keys[j] = merge_key<Key>(in_objects[i]->getPriority(), i);
// cout << "key " << j << "set to " << keys[j] << "\n";
j++;
break;
default:
cerr << "WARNING!!! EARLY EXIT!!!" << endl;
return ami_err;
}
}
unsigned int NonEmptyRuns = j;
// cout << "nonempyruns = " << NonEmptyRuns << "\n";
//build heap from the array of keys
pqheap_t1<merge_key<Key> > mergeheap(keys, NonEmptyRuns);
//cout << "heap is : " << mergeheap << "\n";
//repeatedly extract_min from heap and insert next item from same stream
long extracted = 0;
//rewind output buffer
ami_err = outstream->seek(0);
assert(ami_err == AMI_ERROR_NO_ERROR);
ExtendedEltMergeType<T,Key> out;
while (!mergeheap.empty() && (extracted < K)) {
//find min key and id of stream it comes from
i = mergeheap.min().stream_id();
//write min item to output stream
out = ExtendedEltMergeType<T,Key>(*in_objects[i], bufid, i);
if ((ami_err = outstream->write_item(out)) != AMI_ERROR_NO_ERROR) {
cerr << "WARNING!!! EARLY EXIT!!!" << endl;
return ami_err;
}
//cout << "wrote " << out << "\n";
extracted++; //update nb of extracted elements
//read next item from same input stream
ami_err = instreams[i]->read_item(&(in_objects[i]));
switch(ami_err) {
case AMI_ERROR_END_OF_STREAM:
mergeheap.delete_min();
break;
case AMI_ERROR_NO_ERROR:
//extract the min from the heap and insert next key from the
//same stream
{
Key k = in_objects[i]->getPriority();
mergeheap.delete_min_and_insert(merge_key<Key>(k, i));
}
break;
default:
cerr << "WARNING!!! early breakout!!!" << endl;
return ami_err;
}
//cout << "PQ: " << mergeheap << "\n";
} //while
//delete [] keys;
//!!! KEYS BELONGS NOW TO MERGEHEAP, AND WILL BE DELETED BY THE
//DESTRUCTOR OF MERGEHEAP (CALLED AUUTOMATICALLY ON FUNCTION EXIT)
//IF I DELETE KEYS EXPLICITELY, THEY WILL BE DELETED AGAIN BY
//DESTRUCTOR, AND EVERYTHING SCREWS UP..
buf->put_streams();
MY_LOG_DEBUG_ID("merge_buffer: done");
//cout << "done merging buffer\n";
assert(extracted == outstream->stream_len());
assert(extracted); // something in, something out
return AMI_ERROR_NO_ERROR;
}
//************************************************************/
/* merge the first <K> elements of the input streams; there are <arity>
streams in total; write output in <outstream>;
the input streams are assumed sorted in increasing order of their
keys;
*/
template<class T, class Key>
AMI_err
em_pqueue<T,Key>::merge_streams(ExtendedMergeStream** instreams,
unsigned short arity,
ExtendedMergeStream *outstream, long K) {
MY_LOG_DEBUG_ID("enter merge_streams");
assert(arity> 1);
//Pointers to current leading elements of streams
std::vector<ExtendedEltMergeType<T,Key> > in_objects(arity);
AMI_err ami_err;
//unsigned int i;
unsigned int nonEmptyRuns=0; //count number of non-empty runs
//array initialized with first element from each stream (only non-null keys
//must be included)
MEMORY_LOG("em_pqueue::merge_streams: allocate keys array\n");
merge_key<Key>* keys = new merge_key<Key> [arity];
assert(keys);
//rewind and read the first item from every stream
for (int i = 0; i < arity ; i++ ) {
//rewind stream
if ((ami_err = instreams[i]->seek(0)) != AMI_ERROR_NO_ERROR) {
return ami_err;
}
//read first item
ExtendedEltMergeType<T,Key> *objp;
ami_err = instreams[i]->read_item(&objp);
switch(ami_err) {
case AMI_ERROR_NO_ERROR:
in_objects[i] = *objp;
keys[nonEmptyRuns] = merge_key<Key>(in_objects[i].getPriority(), i);
nonEmptyRuns++;
break;
case AMI_ERROR_END_OF_STREAM:
break;
default:
return ami_err;
}
}
assert(nonEmptyRuns <= arity);
//build heap from the array of keys
pqheap_t1<merge_key<Key> > mergeheap(keys, nonEmptyRuns); /* takes ownership of keys */
//repeatedly extract_min from heap and insert next item from same stream
long extracted = 0;
//rewind output buffer
ami_err = outstream->seek(0);
assert(ami_err == AMI_ERROR_NO_ERROR);
while (!mergeheap.empty() && (extracted < K)) {
//find min key and id of stream it comes from
int id = mergeheap.min().stream_id();
//write min item to output stream
assert(id < nonEmptyRuns);
assert(id >= 0);
assert(mergeheap.size() == nonEmptyRuns);
ExtendedEltMergeType<T,Key> obj = in_objects[id];
if ((ami_err = outstream->write_item(obj)) != AMI_ERROR_NO_ERROR) {
return ami_err;
}
//cout << "wrote " << *in_objects[i] << "\n";
//extract the min from the heap and insert next key from same stream
assert(id < nonEmptyRuns);
assert(id >= 0);
ExtendedEltMergeType<T,Key> *objp;
ami_err = instreams[id]->read_item(&objp);
switch(ami_err) {
case AMI_ERROR_NO_ERROR:
{
in_objects[id] = *objp;
merge_key<Key> tmp = merge_key<Key>(in_objects[id].getPriority(), id);
mergeheap.delete_min_and_insert(tmp);
}
extracted++; //update nb of extracted elements
break;
case AMI_ERROR_END_OF_STREAM:
mergeheap.delete_min();
break;
default:
return ami_err;
}
} //while
//delete [] keys;
//!!! KEYS BELONGS NOW TO MERGEHEAP, AND WILL BE DELETED BY THE
//DESTRUCTOR OF MERGEHEAP (CALLED AUUTOMATICALLY ON FUNCTION EXIT)
//IF I DELETE KEYS EXPLICITELY, THEY WILL BE DELETED AGAIN BY
//DESTRUCTOR, AND EVERYTHING SCREWS UP..
MY_LOG_DEBUG_ID("merge_streams: done");
return AMI_ERROR_NO_ERROR;
}
//************************************************************/
template<class T, class Key>
void
em_pqueue<T,Key>::clear() {
pq->clear();
buff_0->clear();
for(int i=0; i<crt_buf; i++) {
if(buff[i]) {
delete buff[i]; buff[i] = NULL;
}
}
crt_buf = 0;
}
//************************************************************/
template<class T, class Key>
void
em_pqueue<T,Key>::print_range() {
cout << "EM_PQ: [pq=" << pqsize
<< ", b=" << bufsize
<< ", bufs=" << max_nbuf
<< ", ar=" << buf_arity << "]\n";
cout << "PQ: ";
//pq->print_range();
pq->print();
cout << endl;
cout << "B0: ";
// buff_0->print_range();
buff_0->print();
cout << "\n";
for (unsigned short i=0; i < crt_buf; i++) {
cout << "B" << i+1 << ": ";
buff[i]->print_range();
cout << endl;
}
cout.flush();
}
//************************************************************/
template<class T, class Key>
void
em_pqueue<T,Key>::print() {
cout << "EM_PQ: [pq=" << pqsize
<< ", b=" << bufsize
<< ", bufs=" << max_nbuf
<< ", ar=" << buf_arity << "]\n";
cout << "PQ: ";
pq->print();
cout << endl;
cout << "B0: ";
buff_0->print();
cout << "\n";
for (unsigned short i=0; i < crt_buf; i++) {
cout << "B" << i+1 << ": " << endl;
buff[i]->print();
cout << endl;
}
cout.flush();
}
//************************************************************/
template<class T, class Key>
void em_pqueue<T,Key>::print_size() {
//sum up the lengths(nb of elements) of the external buffers
long elen = 0;
cout << "EMPQ: pq=" << pq->size() <<",B0=" << buff_0->get_buf_len() << endl;
cout.flush();
for (unsigned short i=0; i < crt_buf; i++) {
assert(buff[i]);
cout << "B_" << i+1 << ":"; cout.flush();
buff[i]->print_stream_sizes();
elen += buff[i]->get_buf_len();
//cout << endl; cout.flush();
}
cout << "total: " << elen + pq->size() + buff_0->get_buf_len() << endl << endl;
cout.flush();
}
/*****************************************************************/
template<class T,class Key>
void em_pqueue<T,Key>::print_stream_sizes() {
for (unsigned short i=0; i< crt_buf; i++) {
cout << "[";
buff[i]->print_stream_sizes();
cout << "]";
}
cout.flush();
}
#undef XXX
#endif
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