ami_sort_impl.h

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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 AMI_SORT_IMPL_H
#define AMI_SORT_IMPL_H
 
#include "ami_stream.h"
#include "mem_stream.h"
#include "mm.h"
#include "quicksort.h"
#include "queue.h"
#include "replacementHeap.h"
#include "replacementHeapBlock.h"
 
#define SDEBUG if (0)
 
/* if this flag is defined, a run will be split into blocks, each
   block sorted and then all blocks merged */
#define BLOCKED_RUN
 
/* ---------------------------------------------------------------------- */
// set run_size, last_run_size and nb_runs depending on how much memory
// is available
template <class T>
static void initializeRunFormation(AMI_STREAM<T> *instream, size_t &run_size,
                                   size_t &last_run_size, unsigned int &nb_runs)
{
 
    size_t mm_avail = MM_manager.memory_available();
    off_t strlen;
 
#ifdef BLOCKED_RUN
    // not in place, can only use half memory
    mm_avail = mm_avail / 2;
#endif
    run_size = mm_avail / sizeof(T);
 
    strlen = instream->stream_len();
    if (strlen == 0) {
        nb_runs = last_run_size = 0;
    }
    else {
        if (strlen % run_size == 0) {
            nb_runs = strlen / run_size;
            last_run_size = run_size;
        }
        else {
            nb_runs = strlen / run_size + 1;
            last_run_size = strlen % run_size;
        }
    }
 
    SDEBUG cout << "nb_runs=" << nb_runs << ", run_size=" << run_size
                << ", last_run_size=" << last_run_size << "\n";
}
 
/* ---------------------------------------------------------------------- */
/* data is allocated; read run_size elements from stream into data and
   sort them using quicksort */
template <class T, class Compare>
size_t makeRun_Block(AMI_STREAM<T> *instream, T *data, unsigned int run_size,
                     Compare *cmp)
{
    AMI_err err;
    off_t new_run_size = 0;
 
    // read next run from input stream
    err = instream->read_array(data, run_size, &new_run_size);
    assert(err == AMI_ERROR_NO_ERROR || err == AMI_ERROR_END_OF_STREAM);
 
    // sort it in memory in place
    quicksort(data, new_run_size, *cmp);
 
    return new_run_size;
}
 
/* ---------------------------------------------------------------------- */
/* data is allocated; read run_size elements from stream into data and
   sort them using quicksort; instead of reading the whole chunk at
   once, it reads it in blocks, sorts each block and then merges the
   blocks together. Note: it is not in place! it allocates another
   array of same size as data, writes the sorted run into it and
   deteles data, and replaces data with outdata */
template <class T, class Compare>
void makeRun(AMI_STREAM<T> *instream, T *&data, int run_size, Compare *cmp)
{
 
    unsigned int nblocks, last_block_size, crt_block_size, block_size;
 
    block_size = STREAM_BUFFER_SIZE;
 
    if (run_size % block_size == 0) {
        nblocks = run_size / block_size;
        last_block_size = block_size;
    }
    else {
        nblocks = run_size / block_size + 1;
        last_block_size = run_size % block_size;
    }
 
    // create queue of blocks waiting to be merged
    queue<MEM_STREAM<T> *> *blockList;
    MEM_STREAM<T> *str;
    blockList = new queue<MEM_STREAM<T> *>(nblocks);
    for (unsigned int i = 0; i < nblocks; i++) {
        crt_block_size = (i == nblocks - 1) ? last_block_size : block_size;
        makeRun_Block(instream, &(data[i * block_size]), crt_block_size, cmp);
        str = new MEM_STREAM<T>(&(data[i * block_size]), crt_block_size);
        blockList->enqueue(str);
    }
    assert(blockList->length() == nblocks);
 
    // now data consists of sorted blocks: merge them
    ReplacementHeapBlock<T, Compare> rheap(blockList);
    SDEBUG rheap.print(cerr);
    int i = 0;
    T elt;
    T *outdata = new T[run_size];
    while (!rheap.empty()) {
        elt = rheap.extract_min();
        outdata[i] = elt;
        // SDEBUG cerr << "makeRun: written " << elt << endl;
        i++;
    }
    assert(i == run_size && blockList->length() == 0);
    delete blockList;
 
    T *tmp = data;
    delete[] tmp;
    data = outdata;
}
 
/* ---------------------------------------------------------------------- */
 
// partition instream in streams that fit in main memory, sort each
// stream, remember its name, make it persistent and store it on
// disk. if entire stream fits in memory, sort it and store it and
// return it.
 
// assume instream is allocated prior to the call.
//  set nb_runs and allocate runNames.
 
// The comparison object "cmp", of (user-defined) class represented by
// Compare, must have a member function called "compare" which is used
// for sorting the input stream.
 
template <class T, class Compare>
queue<char *> *runFormation(AMI_STREAM<T> *instream, Compare *cmp)
{
 
    size_t run_size, last_run_size, crt_run_size;
    unsigned int nb_runs;
    queue<char *> *runList;
    T *data;
    AMI_STREAM<T> *str;
    char *strname;
 
    assert(instream && cmp);
    SDEBUG cout << "runFormation: ";
    SDEBUG MM_manager.print();
 
    /* leave this in for now, in case some file-based implementations do
       anything funny... -RW */
    // rewind file
    instream->seek(0); // should check error xxx
 
    // estimate run_size, last_run_size and nb_runs
    initializeRunFormation(instream, run_size, last_run_size, nb_runs);
 
    // create runList (if 0 size, queue uses default)
    runList = new queue<char *>(nb_runs);
 
    /* allocate space for a run */
    if (nb_runs <= 1) {
        // don't waste space if input stream is smaller than run_size
        data = new T[last_run_size];
    }
    else {
        data = new T[run_size];
    }
    SDEBUG MM_manager.print();
 
    for (size_t i = 0; i < nb_runs; i++) {
        // while(!instream->eof()) {
        crt_run_size = (i == nb_runs - 1) ? last_run_size : run_size;
 
        SDEBUG cout << "i=" << i << ":  runsize=" << crt_run_size << ", ";
 
        // crt_run_size = makeRun_Block(instream, data, run_size, cmp);
#ifdef BLOCKED_RUN
        makeRun(instream, data, crt_run_size, cmp);
#else
        makeRun_Block(instream, data, crt_run_size, cmp);
#endif
 
        SDEBUG MM_manager.print();
 
        // read next run from input stream
        // err = instream->read_array(data, crt_run_size);
        // assert(err == AMI_ERROR_NO_ERROR);
        // sort it in memory in place
        // quicksort(data, crt_run_size, *cmp);
 
        if (crt_run_size > 0) {
            // create a new stream to hold this run
            str = new AMI_STREAM<T>();
            str->write_array(data, crt_run_size);
            assert(str->stream_len() == crt_run_size);
 
            // remember this run's name
            str->name(&strname); /* deleted after we dequeue */
            runList->enqueue(strname);
            // delete the stream -- should not keep too many streams open
            str->persist(PERSIST_PERSISTENT);
            delete str;
        }
    }
    SDEBUG MM_manager.print();
    // release the run memory!
    delete[] data;
 
    SDEBUG cout << "runFormation: done.\n";
    SDEBUG MM_manager.print();
 
    return runList;
}
 
/* ---------------------------------------------------------------------- */
 
// this is one pass of merge; estimate max possible merge arity <ar>
// and merge the first <ar> streams from runList ; create and return
// the resulting stream (does not add it to the queue -- the calling
// function will do that)
 
// input streams are assumed to be sorted, and are not necessarily of
// the same length.
 
// streamList does not contains streams, but names of streams, which
// must be opened in order to be merged
 
// The comparison object "cmp", of (user-defined) class represented by
// Compare, must have a member function called "compare" which is used
// for sorting the input stream.
 
template <class T, class Compare>
AMI_STREAM<T> *singleMerge(queue<char *> *streamList, Compare *cmp)
{
    AMI_STREAM<T> *mergedStr;
    size_t mm_avail, blocksize;
    unsigned int arity, max_arity;
    T elt;
 
    assert(streamList && cmp);
 
    SDEBUG cout << "singleMerge: ";
 
    // estimate max possible merge arity with available memory (approx M/B)
    mm_avail = MM_manager.memory_available();
    // blocksize = getpagesize();
    // should use AMI function, but there's no stream at this point
    // now use static mtd -RW 5/05
    AMI_STREAM<T>::main_memory_usage(&blocksize, MM_STREAM_USAGE_MAXIMUM);
    max_arity = mm_avail / blocksize;
    if (max_arity < 2) {
        cerr << __FILE__ ":" << __LINE__
             << ": OUT OF MEMORY in singleMerge (going over limit)" << endl;
        max_arity = 2;
    }
    else if (max_arity > MAX_STREAMS_OPEN) {
        max_arity = MAX_STREAMS_OPEN;
    }
    arity =
        (streamList->length() < max_arity) ? streamList->length() : max_arity;
 
    SDEBUG cout << "arity=" << arity << " (max_arity=" << max_arity << ")\n";
 
    /* create the output stream. if this is a complete merge, use finalpath */
    // create output stream
    mergedStr = new AMI_STREAM<T>();
 
    ReplacementHeap<T, Compare> rheap(arity, streamList);
    SDEBUG rheap.print(cerr);
 
    while (!rheap.empty()) {
        // mergedStr->write_item( rheap.extract_min() );
        // xxx should check error here
        elt = rheap.extract_min();
        mergedStr->write_item(elt);
        // SDEBUG cerr << "smerge: written " << elt << endl;
    }
 
    SDEBUG cout << "..done\n";
 
    return mergedStr;
}
 
/* ---------------------------------------------------------------------- */
 
// merge runs whose names are given by runList; this may entail
// multiple passes of singleMerge();
 
// return the resulting output stream
 
// input streams are assumed to be sorted, and are not necessarily of
// the same length.
 
// The comparison object "cmp", of (user-defined) class represented by
// Compare, must have a member function called "compare" which is used
// for sorting the input stream.
 
template <class T, class Compare>
AMI_STREAM<T> *multiMerge(queue<char *> *runList, Compare *cmp)
{
    AMI_STREAM<T> *mergedStr = NULL;
    char *path;
 
    assert(runList && runList->length() > 1 && cmp);
 
    SDEBUG cout << "multiMerge: " << runList->length() << " runs" << endl;
 
    while (runList->length() > 1) {
 
        // merge streams from streamlist into mergedStr
        mergedStr = singleMerge<T, Compare>(runList, cmp);
        // i thought the templates are not needed in the call, but seems to
        // help the compiler..laura
        assert(mergedStr);
 
        // if more runs exist, delete this stream and add it to list
        if (runList->length() > 0) {
            mergedStr->name(&path);
            runList->enqueue(path);
            mergedStr->persist(PERSIST_PERSISTENT);
            delete mergedStr;
        }
    }
 
    assert(runList->length() == 0);
    assert(mergedStr);
    return mergedStr;
}
 
#endif