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yacy_search_server/source/net/yacy/kelondro/index/RowCollection.java

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// RowCollection.java
// (C) 2006 by Michael Peter Christen; mc@yacy.net, Frankfurt a. M., Germany
// first published 12.01.2006 on http://www.anomic.de
//
// $LastChangedDate: 2006-04-02 22:40:07 +0200 (So, 02 Apr 2006) $
// $LastChangedRevision: 1986 $
// $LastChangedBy: orbiter $
//
// LICENSE
//
// 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.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
package net.yacy.kelondro.index;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Random;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Future;
import java.util.concurrent.RejectedExecutionException;
import java.util.concurrent.SynchronousQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import net.yacy.kelondro.logging.Log;
import net.yacy.kelondro.order.Base64Order;
import net.yacy.kelondro.order.ByteOrder;
import net.yacy.kelondro.order.NaturalOrder;
import net.yacy.kelondro.util.FileUtils;
import net.yacy.kelondro.util.MemoryControl;
import net.yacy.kelondro.util.NamePrefixThreadFactory;
import net.yacy.kelondro.util.kelondroException;
public class RowCollection implements Iterable<Row.Entry>, Cloneable {
public static final long growfactorLarge100 = 140L;
public static final long growfactorSmall100 = 120L;
private static final int isortlimit = 20;
private static final int availableCPU = Runtime.getRuntime().availableProcessors();
private static final int exp_chunkcount = 0;
private static final int exp_last_read = 1;
private static final int exp_last_wrote = 2;
private static final int exp_order_type = 3;
private static final int exp_order_bound = 4;
private static final int exp_collection = 5;
public static final ExecutorService sortingthreadexecutor =
(availableCPU > 1)
? new ThreadPoolExecutor(
Runtime.getRuntime().availableProcessors(),
Integer.MAX_VALUE,
120L, TimeUnit.SECONDS,
new SynchronousQueue<Runnable>(),
new NamePrefixThreadFactory("sorting"),
new ThreadPoolExecutor.CallerRunsPolicy())
: null;
private static final ExecutorService partitionthreadexecutor =
(availableCPU > 1)
? new ThreadPoolExecutor(
Runtime.getRuntime().availableProcessors(),
Integer.MAX_VALUE,
120L, TimeUnit.SECONDS,
new SynchronousQueue<Runnable>(),
new NamePrefixThreadFactory("partition"),
new ThreadPoolExecutor.CallerRunsPolicy())
: null;
public final Row rowdef;
protected byte[] chunkcache;
protected int chunkcount;
protected int sortBound;
protected long lastTimeWrote;
protected RowCollection(final RowCollection rc) {
this.rowdef = rc.rowdef;
this.chunkcache = rc.chunkcache;
this.chunkcount = rc.chunkcount;
this.sortBound = rc.sortBound;
this.lastTimeWrote = rc.lastTimeWrote;
}
protected RowCollection(final Row rowdef) {
this.rowdef = rowdef;
this.sortBound = 0;
this.lastTimeWrote = System.currentTimeMillis();
this.chunkcache = new byte[0];
this.chunkcount = 0;
}
public RowCollection(final Row rowdef, final int objectCount) throws RowSpaceExceededException {
this(rowdef);
ensureSize(objectCount);
}
protected RowCollection(final Row rowdef, final int objectCount, final byte[] cache, final int sortBound) {
this.rowdef = rowdef;
this.chunkcache = cache;
this.chunkcount = objectCount;
this.sortBound = sortBound;
this.lastTimeWrote = System.currentTimeMillis();
}
protected RowCollection(final Row rowdef, final Row.Entry exportedCollectionRowEnvironment) {
final int chunkcachelength = exportedCollectionRowEnvironment.cellwidth(1) - (int) exportOverheadSize;
final Row.Entry exportedCollection = exportRow(chunkcachelength).newEntry(exportedCollectionRowEnvironment, 1);
this.rowdef = rowdef;
this.chunkcount = (int) exportedCollection.getColLong(exp_chunkcount);
if ((this.chunkcount > chunkcachelength / rowdef.objectsize)) {
Log.logWarning("RowCollection", "corrected wrong chunkcount; chunkcount = " + this.chunkcount + ", chunkcachelength = " + chunkcachelength + ", rowdef.objectsize = " + rowdef.objectsize);
this.chunkcount = chunkcachelength / rowdef.objectsize; // patch problem
}
this.lastTimeWrote = (exportedCollection.getColLong(exp_last_wrote) + 10957) * day;
final String sortOrderKey = exportedCollection.getColString(exp_order_type, null);
ByteOrder oldOrder = null;
if ((sortOrderKey == null) || (sortOrderKey.equals("__"))) {
oldOrder = null;
} else {
oldOrder = NaturalOrder.bySignature(sortOrderKey);
if (oldOrder == null) oldOrder = Base64Order.bySignature(sortOrderKey);
}
if ((rowdef.objectOrder != null) && (oldOrder != null) && (!(rowdef.objectOrder.signature().equals(oldOrder.signature()))))
throw new kelondroException("old collection order does not match with new order; objectOrder.signature = " + rowdef.objectOrder.signature() + ", oldOrder.signature = " + oldOrder.signature());
this.sortBound = (int) exportedCollection.getColLong(exp_order_bound);
if (sortBound > chunkcount) {
Log.logWarning("RowCollection", "corrected wrong sortBound; sortBound = " + sortBound + ", chunkcount = " + chunkcount);
this.sortBound = chunkcount;
}
this.chunkcache = exportedCollection.getColBytes(exp_collection, false);
}
protected RowCollection(Row rowdef, byte[] chunkcache, int chunkcount, int sortBound, long lastTimeWrote) {
this.rowdef = rowdef;
this.chunkcache = new byte[chunkcache.length];
System.arraycopy(chunkcache, 0, this.chunkcache, 0, chunkcache.length);
this.chunkcount = chunkcount;
this.sortBound = sortBound;
this.lastTimeWrote = lastTimeWrote;
}
public RowCollection clone() {
return new RowCollection(this.rowdef, this.chunkcache, this.chunkcount, this.sortBound, this.lastTimeWrote);
}
public void reset() {
this.chunkcache = new byte[0];
this.chunkcount = 0;
this.sortBound = 0;
}
/**
* calculate the memory that the structure occupies in ram
* @return number of bytes in use
*/
public long mem() {
return this.chunkcache.length;
}
private static final Row exportMeasureRow = exportRow(0 /* no relevance */);
public static final int sizeOfExportedCollectionRows(final Row.Entry exportedCollectionRowEnvironment, final int columnInEnvironment) {
final Row.Entry exportedCollectionEntry = exportMeasureRow.newEntry(exportedCollectionRowEnvironment, columnInEnvironment);
final int chunkcount = (int) exportedCollectionEntry.getColLong(exp_chunkcount);
return chunkcount;
}
private static final long day = 1000 * 60 * 60 * 24;
private static int daysSince2000(final long time) {
return (int) (time / day) - 10957;
}
private static Column exportColumn0, exportColumn1, exportColumn2, exportColumn3, exportColumn4;
protected static final long exportOverheadSize = 14;
private static Row exportRow(final int chunkcachelength) {
/*
return new Row(
"int size-4 {b256}," +
"short lastread-2 {b256}," + // as daysSince2000
"short lastwrote-2 {b256}," + // as daysSince2000
"byte[] orderkey-2," +
"int orderbound-4 {b256}," +
"byte[] collection-" + chunkcachelength,
NaturalOrder.naturalOrder
);
*/
if (exportColumn0 == null) exportColumn0 = new Column("int size-4 {b256}");
if (exportColumn1 == null) exportColumn1 = new Column("short lastread-2 {b256}");
if (exportColumn2 == null) exportColumn2 = new Column("short lastwrote-2 {b256}");
if (exportColumn3 == null) exportColumn3 = new Column("byte[] orderkey-2");
if (exportColumn4 == null) exportColumn4 = new Column("int orderbound-4 {b256}");
/*
* because of a strange bug these objects cannot be initialized as normal
* static final. If I try that, they are not initialized and are assigned null. why?
*/
Row er = new Row(new Column[]{
exportColumn0, exportColumn1, exportColumn2, exportColumn3, exportColumn4,
new Column("byte[] collection-" + chunkcachelength)
},
NaturalOrder.naturalOrder
);
assert er.objectsize == chunkcachelength +exportOverheadSize;
return er;
}
public synchronized byte[] exportCollection() {
// returns null if the collection is empty
sort(); // experimental; supervise CPU load
//uniq();
//trim();
assert this.sortBound == this.chunkcount; // on case the collection is sorted
assert this.size() * this.rowdef.objectsize <= this.chunkcache.length : "this.size() = " + this.size() + ", objectsize = " + this.rowdef.objectsize + ", chunkcache.length = " + this.chunkcache.length;
final Row row = exportRow(this.size() * this.rowdef.objectsize);
final Row.Entry entry = row.newEntry();
assert (sortBound <= chunkcount) : "sortBound = " + sortBound + ", chunkcount = " + chunkcount;
assert (this.chunkcount <= chunkcache.length / rowdef.objectsize) : "chunkcount = " + this.chunkcount + ", chunkcache.length = " + chunkcache.length + ", rowdef.objectsize = " + rowdef.objectsize;
entry.setCol(exp_chunkcount, this.chunkcount);
entry.setCol(exp_last_read, daysSince2000(System.currentTimeMillis()));
entry.setCol(exp_last_wrote, daysSince2000(this.lastTimeWrote));
entry.setCol(exp_order_type, (this.rowdef.objectOrder == null) ? "__".getBytes() :this.rowdef.objectOrder.signature().getBytes());
entry.setCol(exp_order_bound, this.sortBound);
entry.setCol(exp_collection, this.chunkcache);
return entry.bytes();
}
public void saveCollection(final File file) throws IOException {
FileUtils.copy(exportCollection(), file);
}
public Row row() {
return this.rowdef;
}
private final long neededSpaceForEnsuredSize(final int elements, final boolean forcegc) {
assert elements > 0 : "elements = " + elements;
final long needed = elements * rowdef.objectsize;
if (chunkcache.length >= needed) return 0;
assert needed > 0 : "needed = " + needed;
long allocram = needed * growfactorLarge100 / 100L;
allocram -= allocram % rowdef.objectsize;
assert allocram > 0 : "elements = " + elements + ", new = " + allocram;
if (allocram <= Integer.MAX_VALUE && MemoryControl.request(allocram, false)) return allocram;
allocram = needed * growfactorSmall100 / 100L;
allocram -= allocram % rowdef.objectsize;
assert allocram >= 0 : "elements = " + elements + ", new = " + allocram;
if (allocram <= Integer.MAX_VALUE && MemoryControl.request(allocram, forcegc)) return allocram;
return needed;
}
private final void ensureSize(final int elements) throws RowSpaceExceededException {
if (elements == 0) return;
final long allocram = neededSpaceForEnsuredSize(elements, true);
if (allocram == 0) return;
assert chunkcache.length < elements * rowdef.objectsize : "wrong alloc computation (1): elements * rowdef.objectsize = " + (elements * rowdef.objectsize) + ", chunkcache.length = " + chunkcache.length;
assert allocram > chunkcache.length : "wrong alloc computation (2): allocram = " + allocram + ", chunkcache.length = " + chunkcache.length;
if (allocram > Integer.MAX_VALUE || !MemoryControl.request(allocram, true))
throw new RowSpaceExceededException(allocram, "RowCollection grow");
try {
final byte[] newChunkcache = new byte[(int) allocram]; // increase space
System.arraycopy(chunkcache, 0, newChunkcache, 0, chunkcache.length);
chunkcache = newChunkcache;
} catch (OutOfMemoryError e) {
// lets try again after a forced gc()
System.gc();
try {
final byte[] newChunkcache = new byte[(int) allocram]; // increase space
System.arraycopy(chunkcache, 0, newChunkcache, 0, chunkcache.length);
chunkcache = newChunkcache;
} catch (OutOfMemoryError ee) {
throw new RowSpaceExceededException(allocram, "RowCollection grow after OutOfMemoryError " + ee.getMessage());
}
}
}
/**
* compute the needed memory in case of a cache extension. That is, if the cache is full and must
* be copied into a new cache which is larger. In such a case the Collection needs more than the double size
* than is necessary to store the data. This method computes the extra memory that is needed to perform this task.
* @return
*/
protected final long memoryNeededForGrow() {
return neededSpaceForEnsuredSize(chunkcount + 1, false);
}
protected synchronized void trim() {
if (chunkcache.length == 0) return;
long needed = chunkcount * rowdef.objectsize;
assert needed <= chunkcache.length;
if (needed >= chunkcache.length)
return; // in case that the growfactor causes that the cache would
// grow instead of shrink, simply ignore the growfactor
if (MemoryControl.available() + 1000 < needed)
return; // if the swap buffer is not available, we must give up.
// This is not critical. Otherwise we provoke a serious
// problem with OOM
final byte[] newChunkcache = new byte[(int) needed];
System.arraycopy(chunkcache, 0, newChunkcache, 0, Math.min(chunkcache.length, newChunkcache.length));
chunkcache = newChunkcache;
}
public final long lastWrote() {
return lastTimeWrote;
}
protected synchronized final byte[] getKey(final int index) {
assert (index >= 0) : "get: access with index " + index + " is below zero";
assert (index < chunkcount) : "get: access with index " + index + " is above chunkcount " + chunkcount + "; sortBound = " + sortBound;
assert (index * rowdef.objectsize < chunkcache.length);
if ((chunkcache == null) || (rowdef == null)) return null; // case may appear during shutdown
if (index >= chunkcount) return null;
if ((index + 1) * rowdef.objectsize > chunkcache.length) return null; // the whole chunk does not fit into the chunkcache
final byte[] b = new byte[this.rowdef.primaryKeyLength];
System.arraycopy(chunkcache, index * rowdef.objectsize, b, 0, b.length);
return b;
}
public synchronized final Row.Entry get(final int index, final boolean clone) {
assert (index >= 0) : "get: access with index " + index + " is below zero";
assert (index < chunkcount) : "get: access with index " + index + " is above chunkcount " + chunkcount + "; sortBound = " + sortBound;
assert (chunkcache != null && index * rowdef.objectsize < chunkcache.length);
assert sortBound <= chunkcount : "sortBound = " + sortBound + ", chunkcount = " + chunkcount;
if ((chunkcache == null) || (rowdef == null)) return null; // case may appear during shutdown
Row.Entry entry;
final int addr = index * rowdef.objectsize;
synchronized (this) {
if (index >= chunkcount) return null;
if (addr + rowdef.objectsize > chunkcache.length) return null; // the whole chunk does not fit into the chunkcache
entry = rowdef.newEntry(chunkcache, addr, clone);
}
return entry;
}
public synchronized final void set(final int index, final Row.Entry a) throws RowSpaceExceededException {
assert (index >= 0) : "set: access with index " + index + " is below zero";
ensureSize(index + 1);
byte[] column = a.bytes();
assert a.cellwidth(0) == this.rowdef.primaryKeyLength;
assert column.length >= this.rowdef.primaryKeyLength;
final boolean sameKey = match(column, 0, index);
//if (sameKey) System.out.print("$");
a.writeToArray(chunkcache, index * rowdef.objectsize);
if (index >= this.chunkcount) this.chunkcount = index + 1;
if (!sameKey && index < this.sortBound) this.sortBound = index;
this.lastTimeWrote = System.currentTimeMillis();
}
public final void insertUnique(final int index, final Row.Entry a) throws RowSpaceExceededException {
assert (a != null);
if (index < chunkcount) {
// make room
ensureSize(chunkcount + 1);
System.arraycopy(chunkcache, rowdef.objectsize * index, chunkcache, rowdef.objectsize * (index + 1), (chunkcount - index) * rowdef.objectsize);
chunkcount++;
}
// insert entry into gap
set(index, a);
}
public synchronized void addUnique(final Row.Entry row) throws RowSpaceExceededException {
final byte[] r = row.bytes();
addUnique(r, 0, r.length);
}
public synchronized void addUnique(final List<Row.Entry> rows) throws RowSpaceExceededException {
assert this.sortBound == 0 : "sortBound = " + this.sortBound + ", chunkcount = " + this.chunkcount;
final Iterator<Row.Entry> i = rows.iterator();
while (i.hasNext()) addUnique(i.next());
}
public synchronized void add(final byte[] a) throws RowSpaceExceededException {
assert a.length == this.rowdef.objectsize : "a.length = " + a.length + ", objectsize = " + this.rowdef.objectsize;
addUnique(a, 0, a.length);
}
private final void addUnique(final byte[] a, final int astart, final int alength) throws RowSpaceExceededException {
assert (a != null);
assert (astart >= 0) && (astart < a.length) : " astart = " + astart;
assert (!(Log.allZero(a, astart, alength))) : "a = " + NaturalOrder.arrayList(a, astart, alength);
assert (alength > 0);
assert (astart + alength <= a.length);
assert alength == rowdef.objectsize : "alength =" + alength + ", rowdef.objectsize = " + rowdef.objectsize;
final int l = Math.min(rowdef.objectsize, Math.min(alength, a.length - astart));
ensureSize(chunkcount + 1);
System.arraycopy(a, astart, chunkcache, rowdef.objectsize * chunkcount, l);
chunkcount++;
// if possible, increase the sortbound value to suppress unnecessary sorting
if (this.chunkcount == 1) {
assert this.sortBound == 0;
this.sortBound = 1;
} else if (
this.sortBound + 1 == chunkcount &&
this.rowdef.objectOrder.compare(chunkcache, rowdef.objectsize * (chunkcount - 2),
chunkcache, rowdef.objectsize * (chunkcount - 1), rowdef.primaryKeyLength) == -1) {
this.sortBound = chunkcount;
}
this.lastTimeWrote = System.currentTimeMillis();
}
protected final void addSorted(final byte[] a, final int astart, final int alength) throws RowSpaceExceededException {
assert (a != null);
assert (astart >= 0) && (astart < a.length) : " astart = " + astart;
assert (!(Log.allZero(a, astart, alength))) : "a = " + NaturalOrder.arrayList(a, astart, alength);
assert (alength > 0);
assert (astart + alength <= a.length);
assert alength == rowdef.objectsize : "alength =" + alength + ", rowdef.objectsize = " + rowdef.objectsize;
final int l = Math.min(rowdef.objectsize, Math.min(alength, a.length - astart));
ensureSize(chunkcount + 1);
System.arraycopy(a, astart, chunkcache, rowdef.objectsize * chunkcount, l);
this.chunkcount++;
this.sortBound = this.chunkcount;
this.lastTimeWrote = System.currentTimeMillis();
}
public synchronized final void addAllUnique(final RowCollection c) throws RowSpaceExceededException {
if (c == null) return;
assert(rowdef.objectsize == c.rowdef.objectsize);
ensureSize(chunkcount + c.size());
System.arraycopy(c.chunkcache, 0, chunkcache, rowdef.objectsize * chunkcount, rowdef.objectsize * c.size());
chunkcount += c.size();
}
/**
* This method removes the entry at position p ensuring the order of the remaining
* entries if specified by keepOrder.
* Note: Keeping the order is expensive. If you want to remove more than one element in
* a batch with this method, it'd be better to do the removes without order keeping and doing
* the sort after all the removes are done.
*
* @param p element at this position will be removed
* @param keepOrder keep the order of remaining entries
*/
public synchronized final void removeRow(final int p, final boolean keepOrder) {
assert p >= 0 : "p = " + p;
assert p < chunkcount : "p = " + p + ", chunkcount = " + chunkcount;
assert chunkcount > 0 : "chunkcount = " + chunkcount;
assert sortBound <= chunkcount : "sortBound = " + sortBound + ", chunkcount = " + chunkcount;
if (keepOrder && (p < sortBound)) {
// remove by shift (quite expensive for big collections)
final int addr = p * this.rowdef.objectsize;
System.arraycopy(
chunkcache, addr + this.rowdef.objectsize,
chunkcache, addr,
(chunkcount - p - 1) * this.rowdef.objectsize);
sortBound--; // this is only correct if p < sortBound, but this was already checked above
} else {
// remove by copying the top-element to the remove position
if (p != chunkcount - 1) {
System.arraycopy(
chunkcache, (chunkcount - 1) * this.rowdef.objectsize,
chunkcache, p * this.rowdef.objectsize,
this.rowdef.objectsize);
}
// we moved the last element to the remove position: (p+1)st element
// only the first p elements keep their order (element p is already outside the order)
if (sortBound > p) sortBound = p;
}
chunkcount--;
this.lastTimeWrote = System.currentTimeMillis();
}
/**
* removes the last entry from the collection
* @return
*/
public synchronized Row.Entry removeOne() {
if (chunkcount == 0) return null;
final Row.Entry r = get(chunkcount - 1, true);
if (chunkcount == sortBound) sortBound--;
chunkcount--;
this.lastTimeWrote = System.currentTimeMillis();
return r;
}
public synchronized List<Row.Entry> top(int count) {
ArrayList<Row.Entry> list = new ArrayList<Row.Entry>();
if (chunkcount == 0) return list;
Row.Entry entry;
int cursor = chunkcount - 1;
while (count > 0 && cursor >= 0) {
entry = get(cursor, true);
list.add(entry);
count--;
cursor--;
}
return list;
}
public synchronized byte[] smallestKey() {
if (chunkcount == 0) return null;
this.sort();
final Row.Entry r = get(0, false);
final byte[] b = r.getPrimaryKeyBytes();
return b;
}
public synchronized byte[] largestKey() {
if (chunkcount == 0) return null;
this.sort();
final Row.Entry r = get(chunkcount - 1, false);
final byte[] b = r.getPrimaryKeyBytes();
return b;
}
public synchronized void clear() {
if (this.chunkcache.length == 0) return;
this.chunkcache = new byte[0];
this.chunkcount = 0;
this.sortBound = 0;
this.lastTimeWrote = System.currentTimeMillis();
}
public int size() {
return this.chunkcount;
}
public boolean isEmpty() {
return this.chunkcount == 0;
}
public int sorted() {
return this.sortBound;
}
public synchronized Iterator<byte[]> keys(final boolean keepOrderWhenRemoving) {
// iterates byte[] - type entries
return new keyIterator(keepOrderWhenRemoving);
}
/**
* Iterator for kelondroRowCollection.
* It supports remove() though it doesn't contain the order of the underlying
* collection during removes.
*
*/
private class keyIterator implements Iterator<byte[]> {
private int p;
private final boolean keepOrderWhenRemoving;
private keyIterator(final boolean keepOrderWhenRemoving) {
this.p = 0;
this.keepOrderWhenRemoving = keepOrderWhenRemoving;
}
public boolean hasNext() {
return p < chunkcount;
}
public byte[] next() {
return getKey(p++);
}
public void remove() {
p--;
removeRow(p, keepOrderWhenRemoving);
}
}
/**
* return an iterator for the row entries in this object
*/
public Iterator<Row.Entry> iterator() {
// iterates kelondroRow.Entry - type entries
return new rowIterator();
}
/**
* Iterator for kelondroRowCollection.
* It supports remove() and keeps the order of the underlying
* collection during removes.
*/
private class rowIterator implements Iterator<Row.Entry> {
private int p;
public rowIterator() {
p = 0;
}
public boolean hasNext() {
return p < chunkcount;
}
public Row.Entry next() {
return get(p++, true);
}
public void remove() {
p--;
removeRow(p, true);
}
}
public synchronized final void sort() {
assert (this.rowdef.objectOrder != null);
if (this.sortBound == this.chunkcount) return; // this is already sorted
if (this.chunkcount < isortlimit) {
isort(0, this.chunkcount, new byte[this.rowdef.objectsize]);
this.sortBound = this.chunkcount;
assert this.isSorted();
return;
}
final byte[] swapspace = new byte[this.rowdef.objectsize];
final int p = partition(0, this.chunkcount, this.sortBound, swapspace);
if (sortingthreadexecutor != null &&
!sortingthreadexecutor.isShutdown() &&
availableCPU > 1 &&
this.chunkcount > 8000 &&
p > isortlimit * 5 &&
this.chunkcount - p > isortlimit * 5
) {
// sort this using multi-threading
Future<Integer> part0, part1;
int p0 = -1, p1 = -1;
try {
part0 = partitionthreadexecutor.submit(new partitionthread(this, 0, p, 0));
} catch (RejectedExecutionException e) {
part0 = null;
try {p0 = new partitionthread(this, 0, p, 0).call().intValue();} catch (Exception ee) {}
}
try {
part1 = partitionthreadexecutor.submit(new partitionthread(this, p, this.chunkcount, p));
} catch (RejectedExecutionException e) {
part1 = null;
try {p1 = new partitionthread(this, p, this.chunkcount, p).call().intValue();} catch (Exception ee) {}
}
try {
if (part0 != null) p0 = part0.get().intValue();
Future<Object> sort0, sort1, sort2, sort3;
try {
sort0 = sortingthreadexecutor.submit(new qsortthread(this, 0, p0, 0));
} catch (RejectedExecutionException e) {
sort0 = null;
try {new qsortthread(this, 0, p0, 0).call();} catch (Exception ee) {}
}
try {
sort1 = sortingthreadexecutor.submit(new qsortthread(this, p0, p, p0));
} catch (RejectedExecutionException e) {
sort1 = null;
try {new qsortthread(this, p0, p, p0).call();} catch (Exception ee) {}
}
if (part1 != null) p1 = part1.get().intValue();
try {
sort2 = sortingthreadexecutor.submit(new qsortthread(this, p, p1, p));
} catch (RejectedExecutionException e) {
sort2 = null;
try {new qsortthread(this, p, p1, p).call();} catch (Exception ee) {}
}
try {
sort3 = sortingthreadexecutor.submit(new qsortthread(this, p1, this.chunkcount, p1));
} catch (RejectedExecutionException e) {
sort3 = null;
try {new qsortthread(this, p1, this.chunkcount, p1).call();} catch (Exception ee) {}
}
// wait for all results
if (sort0 != null) sort0.get();
if (sort1 != null) sort1.get();
if (sort2 != null) sort2.get();
if (sort3 != null) sort3.get();
} catch (final InterruptedException e) {
Log.logSevere("RowCollection", "", e);
} catch (final ExecutionException e) {
Log.logSevere("RowCollection", "", e);
}
} else {
qsort(0, p, 0, swapspace);
qsort(p + 1, this.chunkcount, 0, swapspace);
}
this.sortBound = this.chunkcount;
//assert this.isSorted();
}
/*
public synchronized final void sort2() {
assert (this.rowdef.objectOrder != null);
if (this.sortBound == this.chunkcount) return; // this is already sorted
if (this.chunkcount < isortlimit) {
isort(0, this.chunkcount, new byte[this.rowdef.objectsize]);
this.sortBound = this.chunkcount;
assert this.isSorted();
return;
}
final byte[] swapspace = new byte[this.rowdef.objectsize];
final int p = partition(0, this.chunkcount, this.sortBound, swapspace);
if ((sortingthreadexecutor != null) &&
(!sortingthreadexecutor.isShutdown()) &&
(availableCPU > 1) &&
(this.chunkcount > 4000)) {
// sort this using multi-threading
final Future<Object> part = sortingthreadexecutor.submit(new qsortthread(this, 0, p, 0));
//CompletionService<Object> sortingthreadcompletion = new ExecutorCompletionService<Object>(sortingthreadexecutor);
//Future<Object> part = sortingthreadcompletion.submit(new qsortthread(this, 0, p, 0));
qsort(p + 1, this.chunkcount, 0, swapspace);
try {
part.get();
} catch (final InterruptedException e) {
Log.logSevere("RowCollection", "", e);
} catch (final ExecutionException e) {
Log.logSevere("RowCollection", "", e);
}
} else {
qsort(0, p, 0, swapspace);
qsort(p + 1, this.chunkcount, 0, swapspace);
}
this.sortBound = this.chunkcount;
//assert this.isSorted();
}
*/
private static class qsortthread implements Callable<Object> {
private RowCollection rc;
int L, R, S;
public qsortthread(final RowCollection rc, final int L, final int R, final int S) {
this.rc = rc;
this.L = L;
this.R = R;
this.S = S;
}
public Object call() throws Exception {
rc.qsort(L, R, S, new byte[rc.rowdef.objectsize]);
return null;
}
}
final void qsort(final int L, final int R, final int S, final byte[] swapspace) {
if (R - L < isortlimit) {
isort(L, R, swapspace);
return;
}
assert R > L: "L = " + L + ", R = " + R + ", S = " + S;
final int p = partition(L, R, S, swapspace);
assert p >= L: "L = " + L + ", R = " + R + ", S = " + S + ", p = " + p;
assert p < R: "L = " + L + ", R = " + R + ", S = " + S + ", p = " + p;
qsort(L, p, 0, swapspace);
qsort(p + 1, R, 0, swapspace);
}
public static class partitionthread implements Callable<Integer> {
RowCollection rc;
int L, R, S;
public partitionthread(final RowCollection rc, final int L, final int R, final int S) {
this.rc = rc;
this.L = L;
this.R = R;
this.S = S;
}
public Integer call() throws Exception {
return Integer.valueOf(rc.partition(L, R, S, new byte[rc.rowdef.objectsize]));
}
}
/**
* @param L is the first element in the sequence
* @param R is the right bound of the sequence, and outside of the sequence
* @param S is the bound of the sorted elements in the sequence
* @param swapspace
* @return
*/
final int partition(final int L, final int R, int S, final byte[] swapspace) {
assert (L < R - 1): "L = " + L + ", R = " + R + ", S = " + S;
assert (R - L >= isortlimit): "L = " + L + ", R = " + R + ", S = " + S + ", isortlimit = " + isortlimit;
int p = L;
int q = R - 1;
int pivot = pivot(L, R, S);
if (this.rowdef.objectOrder instanceof Base64Order) {
while (p <= q) {
// wenn pivot < S: pivot befindet sich in sortierter Sequenz von L bis S - 1
// d.h. alle Werte von L bis pivot sind kleiner als das pivot
// zu finden ist ein minimales p <= q so dass chunk[p] >= pivot
if ((pivot < S) && (p < pivot)) {
//System.out.println("+++ saved " + (pivot - p) + " comparisments");
p = pivot;
S = 0;
} else {
while ((p < R - 1) && (compare(pivot, p) >= 0)) p++; // chunkAt[p] < pivot
}
// nun gilt chunkAt[p] >= pivot
while ((q > L) && (compare(pivot, q) <= 0)) q--; // chunkAt[q] > pivot
if (p <= q) {
pivot = swap(p, q, pivot, swapspace);
p++;
q--;
}
}
} else {
while (p <= q) {
if ((pivot < S) && (p < pivot)) {
p = pivot;
S = 0;
} else {
while ((p < R - 1) && (compare(pivot, p) >= 0)) p++; // chunkAt[p] < pivot
}
while ((q > L) && (compare(pivot, q) <= 0)) q--; // chunkAt[q] > pivot
if (p <= q) {
pivot = swap(p, q, pivot, swapspace);
p++;
q--;
}
}
}
// now p is the beginning of the upper sequence
// finally, the pivot element should be exactly between the two sequences
// distinguish two cases: pivot in lower and upper sequence
// to do this it is sufficient to compare the index, not the entry content
if (pivot < p) {
// switch the pivot with the element _below_ p, the element in p belongs to the upper sequence
// and does not fit into the lower sequence
swap(pivot, p - 1, pivot, swapspace);
return p - 1;
} else if (pivot > p) {
// switch the pivot with p, they are both in the same sequence
swap(pivot, p, pivot, swapspace);
return p;
}
assert pivot == p;
return p;
}
private final int pivot(final int L, final int R, final int S) {
if (S == 0 || S < L) {
// the collection has no ordering
// or
// the collection has an ordering, but this is not relevant for this pivot
// because the ordered zone is outside of ordering zone
final int m = picMiddle(L, (3 * L + R - 1) / 4, (L + R - 1) / 2, (L + 3 * R - 3) / 4, R - 1);
assert L <= m;
assert m < R;
return m;
}
if (S < R) {
// the collection has an ordering
// and part of the ordered zone is inside the to-be-ordered zone
final int m = picMiddle(L, L + (S - L) / 3, (L + R - 1) / 2, S, R - 1);
assert L <= m;
assert m < R;
return m;
}
// use the sorted set to find good pivot:
// the sort range is fully inside the sorted area:
// the middle element must be the best
// (however, it should be skipped because there is no point in sorting this)
return (L + R - 1) / 2;
}
private final int picMiddle(final int a, final int b, final int c, final int d, final int e) {
return picMiddle(picMiddle(a, b, c), d, e);
}
private final int picMiddle(final int a, final int b, final int c) {
if (compare(a, b) > 0) {
if (compare(c, a) > 0) return a;
if (compare(b, c) > 0) return b;
} else {
if (compare(a, c) > 0) return a;
if (compare(c, b) > 0) return b;
}
return c;
//if (c < a && a < b || a > b && c > a) return a;
//if (a < b && c > b || c < b && a > b) return b;
}
/*
private final int picMiddle(final int[] list, int len) {
assert len % 2 != 0;
assert len <= list.length;
final int cut = list.length / 2;
for (int i = 0; i < cut; i++) {remove(list, len, min(list, len)); len--;}
for (int i = 0; i < cut; i++) {remove(list, len, max(list, len)); len--;}
// the remaining element must be the middle element
assert len == 1;
return list[0];
}
private final void remove(final int[] list, final int len, final int idx) {
if (idx == len - 1) return;
list[idx] = list[len - 1]; // shift last element to front
}
private final int min(final int[] list, int len) {
assert len > 0;
int f = 0;
while (len-- > 0) {
if (compare(list[f], list[len]) > 0) f = len;
}
return f;
}
private final int max(final int[] list, int len) {
assert len > 0;
int f = 0;
while (len-- > 0) {
if (compare(list[f], list[len]) < 0) f = len;
}
return f;
}
*/
private final void isort(final int L, final int R, final byte[] swapspace) {
for (int i = L + 1; i < R; i++)
for (int j = i; j > L && compare(j - 1, j) > 0; j--)
swap(j, j - 1, 0, swapspace);
}
private final int swap(final int i, final int j, final int p, final byte[] swapspace) {
if (i == j) return p;
System.arraycopy(chunkcache, this.rowdef.objectsize * i, swapspace, 0, this.rowdef.objectsize);
System.arraycopy(chunkcache, this.rowdef.objectsize * j, chunkcache, this.rowdef.objectsize * i, this.rowdef.objectsize);
System.arraycopy(swapspace, 0, chunkcache, this.rowdef.objectsize * j, this.rowdef.objectsize);
if (i == p) return j; else if (j == p) return i; else return p;
}
protected synchronized void uniq() {
assert (this.rowdef.objectOrder != null);
// removes double-occurrences of chunks
// this works only if the collection was ordered with sort before
// if the collection is large and the number of deletions is also large,
// then this method may run a long time with 100% CPU load which is caused
// by the large number of memory movements.
if (chunkcount < 2) return;
int i = chunkcount - 2;
final long t = System.currentTimeMillis(); // for time-out
int d = 0;
try {
while (i >= 0) {
if (match(i, i + 1)) {
removeRow(i + 1, true);
d++;
}
i--;
if (System.currentTimeMillis() - t > 60000) {
Log.logWarning("RowCollection", "uniq() time-out at " + i + " (backwards) from " + chunkcount + " elements after " + (System.currentTimeMillis() - t) + " milliseconds; " + d + " deletions so far");
return;
}
}
} catch (final RuntimeException e) {
Log.logWarning("RowCollection", e.getMessage(), e);
}
}
public synchronized ArrayList<RowCollection> removeDoubles() throws RowSpaceExceededException {
assert (this.rowdef.objectOrder != null);
// removes double-occurrences of chunks
// in contrast to uniq() this removes also the remaining, non-double entry that had a double-occurrence to the others
// all removed chunks are returned in an array
this.sort();
final ArrayList<RowCollection> report = new ArrayList<RowCollection>();
if (chunkcount < 2) return report;
int i = chunkcount - 2;
boolean u = true;
RowCollection collection = new RowCollection(this.rowdef, 2);
try {
while (i >= 0) {
if (match(i, i + 1)) {
collection.addUnique(get(i + 1, false));
removeRow(i + 1, false);
if (i + 1 < chunkcount - 1) u = false;
} else if (!collection.isEmpty()) {
// finish collection of double occurrences
collection.addUnique(get(i + 1, false));
removeRow(i + 1, false);
if (i + 1 < chunkcount - 1) u = false;
collection.trim();
report.add(collection);
collection = new RowSet(this.rowdef, 2);
}
i--;
}
} catch (final RuntimeException e) {
Log.logWarning("kelondroRowCollection", e.getMessage(), e);
} finally {
if (!u) this.sort();
}
return report;
}
public synchronized boolean isSorted() {
assert (this.rowdef.objectOrder != null);
if (chunkcount <= 1) return true;
if (chunkcount != this.sortBound) return false;
/*
for (int i = 0; i < chunkcount - 1; i++) {
//System.out.println("*" + new String(get(i).getColBytes(0)));
if (compare(i, i + 1) > 0) {
System.out.println("?" + new String(get(i + 1, false).getColBytes(0)));
return false;
}
}
*/
return true;
}
public synchronized String toString() {
final StringBuilder s = new StringBuilder();
final Iterator<Row.Entry> i = iterator();
if (i.hasNext()) s.append(i.next().toString());
while (i.hasNext()) s.append(", " + (i.next()).toString());
return new String(s);
}
private final int compare(final int i, final int j) {
assert (chunkcount * this.rowdef.objectsize <= chunkcache.length) : "chunkcount = " + chunkcount + ", objsize = " + this.rowdef.objectsize + ", chunkcache.length = " + chunkcache.length;
assert (i >= 0) && (i < chunkcount) : "i = " + i + ", chunkcount = " + chunkcount;
assert (j >= 0) && (j < chunkcount) : "j = " + j + ", chunkcount = " + chunkcount;
assert (this.rowdef.objectOrder != null);
if (i == j) return 0;
//assert (!bugappearance(chunkcache, i * this.rowdef.objectsize + colstart, this.rowdef.primaryKeyLength));
//assert (!bugappearance(chunkcache, j * this.rowdef.objectsize + colstart, this.rowdef.primaryKeyLength));
final int c = this.rowdef.objectOrder.compare(
chunkcache,
i * this.rowdef.objectsize,
chunkcache,
j * this.rowdef.objectsize,
this.rowdef.primaryKeyLength);
return c;
}
protected synchronized int compare(final byte[] a, final int astart, final int chunknumber) {
assert (chunknumber < chunkcount);
assert a.length - astart >= this.rowdef.primaryKeyLength;
final int len = Math.min(a.length - astart, this.rowdef.primaryKeyLength);
return rowdef.objectOrder.compare(a, astart, chunkcache, chunknumber * this.rowdef.objectsize, len);
}
protected final boolean match(final int i, final int j) {
assert (chunkcount * this.rowdef.objectsize <= chunkcache.length) : "chunkcount = " + chunkcount + ", objsize = " + this.rowdef.objectsize + ", chunkcache.length = " + chunkcache.length;
assert (i >= 0) && (i < chunkcount) : "i = " + i + ", chunkcount = " + chunkcount;
assert (j >= 0) && (j < chunkcount) : "j = " + j + ", chunkcount = " + chunkcount;
if (i >= chunkcount) return false;
if (j >= chunkcount) return false;
assert (this.rowdef.objectOrder != null);
if (i == j) return true;
int astart = i * this.rowdef.objectsize;
int bstart = j * this.rowdef.objectsize;
int k = this.rowdef.primaryKeyLength;
while (k-- != 0) {
if (chunkcache[astart++] != chunkcache[bstart++]) return false;
}
return true;
}
protected synchronized boolean match(final byte[] a, int astart, final int chunknumber) {
if (chunknumber >= chunkcount) return false;
int p = chunknumber * this.rowdef.objectsize;
assert a.length - astart >= this.rowdef.primaryKeyLength;
int len = Math.min(a.length - astart, this.rowdef.primaryKeyLength);
while (len-- != 0) {
if (a[astart++] != chunkcache[p++]) return false;
}
return true;
}
public synchronized void close() {
chunkcache = null;
}
private static long d(final long a, final long b) {
if (b == 0) return a;
return a / b;
}
private static Random random = null;
private static String randomHash() {
return
Base64Order.enhancedCoder.encodeLong(random.nextLong(), 4) +
Base64Order.enhancedCoder.encodeLong(random.nextLong(), 4) +
Base64Order.enhancedCoder.encodeLong(random.nextLong(), 4);
}
public static void test(final int testsize) throws RowSpaceExceededException {
final Row r = new Row(new Column[]{
new Column("hash", Column.celltype_string, Column.encoder_bytes, 12, "hash")},
Base64Order.enhancedCoder);
RowCollection a = new RowCollection(r, testsize);
a.add("AAAAAAAAAAAA".getBytes());
a.add("BBBBBBBBBBBB".getBytes());
a.add("BBBBBBBBBBBB".getBytes());
a.add("BBBBBBBBBBBB".getBytes());
a.add("CCCCCCCCCCCC".getBytes());
final ArrayList<RowCollection> del = a.removeDoubles();
System.out.println(del + "rows double");
final Iterator<Row.Entry> j = a.iterator();
while (j.hasNext()) System.out.println(new String(j.next().bytes()));
System.out.println("kelondroRowCollection test with size = " + testsize);
a = new RowCollection(r, testsize);
long t0 = System.nanoTime();
random = new Random(0);
for (int i = 0; i < testsize; i++) a.add(randomHash().getBytes());
random = new Random(0);
for (int i = 0; i < testsize; i++) a.add(randomHash().getBytes());
a.sort();
a.uniq();
long t1 = System.nanoTime();
System.out.println("create a : " + (t1 - t0) + " nanoseconds, " + d(testsize, (t1 - t0)) + " entries/nanoseconds; a.size() = " + a.size());
final RowCollection c = new RowCollection(r, testsize);
random = new Random(0);
t0 = System.nanoTime();
for (int i = 0; i < testsize; i++) {
c.add(randomHash().getBytes());
}
t1 = System.nanoTime();
System.out.println("create c : " + (t1 - t0) + " nanoseconds, " + d(testsize, (t1 - t0)) + " entries/nanoseconds");
final RowCollection d = new RowCollection(r, testsize);
for (int i = 0; i < testsize; i++) {
d.add(c.get(i, false).getColBytes(0, false));
}
final long t2 = System.nanoTime();
System.out.println("copy c -> d: " + (t2 - t1) + " nanoseconds, " + d(testsize, (t2 - t1)) + " entries/nanoseconds");
//availableCPU = 1;
c.sort();
final long t3 = System.nanoTime();
System.out.println("sort c (1) : " + (t3 - t2) + " nanoseconds, " + d(testsize, (t3 - t2)) + " entries/nanoseconds");
//availableCPU = 2;
d.sort();
final long t4 = System.nanoTime();
System.out.println("sort d (2) : " + (t4 - t3) + " nanoseconds, " + d(testsize, (t4 - t3)) + " entries/nanoseconds");
c.uniq();
final long t5 = System.nanoTime();
System.out.println("uniq c : " + (t5 - t4) + " nanoseconds, " + d(testsize, (t5 - t4)) + " entries/nanoseconds");
d.uniq();
final long t6 = System.nanoTime();
System.out.println("uniq d : " + (t6 - t5) + " nanoseconds, " + d(testsize, (t6 - t5)) + " entries/nanoseconds");
random = new Random(0);
final RowSet e = new RowSet(r, testsize);
for (int i = 0; i < testsize; i++) {
e.put(r.newEntry(randomHash().getBytes()));
}
final long t7 = System.nanoTime();
System.out.println("create e : " + (t7 - t6) + " nanoseconds, " + d(testsize, (t7 - t6)) + " entries/nanoseconds");
e.sort();
final long t8 = System.nanoTime();
System.out.println("sort e (2) : " + (t8 - t7) + " nanoseconds, " + d(testsize, (t8 - t7)) + " entries/nanoseconds");
e.uniq();
final long t9 = System.nanoTime();
System.out.println("uniq e : " + (t9 - t8) + " nanoseconds, " + d(testsize, (t9 - t8)) + " entries/nanoseconds");
final boolean cis = c.isSorted();
final long t10 = System.nanoTime();
System.out.println("c isSorted = " + ((cis) ? "true" : "false") + ": " + (t10 - t9) + " nanoseconds");
final boolean dis = d.isSorted();
final long t11 = System.nanoTime();
System.out.println("d isSorted = " + ((dis) ? "true" : "false") + ": " + (t11 - t10) + " nanoseconds");
final boolean eis = e.isSorted();
final long t12 = System.nanoTime();
System.out.println("e isSorted = " + ((eis) ? "true" : "false") + ": " + (t12 - t11) + " nanoseconds");
random = new Random(0);
boolean allfound = true;
for (int i = 0; i < testsize; i++) {
final String rh = randomHash();
if (e.get(rh.getBytes()) == null) {
allfound = false;
System.out.println("not found hash " + rh + " at attempt " + i);
break;
}
}
final long t13 = System.nanoTime();
System.out.println("e allfound = " + ((allfound) ? "true" : "false") + ": " + (t13 - t12) + " nanoseconds");
boolean noghosts = true;
for (int i = 0; i < testsize; i++) {
if (e.get(randomHash().getBytes()) != null) {
noghosts = false;
break;
}
}
final long t14 = System.nanoTime();
System.out.println("e noghosts = " + ((noghosts) ? "true" : "false") + ": " + (t14 - t13) + " nanoseconds");
System.out.println("Result size: c = " + c.size() + ", d = " + d.size() + ", e = " + e.size());
System.out.println();
if (sortingthreadexecutor != null) sortingthreadexecutor.shutdown();
}
public static void main(final String[] args) {
//test(1000);
try {
test(50000);
} catch (RowSpaceExceededException e) {
e.printStackTrace();
}
//test(100000);
//test(1000000);
/*
System.out.println(new java.util.Date(10957 * day));
System.out.println(new java.util.Date(0));
System.out.println(daysSince2000(System.currentTimeMillis()));
*/
}
}
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