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A fast java serialization drop in-replacement and some serialization based utils such as Structs and OffHeap Memory.
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/*
* Copyright 2014 Ruediger Moeller.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.nustaq.offheap;
import org.nustaq.logging.FSTLogger;
import org.nustaq.offheap.bytez.ByteSource;
import org.nustaq.offheap.bytez.bytesource.AsciiStringByteSource;
import org.nustaq.offheap.bytez.bytesource.BytezByteSource;
import org.nustaq.offheap.bytez.Bytez;
import org.nustaq.offheap.bytez.bytesource.LeftCutStringByteSource;
import org.nustaq.offheap.bytez.bytesource.UTFStringByteSource;
import org.nustaq.offheap.bytez.malloc.MMFBytez;
import org.nustaq.offheap.bytez.malloc.MallocBytez;
import org.nustaq.offheap.bytez.malloc.MallocBytezAllocator;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ConcurrentModificationException;
import java.util.Iterator;
/**
* Baseclass of offheap maps.
* FST OffHeap Maps enable to store key/value pairs in offheap memory. Additionally it provides
* and iterator interface for all values. In order to also iterate keys, add each key to its value object,
* as this OffHeap map does not support iteration of keys out of the box.
*
* See subclasses for directly applicable classes (E.g. FSTStringOffheapMap)
*
* The base is a generic bytesource to bytesource map. Note that key should be as short as possible (4-20 bytes) and
* should have their most modified digit at the last character of their value.
* e.g. [0,0,0,0,123,44] where '44' changes with each new key. Else on-heap memory consumption will grow.
* Performance of lookup degrades with growing key size.
*
* In case entries are updated frequently with values of different size, avoid fragementation
* by adding extra space to each entry. Override getEntryLengthForContentLength for this.
*/
public class FSTBinaryOffheapMap {
// FIXME: Testcase for mem overflow
public static final long MB = 1024 * 1024;
public static final long GB = 1024 * MB;
public static final int CUSTOM_FILEHEADER_LEN = 8000; // 8k for application
public static final int CORE_HEADER_LEN = 8;
public static final int FILE_HEADER_LEN = CORE_HEADER_LEN +CUSTOM_FILEHEADER_LEN; // 0 - numelems, 4 - magic num
final static int HEADER_TAG = 0xe5e1; // can be used to recover corrupted data
public static final int KEY_OFFSET_IN_HEADER = 16;
private BytezByteSource tmpValueBytez;
protected OffHeapByteTree index;
protected Bytez memory;
protected Bytez customHeader;
protected MallocBytezAllocator alloc;
protected int numElem;
protected int keyLen;
protected long bytezOffset;
protected FreeList freeList;// FIXME: missing merge/split of different block sizes
protected String mappedFile;
protected int mutationCount;
public FSTBinaryOffheapMap(String mappedFile, int keyLen, long sizeMemBytes, int numberOfElems) throws Exception {
initFromFile(mappedFile, keyLen, sizeMemBytes, numberOfElems);
}
Thread debug;
private void checkThread() {
// if ( debug == null )
// debug = Thread.currentThread();
// else {
// if ( debug != Thread.currentThread() )
// throw new RuntimeException( "unexpected concurrency "+debug.getName()+" curr:" + Thread.currentThread().getName() );
// }
}
public Bytez getCustomFileHeader() {
return customHeader;
}
protected void initFromFile(String file, int keyLen, long sizeMemBytes, int numberOfElems) throws Exception {
checkThread();
numElem = 0;
bytezOffset = FILE_HEADER_LEN;
freeList = new FreeList(); // FIXME: missing merge/split of different block sizes
this.mappedFile = file;
if ( new File(file).exists() )
resetMem(file, new File(file).length());
else
resetMem(file, sizeMemBytes);
this.keyLen = keyLen;
if ( memory.getInt(4) != HEADER_TAG || memory.getInt(0) <= 0 ) {
// newly created or empty file
index = new OffHeapByteTree(keyLen,OffHeapByteTree.estimateMBytesForIndex(keyLen,numberOfElems));
memory.putInt(4,HEADER_TAG);
System.out.println("new file detected "+file);
} else {
// FIXME: be more resilent in case of corruption ..
numElem = memory.getInt(0);
index = new OffHeapByteTree(keyLen,OffHeapByteTree.estimateMBytesForIndex(keyLen,numElem*2));
long off = FILE_HEADER_LEN;
int elemCount = 0;
BytezByteSource byteIter = new BytezByteSource(memory,0,0);
long tim = System.currentTimeMillis();
while (elemCount < numElem) {
int len = getLenFromHeader(off);
boolean removed = memory.get(off+4) != 0;
if ( ! removed ) {
elemCount++;
byteIter.setOff(off + KEY_OFFSET_IN_HEADER); // 16 = offset of key in header
byteIter.setLen(keyLen);
index.put(byteIter, off);
bytezOffset = off+getHeaderLen()+len;
} else {
addToFreeList(off);
}
off+= getHeaderLen() + len;
}
FSTLogger.getLogger(getClass()).log(FSTLogger.Level.INFO,"boot "+numElem+" records in "+(System.currentTimeMillis()-tim)+"ms",null);
}
}
private void resetMem(String file, long sizeMemBytes) throws Exception {
checkThread();
mutationCount++;
memory = new MMFBytez(file,sizeMemBytes,false);
customHeader = memory.slice(CORE_HEADER_LEN, CUSTOM_FILEHEADER_LEN);
tmpValueBytez = new BytezByteSource(memory,0,0);
}
public FSTBinaryOffheapMap(int keyLen, long sizeMemBytes, int numberOfElems) {
init(keyLen, sizeMemBytes, numberOfElems);
}
protected void init(int keyLen, long sizeMemBytes, int numberOfElems) {
checkThread();
numElem = 0;
bytezOffset = FILE_HEADER_LEN;
freeList = new FreeList(); // FIXME: missing merge/split of different block sizes
alloc = new MallocBytezAllocator();
memory = alloc.alloc(sizeMemBytes);
customHeader = memory.slice(CORE_HEADER_LEN,CUSTOM_FILEHEADER_LEN);
tmpValueBytez = new BytezByteSource(memory,0,0);
this.keyLen = keyLen;
index = new OffHeapByteTree(keyLen,OffHeapByteTree.estimateMBytesForIndex(keyLen,numberOfElems));
memory.putInt(4, HEADER_TAG);
}
@Override
protected void finalize() throws Throwable {
free();
}
public void free() {
checkThread();
mutationCount++;
if ( alloc != null ) {
alloc.freeAll();
alloc = null;
}
if ( memory instanceof MMFBytez ) {
((MMFBytez) memory).freeAndClose();
memory = null;
}
// index.free();
index = null;
}
public void putBinary( ByteSource key, ByteSource value ) {
checkThread();
if ( key.length() != keyLen )
throw new RuntimeException("key must have length "+keyLen);
mutationCount++;
long put = index.get(key);
if ( put != 0 ) {
int lenFromHeader = getLenFromHeader(put);
if (value.length() <= lenFromHeader) {
// replace
setEntry(put, lenFromHeader, value);
index.put(key, put);
return;
}
// set removed and fall through to add
index.put(key, addEntry(key, value));
removeEntry(put);
} else {
// add
index.put(key, addEntry(key, value));
incElems();
}
}
protected void removeEntry(long offset) {
checkThread();
mutationCount++;
addToFreeList(offset);
memory.put(offset + 4, (byte) 1);
}
protected void addToFreeList(long offset) {
freeList.addToFree(offset, getLenFromHeader(offset) + getHeaderLen());
}
protected void setEntry(long off, int entryLen, ByteSource value) {
checkThread();
mutationCount++;
writeEntryHeader(off, entryLen, (int) value.length(), false);
off += getHeaderLen();
for ( int i = 0; i < value.length(); i++ ) {
memory.put( off++, value.get(i) );
}
}
protected long addEntry(ByteSource key, ByteSource value) {
checkThread();
mutationCount++;
long valueLength = value.length();
long newOffset = freeList.findFreeBlock( (int) valueLength + getHeaderLen() );
if ( newOffset > 0) {
// System.out.println("reuse len "+getLenFromHeader(newOffset)+" at "+newOffset+" entrylen "+(getLenFromHeader(newOffset)+getHeaderLen()));
writeEntryHeader(newOffset,getLenFromHeader(newOffset),(int) valueLength,false);
long l = newOffset;
// put key
for ( int ii = 0; ii < keyLen; ii++ ) {
memory.put( 16+l+ii, key.get(ii) );
}
l += getHeaderLen();
// put value
for ( int ii = 0; ii < valueLength; ii++ ) {
memory.put( l++, value.get(ii) );
}
return newOffset;
}
int entryLen = getEntryLengthForContentLength(value.length());
// size to power of 2
entryLen = freeList.computeLen(entryLen+getHeaderLen())-getHeaderLen();
if ( memory.length() <= bytezOffset+entryLen+getHeaderLen()) {
resizeStore(bytezOffset + entryLen + getHeaderLen());
// return addEntry(key,value); // fixme loses one freelist entry
}
long res = bytezOffset;
writeEntryHeader(bytezOffset, entryLen,(int)value.length(),false);
// put key
for ( int ii = 0; ii < keyLen; ii++ ) {
memory.put( 16+bytezOffset+ii, key.get(ii) );
}
long off = bytezOffset+getHeaderLen();
for ( int i = 0; i < value.length(); i++ ) {
memory.put( off++, value.get(i) );
}
bytezOffset+=entryLen+getHeaderLen();
return res;
}
private void resizeStore(long required) {
resizeStore(required,GB);
}
/**
* PRIVILEGED method. You gotta know what your doing here ..
*
* currently a very expensive operation .. frees everything, resize file and remap.
* Remapping involves rebuild of index.
* @param required
*/
public void resizeStore(long required, long maxgrowbytes) {
if ( mappedFile == null )
throw new RuntimeException("store is full. Required: "+required);
if ( required <= memory.length() )
return;
mutationCount++;
long newSize = Math.min(required*2,required+maxgrowbytes);
System.out.println("resizing underlying "+mappedFile+" to "+newSize+" numElem:"+numElem);
long tim = System.currentTimeMillis();
((MMFBytez) memory).freeAndClose();
memory = null;
try {
resetMem(mappedFile, newSize);
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("resizing done in "+(System.currentTimeMillis()-tim)+" numElemAfter:"+numElem);
}
/**
* get an entry. the returned ByteSource must be processed immediately as it will be reused
* internally on next get
* Warning: Concurrent Modification (e.g. add remove elements during iteration) is NOT SUPPORTED
* and NOT CHECKED. Collect keys to change inside iteration and perform changes after iteration is
* finished.
* @param key
* @return
*/
public BytezByteSource getBinary( ByteSource key ) {
checkThread();
if ( key.length() != keyLen )
throw new RuntimeException("key must have length "+keyLen);
long aLong = index.get(key);
if ( aLong == 0 ) {
return null;
}
long off = aLong;
int len = getContentLenFromHeader(off);
off+= getHeaderLen();
tmpValueBytez.setLen(len);
tmpValueBytez.setOff(off);
return tmpValueBytez;
}
/**
* remove the key from the binary map
* @param key
*/
public void removeBinary( ByteSource key ) {
checkThread();
if ( key.length() != keyLen )
throw new RuntimeException("key must have length "+keyLen);
mutationCount++;
long rem = index.get(key);
if ( rem != 0 ) {
index.remove(key);
decElems();
removeEntry(rem);
}
}
protected void decElems() {
numElem--;
memory.putInt(0, numElem);
}
protected void incElems() {
numElem++;
memory.putInt(0, numElem);
}
/**
* called upon add, allows to reserve extra space for later growth per entry
* @param lengthOfEntry
* @return
*/
protected int getEntryLengthForContentLength(long lengthOfEntry) {
return (int) lengthOfEntry;
}
protected void writeEntryHeader( long offset, int entryLen, int contentLen, boolean removed ) {
checkThread();
mutationCount++;
memory.putInt( offset, entryLen );
memory.put( offset + 4, (byte) (removed ? 1 : 0));
memory.putInt( offset + 8, contentLen);
memory.putInt( offset + 12, HEADER_TAG);
}
protected int getHeaderLen() {
return 4+4+4+4+keyLen; // 0-3 len, 4 removed flag, 5-7 free, 8-11 content len, 12-15 magic num, 16... key
}
// overall content size (excl header)
protected int getLenFromHeader(long off) {
return memory.getInt(off);
}
protected int getContentLenFromHeader(long off) {
return memory.getInt(off+8);
}
public Iterator binaryValues() {
checkThread();
return new Iterator() {
long off = FILE_HEADER_LEN;
int elemCount = 0;
int mutSnap = mutationCount;
BytezByteSource byteIter = new BytezByteSource(memory,0,0);
@Override
public boolean hasNext() {
return elemCount < numElem;
}
@Override
public ByteSource next() {
checkThread();
int contentLen = getContentLenFromHeader(off);
int len = getLenFromHeader(off);
boolean removed = memory.get(off+4) != 0;
off+= getHeaderLen();
while ( removed ) {
off += len;
len = getLenFromHeader(off);
contentLen = getContentLenFromHeader(off);
removed = memory.get(off+4) != 0;
off+= getHeaderLen();
}
elemCount++;
byteIter.setOff(off);
byteIter.setLen(contentLen);
off+=len;
if ( mutSnap != mutationCount )
throw new ConcurrentModificationException("in offheap map snap:"+mutSnap+" current:"+mutationCount);
return byteIter;
}
@Override
public void remove() {
throw new RuntimeException("unimplemented");
}
};
}
public String printBinaryKey(ByteSource key) {
StringBuilder res = new StringBuilder();
for ( int i = 0; i < key.length(); i++ ) {
byte b = key.get(i);
if ( b > 31 ) {
res.append((char) b);
} else {
res.append('_');
}
}
return res.toString();
}
public KeyValIter binaryKeys() {
checkThread();
return new KeyValIter() {
long off = FILE_HEADER_LEN;
int elemCount = 0;
int mutSnap = mutationCount;
BytezByteSource byteIter = new BytezByteSource(memory,0,0);
BytezByteSource byteVal = new BytezByteSource(memory,0,0);
long valueAddress;
@Override
public boolean hasNext() {
return elemCount < numElem;
}
@Override
public ByteSource next() {
checkThread();
int len = getLenFromHeader(off);
int contentLen = getContentLenFromHeader(off);
boolean removed = memory.get(off+4) != 0;
off+= getHeaderLen();
while ( removed ) {
off += len;
len = getLenFromHeader(off);
contentLen = getContentLenFromHeader(off);
removed = memory.get(off+4) != 0;
off+= getHeaderLen();
}
elemCount++;
valueAddress = off;
byteVal.setOff(off);
byteVal.setLen(contentLen);
byteIter.setOff(off-getHeaderLen()+16);
byteIter.setLen(keyLen);
off+=len;
if ( mutSnap != mutationCount )
throw new ConcurrentModificationException("in offheap map snap:"+mutSnap+" current:"+mutationCount);
return byteIter;
}
@Override
public void remove() {
throw new RuntimeException("unimplemented");
}
@Override
public ByteSource getValueBytes() {
return byteVal;
}
@Override
public long getValueAddress() {
return valueAddress;
}
};
}
public long getFreeMem() {
return memory.length()-bytezOffset;
}
public long getUsedMem() {
return bytezOffset;
}
public int getCapacityMB() { return (int) (memory.length()/1024l/1024l); }
public int getSize() {
return numElem;
}
public void dumpIndexStats() {
index.dumpStats();
}
public String getFileName() {
return mappedFile;
}
public static interface KeyValIter extends Iterator {
public ByteSource getValueBytes();
public long getValueAddress();
}
public static void main(String[] args) throws Exception {
FSTAsciiStringOffheapMap map = new FSTAsciiStringOffheapMap("/tmp/omap.bin",64,10000, 10);
if ( false ) {
for ( int i = 0; i < 1000; i++ ) {
map.put(""+i, "Hello"+i);
}
}
for ( int i = 0; i < 1000; i++ ) {
System.out.println(map.get("" + i));
}
}
}
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