package ivory.lsh.pwsim;
import ivory.core.RetrievalEnvironment;
import ivory.lsh.data.BitsSignatureTable;
import ivory.lsh.data.PairOfIntSignature;
import ivory.lsh.data.Permutation;
import ivory.lsh.data.PermutationByBit;
import ivory.lsh.data.Signature;
import ivory.lsh.driver.PwsimEnvironment;
import java.io.IOException;
import java.lang.reflect.Constructor;
import java.net.URI;
import java.util.Iterator;
import java.util.List;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.GnuParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.hadoop.conf.Configured;
import org.apache.hadoop.filecache.DistributedCache;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.IntWritable;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Writable;
import org.apache.hadoop.mapred.FileInputFormat;
import org.apache.hadoop.mapred.FileOutputFormat;
import org.apache.hadoop.mapred.JobClient;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Partitioner;
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
import org.apache.hadoop.mapred.SequenceFileInputFormat;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.hadoop.util.Tool;
import org.apache.hadoop.util.ToolRunner;
import org.apache.log4j.Level;
import org.apache.log4j.Logger;
import tl.lin.data.array.ArrayListOfIntsWritable;
import edu.umd.cloud9.io.SequenceFileUtils;
@SuppressWarnings("deprecation")
public class GenerateChunkedPermutedTables extends Configured implements Tool {
private static final Logger sLogger = Logger.getLogger(GenerateChunkedPermutedTables.class);
static {
sLogger.setLevel(Level.WARN);
}
static enum Count {
Signatures, Chunks, SignaturesInChunks
}
private void printUsage() {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp( this.getClass().getCanonicalName(), options );
}
/**
* @author ferhanture
*
* Maps each signature to Q random permutations, usign the permuters stored in local cache
* file <docno,signature> --> <(permno,signature),docno>
*/
@SuppressWarnings("unchecked")
public static class MyMapper extends MapReduceBase implements
Mapper<IntWritable, Signature, PairOfIntSignature, IntWritable> {
static Path[] localFiles;
static List<Writable> randomPermutations;
static int numOfPermutations, numOfBits;
static Signature permutedSignature;
static Constructor pairConstructor;
static PairOfIntSignature pair;
private String getFilename(String s) {
return s.substring(s.lastIndexOf("/") + 1);
}
public void configure(JobConf job) {
numOfPermutations = job.getInt("Ivory.NumOfPermutations", -1);
numOfBits = job.getInt("Ivory.NumOfBits", -1);
Class signatureClass = null;
try {
Class pairClass = Class.forName(job.get("Ivory.PairClass"));
pairConstructor = pairClass.getConstructor(int.class, Signature.class);
signatureClass = Class.forName(job.get("Ivory.SignatureClass"));
Constructor intConstructor = signatureClass.getConstructor(int.class);
permutedSignature = (Signature) intConstructor.newInstance(numOfBits);
pair = (PairOfIntSignature) pairConstructor.newInstance(0, permutedSignature);
} catch (Exception e) {
throw new RuntimeException("config exception: \n" + e.toString());
}
sLogger.debug("Reading permutations file....");
String randomPermsFile = job.get("Ivory.RandomPermsFile");
try {
randomPermsFile = getFilename(randomPermsFile);
localFiles = DistributedCache.getLocalCacheFiles(job);
for (Path localFile : localFiles) {
if (localFile.toString().contains(randomPermsFile)) {
randomPermutations = SequenceFileUtils.readValues(localFile, FileSystem.getLocal(job));
}
}
if (randomPermutations == null) throw new RuntimeException("Not found in local cache: " + randomPermsFile);
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException("Error reading random permutations " + randomPermsFile);
}
sLogger.debug("Done reading file.");
}
public void map(IntWritable docno, Signature signature,
OutputCollector<PairOfIntSignature, IntWritable> output, Reporter reporter)
throws IOException {
// Map each signature to Q random permutations
for (int i = 0; i < numOfPermutations; i++) {
signature.perm((ArrayListOfIntsWritable) randomPermutations.get(i), permutedSignature);
pair.setInt(i);
pair.setSignature(permutedSignature);
output.collect(pair, docno);
}
reporter.incrCounter(Count.Signatures, 1);
}
}
public static class MyPartitioner implements Partitioner<PairOfIntSignature, IntWritable> {
// partition with permutation number only
public int getPartition(PairOfIntSignature key, IntWritable value, int numReducers) {
return key.getInt() % numReducers;
}
public void configure(JobConf conf) {
}
}
public static class MyReducer extends MapReduceBase implements
Reducer<PairOfIntSignature, IntWritable, IntWritable, BitsSignatureTable> {
static int permNo = -1;
Signature[] signatures = null;
int[] docNos = null;
int curTableSize = 0;
int overlapSize = -1;
int chunckSize = -1;
public void configure(JobConf conf) {
// sLogger.setLevel(Level.DEBUG);
overlapSize = conf.getInt("Ivory.OverlapSize", -1);
chunckSize = conf.getInt("Ivory.ChunckSize", -1);
if (overlapSize >= chunckSize)
throw new RuntimeException("Invalid Ivory.OverlapSize(" +
overlapSize + ") or Ivory.ChunkSize(" + chunckSize + ")");
signatures = new Signature[chunckSize];
docNos = new int[chunckSize];
}
BitsSignatureTable table = new BitsSignatureTable();
IntWritable outKey = new IntWritable();
OutputCollector<IntWritable, BitsSignatureTable> mOutput = null;
PairOfIntSignature lastKey = null;
Reporter mReporter = null;
public void reduce(PairOfIntSignature key, Iterator<IntWritable> val,
OutputCollector<IntWritable, BitsSignatureTable> output, Reporter reporter)
throws IOException {
mReporter = reporter;
mOutput = output;
lastKey = key;
while (val.hasNext()) {
docNos[curTableSize] = val.next().get();
signatures[curTableSize] = key.getSignature();
curTableSize++;
if (curTableSize == chunckSize) {
table.set(signatures, docNos, curTableSize);
outKey.set(key.getInt());
output.collect(outKey, table);
reporter.incrCounter(Count.SignaturesInChunks, table.getNumOfSignatures());
reporter.incrCounter(Count.Chunks, 1);
shiftOverlap();
}
}
}
private void shiftOverlap() {
if (overlapSize >= curTableSize)
return;
// overlapSize < curTableSize ==> shift up
int j = 0;
for (int i = curTableSize - overlapSize; i < curTableSize; i++) {
signatures[j] = signatures[i];
docNos[j] = docNos[i];
j++;
}
curTableSize = j;
}
@Override
public void close() throws IOException {
if (curTableSize == 0 || mOutput == null)
return;
table.set(signatures, docNos, curTableSize);
outKey.set(lastKey.getInt());
mOutput.collect(outKey, table);
mReporter.incrCounter(Count.SignaturesInChunks, table.getNumOfSignatures());
mReporter.incrCounter(Count.Chunks, 1);
// sLogger.debug(nSignaturesRead);
}
}
// create Q permutation functions and write them to file
public static String createPermutations(FileSystem fs, JobConf job, String rootPath, int numBits,
int numOfPermutations) throws Exception {
String randomPermFile = PwsimEnvironment.getPermutationsFile(rootPath, fs, numBits, numOfPermutations);
if (fs.exists(new Path(randomPermFile))) {
sLogger.info("Random permutations output path already exists!");
return randomPermFile;
}
SequenceFile.Writer writer = SequenceFile.createWriter(fs, job, new Path(randomPermFile),
IntWritable.class, ArrayListOfIntsWritable.class);
Permutation p = new PermutationByBit(numBits);
for (int i = 0; i < numOfPermutations; i++) {
ArrayListOfIntsWritable perm = p.nextPermutation();
writer.append(new IntWritable(i), perm);
sLogger.debug(i + ":" + perm);
}
writer.close();
sLogger.info("Random permutations written.");
return randomPermFile;
}
public int run(String[] args) throws Exception {
sLogger.setLevel(Level.INFO);
JobConf job = new JobConf(getConf(), GenerateChunkedPermutedTables.class);
if ( parseArgs(args, job) < 0 ) {
printUsage();
System.exit(-1);
}
FileSystem fs = FileSystem.get(job);
job.setJobName(this.getClass().getCanonicalName() + "_" + numOfPermutations + "_" + signatureType + "_" + numOfBits);
PwsimEnvironment.setClassTypes(signatureType, job);
if (fs.exists(new Path(outputPath))) {
sLogger.info("Permuted tables already exist! Quitting...");
return 0;
}
// create Q permutation functions and write them to file
String randomPermFile = createPermutations(fs, job, workDir, numOfBits, numOfPermutations);
job.set("Ivory.RandomPermsFile", randomPermFile);
DistributedCache.addCacheFile(new URI(randomPermFile), job);
FileInputFormat.addInputPath(job, new Path(trgInputPath));
if (srcInputPath != null) {
FileInputFormat.addInputPath(job, new Path(srcInputPath));
}
Path[] paths = FileInputFormat.getInputPaths(job);
for (Path path : paths) {
sLogger.info("Added input: " + path);
}
FileOutputFormat.setOutputPath(job, new Path(outputPath));
FileOutputFormat.setCompressOutput(job, false);
job.setInt("Ivory.NumOfPermutations", numOfPermutations);
job.setInt("Ivory.NumOfBits", numOfBits);
job.setInt("Ivory.OverlapSize", chunkOverlapSize);
job.setInt("Ivory.ChunckSize", chunkSize);
job.set("mapred.child.java.opts", "-Xmx2048m");
job.setInt("mapred.task.timeout", 600000000);
job.setJarByClass(GenerateChunkedPermutedTables.class);
job.setNumMapTasks(100);
job.setNumReduceTasks(numOfPermutations);
job.setInputFormat(SequenceFileInputFormat.class);
job.setMapOutputKeyClass(Class.forName(job.get("Ivory.PairClass")));
job.setMapOutputValueClass(IntWritable.class);
job.setOutputKeyClass(IntWritable.class);
job.setOutputValueClass(BitsSignatureTable.class);
job.setMapperClass(MyMapper.class);
job.setReducerClass(MyReducer.class);
job.setPartitionerClass(MyPartitioner.class);
job.setOutputFormat(SequenceFileOutputFormat.class);
sLogger.info("Running job " + job.getJobName() + "...");
sLogger.info("Output path: " + outputPath);
sLogger.info("Number of bits/signature(D): " + numOfBits);
sLogger.info("Number of permutations(Q): " + numOfPermutations);
sLogger.info("Overlap size: " + chunkOverlapSize);
sLogger.info("Chunk size: " + chunkSize);
long startTime = System.currentTimeMillis();
JobClient.runJob(job);
System.out.println("Job finished in " + (System.currentTimeMillis() - startTime) / 1000.0 + " seconds");
return 0;
}
private Options options;
private int numOfPermutations, numOfBits, chunkOverlapSize, slidingWindowSize, chunkSize;
private String signatureType, trgInputPath, srcInputPath, outputPath, workDir, srcWorkDir;
private static final String SOURCE_INPUT_OPTION = "sourceindex";
private static final String INPUT_OPTION = "index";
private static final String SIGNLENG_OPTION = "num_bits";
private static final String SIGNTYPE_OPTION = "type";
private static final String NUMPERMS_OPTION = "Q";
private static final String OVERLAPSIZE_OPTION = "overlap";
private static final String LIBJARS_OPTION = "libjars";
private static final String WINDOWSIZE_OPTION = "B";
@SuppressWarnings("static-access")
private int parseArgs(String[] args, JobConf conf) throws Exception {
FileSystem fs = FileSystem.get(conf);
options = new Options();
options.addOption(OptionBuilder.withDescription("path to source-language index directory").withArgName("path").hasArg().create(SOURCE_INPUT_OPTION));
options.addOption(OptionBuilder.withDescription("path to (target-language) index directory").withArgName("path").hasArg().isRequired().create(INPUT_OPTION));
options.addOption(OptionBuilder.withDescription("length of signature").withArgName("number of bits").hasArg().isRequired().create(SIGNLENG_OPTION));
options.addOption(OptionBuilder.withDescription("type of signature").withArgName("random|minhash|simhash").hasArg().isRequired().create(SIGNTYPE_OPTION));
options.addOption(OptionBuilder.withDescription("sliding window size").withArgName("window").hasArg().create(WINDOWSIZE_OPTION));
options.addOption(OptionBuilder.withDescription("number of permutations (tables)").withArgName("permutations").hasArg().isRequired().create(NUMPERMS_OPTION));
options.addOption(OptionBuilder.withDescription("size of overlap between chunks (default: window size)").withArgName("overlap size").hasArg().create(OVERLAPSIZE_OPTION));
options.addOption(OptionBuilder.withDescription("Hadoop option to load external jars").withArgName("jar packages").hasArg().create(LIBJARS_OPTION));
CommandLine cmdline;
CommandLineParser parser = new GnuParser();
try {
cmdline = parser.parse(options, args);
} catch (ParseException exp) {
System.err.println("Error parsing command line: " + exp.getMessage());
return -1;
}
srcWorkDir = cmdline.hasOption(SOURCE_INPUT_OPTION) ? cmdline.getOptionValue(SOURCE_INPUT_OPTION) : null;
workDir = cmdline.getOptionValue(INPUT_OPTION);
numOfBits = Integer.parseInt(cmdline.getOptionValue(SIGNLENG_OPTION));
signatureType = cmdline.getOptionValue(SIGNTYPE_OPTION);
numOfPermutations = Integer.parseInt(cmdline.getOptionValue(NUMPERMS_OPTION));
slidingWindowSize = cmdline.hasOption(WINDOWSIZE_OPTION) ? Integer.parseInt(cmdline.getOptionValue(WINDOWSIZE_OPTION)) : 0;
srcInputPath = PwsimEnvironment.getSignaturesDir(srcWorkDir, numOfBits, signatureType);
trgInputPath = PwsimEnvironment.getSignaturesDir(workDir, numOfBits, signatureType);
if (cmdline.hasOption(OVERLAPSIZE_OPTION)){
chunkOverlapSize = Integer.parseInt(cmdline.getOptionValue(OVERLAPSIZE_OPTION));
}else {
if (slidingWindowSize == 0) {
throw new RuntimeException("Either provide option --" + WINDOWSIZE_OPTION + " or --" + OVERLAPSIZE_OPTION);
}else {
chunkOverlapSize = slidingWindowSize;
}
}
outputPath = PwsimEnvironment.getTablesDir(workDir, fs, signatureType, numOfBits, chunkOverlapSize, numOfPermutations);
RetrievalEnvironment targetEnv = new RetrievalEnvironment(workDir, fs);
RetrievalEnvironment srcEnv = new RetrievalEnvironment(srcWorkDir, fs);
int collSize = targetEnv.readCollectionDocumentCount() + srcEnv.readCollectionDocumentCount();
// split table into 10 chunks by default, limit chunk size to range (100k,2m)
chunkSize = collSize / 10;
if (chunkSize < 100000) {
chunkSize = 100000;
} else if (chunkSize > 2000000) {
chunkSize = 2000000;
}
if (numOfPermutations < 0 || numOfBits < 0 || chunkOverlapSize < slidingWindowSize) {
return -1;
}
return 0;
}
public static void main(String[] args) throws Exception {
ToolRunner.run(new GenerateChunkedPermutedTables(), args);
return;
}
}