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Declarative Machine Learning
/*
* Licensed to the Apache Software Foundation (ASF) under one
* or more contributor license agreements. See the NOTICE file
* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you 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.apache.sysml.runtime.matrix;
import java.io.DataInput;
import java.io.DataOutput;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.HashSet;
import org.apache.hadoop.filecache.DistributedCache;
import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.PathFilter;
import org.apache.hadoop.io.ByteWritable;
import org.apache.hadoop.io.Writable;
import org.apache.hadoop.io.WritableComparable;
import org.apache.hadoop.mapred.Counters.Group;
import org.apache.hadoop.mapred.FileOutputFormat;
import org.apache.hadoop.mapred.JobClient;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.RunningJob;
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.sysml.conf.ConfigurationManager;
import org.apache.sysml.conf.DMLConfig;
import org.apache.sysml.runtime.instructions.MRJobInstruction;
import org.apache.sysml.runtime.matrix.data.InputInfo;
import org.apache.sysml.runtime.matrix.data.MatrixBlock;
import org.apache.sysml.runtime.matrix.data.OutputInfo;
import org.apache.sysml.runtime.matrix.data.TaggedFirstSecondIndexes;
import org.apache.sysml.runtime.matrix.mapred.CSVAssignRowIDMapper;
import org.apache.sysml.runtime.matrix.mapred.CSVAssignRowIDReducer;
import org.apache.sysml.runtime.matrix.mapred.CSVReblockMapper;
import org.apache.sysml.runtime.matrix.mapred.CSVReblockReducer;
import org.apache.sysml.runtime.matrix.mapred.MRJobConfiguration;
import org.apache.sysml.runtime.matrix.mapred.MRJobConfiguration.ConvertTarget;
import org.apache.sysml.runtime.matrix.mapred.MRJobConfiguration.MatrixChar_N_ReducerGroups;
import org.apache.sysml.runtime.transform.TfUtils;
import org.apache.sysml.runtime.util.MapReduceTool;
@SuppressWarnings("deprecation")
public class CSVReblockMR
{
public static final String NUM_ROWS_IN_MATRIX="num.rows.in.matrix.";
public static final String NUM_COLS_IN_MATRIX="num.cols.in.matrix.";
public static final String ROWID_FILE_NAME="rowid.file.name";
public static final String SMALLEST_FILE_NAME_PER_INPUT="smallest.file.name.per.input";
private CSVReblockMR() {
//prevent instantiation via private constructor
}
public static final PathFilter hiddenFileFilter = new PathFilter(){
public boolean accept(Path p){
String name = p.getName();
return !name.startsWith("_") && !name.startsWith(".");
}
};
@SuppressWarnings("rawtypes")
public static class OffsetCount implements WritableComparable
{
public String filename;
public long fileOffset;
public long count;
public OffsetCount()
{
filename="";
fileOffset=0;
count=0;
}
public OffsetCount(String fname, long off, long cnt)
{
filename=fname;
fileOffset=off;
count=cnt;
}
public OffsetCount(OffsetCount that)
{
this.filename=that.filename;
this.fileOffset=that.fileOffset;
this.count=that.count;
}
@Override
public void readFields(DataInput in) throws IOException {
filename=in.readLine();
fileOffset=in.readLong();
count=in.readLong();
}
@Override
public void write(DataOutput out) throws IOException {
out.writeBytes(filename+'\n');
out.writeLong(fileOffset);
out.writeLong(count);
}
public String toString()
{
return filename+", "+fileOffset+", "+count;
}
public int compareTo(OffsetCount that) {
int ret=this.filename.compareTo(that.filename);
if(ret!=0)
return ret;
else if(this.fileOffsetthat.fileOffset)
return 1;
else return 0;
}
@Override
public int compareTo(Object o) {
if( !(o instanceof OffsetCount) )
return -1;
return compareTo((OffsetCount)o);
}
@Override
public boolean equals(Object o) {
if( !(o instanceof OffsetCount) )
return false;
OffsetCount that = (OffsetCount)o;
return (filename.equals(that.filename) && fileOffset==that.fileOffset);
}
@Override
public int hashCode() {
throw new RuntimeException("hashCode() should never be called on instances of this class.");
}
}
public static class BlockRow implements Writable
{
public int indexInBlock = 0;
public MatrixBlock data = null;
@Override
public void readFields(DataInput in) throws IOException {
indexInBlock=in.readInt();
if( data == null )
data = new MatrixBlock();
data.readFields(in);
}
@Override
public void write(DataOutput out) throws IOException {
out.writeInt(indexInBlock);
data.write(out);
}
}
public static class AssignRowIDMRReturn
{
public Path counterFile=null;
public long[] rlens=null;
public long[] clens=null;
public String toString()
{
StringBuilder sb = new StringBuilder();
sb.append(counterFile.toString());
sb.append("\n");
for(long rlen: rlens) {
sb.append(rlen);
sb.append(", ");
}
sb.append("\n");
for(long clen: clens) {
sb.append(clen);
sb.append(", ");
}
return sb.toString();
}
}
/**
* Method to find the first (part)file in the order given by fs.listStatus() among all (part)files in inpathPath.
*
* @param job
* @param inputPath
* @return
* @throws IOException
* @throws FileNotFoundException
*/
public static String findSmallestFile(JobConf job, String inputPath) throws FileNotFoundException, IOException {
String smallestFile = null;
Path p=new Path(inputPath);
FileSystem fs = p.getFileSystem(job);
if(!fs.isDirectory(p))
smallestFile=p.makeQualified(fs).toString();
else
{
FileStatus[] stats=fs.listStatus(p, hiddenFileFilter);
if(stats.length==0)
smallestFile="";
else
{
smallestFile=stats[0].getPath().toString();
for(int j=1; j0 && rlens[i]!=ret1.rlens[i]) || (clens[i]>0 && clens[i]!=ret1.clens[i]) )
throw new RuntimeException("Dimension doesn't mach for input matrix "+i+", expected ("+rlens[i]+", "+clens[i]+") but real ("+ret1.rlens[i]+", "+ret1.clens[i]+")");
JobReturn ret= CSVReblockMR.runCSVReblockJob(null, inputs, inputInfos, ret1.rlens, ret1.clens, brlens, bclens, reblockInstructions,
otherInstructionsInReducer, numReducers, replication, resultIndexes, outputs, outputInfos, ret1.counterFile, smallestFiles);
return ret;
}
public static AssignRowIDMRReturn runAssignRowIDMRJob(String[] inputs, InputInfo[] inputInfos, int[] brlens, int[] bclens,
String reblockInstructions, int replication, String[] smallestFiles)
throws Exception
{
return runAssignRowIDMRJob(inputs, inputInfos, brlens, bclens, reblockInstructions, replication, smallestFiles, false, null, null);
}
public static AssignRowIDMRReturn runAssignRowIDMRJob(String[] inputs, InputInfo[] inputInfos, int[] brlens, int[] bclens,
String reblockInstructions, int replication, String[] smallestFiles, boolean transform, String naStrings, String specFile)
throws Exception
{
AssignRowIDMRReturn ret=new AssignRowIDMRReturn();
JobConf job;
job = new JobConf(CSVReblockMR.class);
job.setJobName("Assign-RowID-MR");
byte[] realIndexes=new byte[inputs.length];
for(byte b=0; b mapoutputIndexes=MRJobConfiguration.setUpOutputIndexesForMapper(job, realIndexes, null,
reblockInstructions, null, otherInstructionsInReducer, resultIndexes);
MatrixChar_N_ReducerGroups ret=MRJobConfiguration.computeMatrixCharacteristics(job, realIndexes,
null, reblockInstructions, null, null, otherInstructionsInReducer,
resultIndexes, mapoutputIndexes, false);
MatrixCharacteristics[] stats=ret.stats;
//set up the number of reducers
int numRed = WriteCSVMR.determineNumReducers(rlens, clens, ConfigurationManager.getConfig().getIntValue(DMLConfig.NUM_REDUCERS), ret.numReducerGroups);
job.setNumReduceTasks( numRed );
// Print the complete instruction
//if (LOG.isTraceEnabled())
// inst.printCompelteMRJobInstruction(stats);
// Update resultDimsUnknown based on computed "stats"
byte[] resultDimsUnknown = new byte[resultIndexes.length];
for ( int i=0; i < resultIndexes.length; i++ ) {
if ( stats[i].getRows() == -1 || stats[i].getCols() == -1 ) {
resultDimsUnknown[i] = (byte) 1;
}
else {
resultDimsUnknown[i] = (byte) 0;
}
}
//set up the multiple output files, and their format information
MRJobConfiguration.setUpMultipleOutputs(job, resultIndexes, resultDimsUnknown, outputs, outputInfos, true, true);
// configure mapper and the mapper output key value pairs
job.setMapperClass(CSVReblockMapper.class);
job.setMapOutputKeyClass(TaggedFirstSecondIndexes.class);
job.setMapOutputValueClass(BlockRow.class);
//configure reducer
job.setReducerClass(CSVReblockReducer.class);
//turn off adaptivemr
job.setBoolean("adaptivemr.map.enable", false);
//set unique working dir
MRJobConfiguration.setUniqueWorkingDir(job);
Path cachefile=new Path(counterFile, "part-00000");
DistributedCache.addCacheFile(cachefile.toUri(), job);
DistributedCache.createSymlink(job);
job.set(ROWID_FILE_NAME, cachefile.toString());
RunningJob runjob=JobClient.runJob(job);
MapReduceTool.deleteFileIfExistOnHDFS(counterFile, job);
/* Process different counters */
Group group=runjob.getCounters().getGroup(MRJobConfiguration.NUM_NONZERO_CELLS);
for(int i=0; i\n"+stats[i]);
}
return new JobReturn(stats, outputInfos, runjob.isSuccessful());
}
}