src/main/java/org/apache/sysds/runtime/io/WriterBinaryBlock.java - systemds - Git at Google

 /*
  * 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.sysds.runtime.io;

 import java.io.IOException;

 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile.Writer;
 import org.apache.hadoop.mapred.JobConf;
 import org.apache.sysds.conf.ConfigurationManager;
 import org.apache.sysds.runtime.DMLRuntimeException;
 import org.apache.sysds.runtime.compress.CompressedMatrixBlock;
 import org.apache.sysds.runtime.matrix.data.MatrixBlock;
 import org.apache.sysds.runtime.matrix.data.MatrixIndexes;
 import org.apache.sysds.runtime.util.HDFSTool;

 public class WriterBinaryBlock extends MatrixWriter {
 	protected int _replication = -1;

 	public WriterBinaryBlock(int replication) {
 		_replication = replication;
 	}

 	@Override
 	public final void writeMatrixToHDFS(MatrixBlock src, String fname, long rlen, long clen, int blen, long nnz,
 		boolean diag) throws IOException, DMLRuntimeException {
 		// prepare file access
 		JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
 		Path path = new Path(fname);
 		FileSystem fs = IOUtilFunctions.getFileSystem(path, job);

 		// if the file already exists on HDFS, remove it.
 		HDFSTool.deleteFileIfExistOnHDFS(fname);

 		// set up preferred custom serialization framework for binary block format
 		if(HDFSTool.USE_BINARYBLOCK_SERIALIZATION)
 			HDFSTool.addBinaryBlockSerializationFramework(job);

 		if(src instanceof CompressedMatrixBlock)
 			src = CompressedMatrixBlock.getUncompressed(src, "Decompressing for binary write");

 		// core write sequential/parallel
 		if(diag)
 			writeDiagBinaryBlockMatrixToHDFS(path, job, fs, src, rlen, clen, blen);
 		else
 			writeBinaryBlockMatrixToHDFS(path, job, fs, src, rlen, clen, blen);

 		IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
 	}

 	@Override
 	public final void writeEmptyMatrixToHDFS(String fname, long rlen, long clen, int blen)
 		throws IOException, DMLRuntimeException {
 		JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
 		Path path = new Path(fname);
 		FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
 		final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);
 		try {
 			MatrixIndexes index = new MatrixIndexes(1, 1);
 			MatrixBlock block = new MatrixBlock((int) Math.max(Math.min(rlen, blen), 1),
 				(int) Math.max(Math.min(clen, blen), 1), true);
 			writer.append(index, block);
 		}
 		finally {
 			IOUtilFunctions.closeSilently(writer);
 		}

 		IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
 	}

 	protected void writeBinaryBlockMatrixToHDFS(Path path, JobConf job, FileSystem fs, MatrixBlock src, long rlen,
 		long clen, int blen) throws IOException, DMLRuntimeException {
 		// sequential write
 		writeBinaryBlockMatrixToSequenceFile(path, job, fs, src, blen, 0, (int) rlen);
 	}

 	protected final void writeBinaryBlockMatrixToSequenceFile(Path path, JobConf job, FileSystem fs, MatrixBlock src,
 		int blen, int rl, int ru) throws IOException {
 		boolean sparse = src.isInSparseFormat();
 		int rlen = src.getNumRows();
 		int clen = src.getNumColumns();

 		final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);

 		try { // 2) bound check for src block
 			if(src.getNumRows() > rlen || src.getNumColumns() > clen) {
 				throw new IOException("Matrix block [1:" + src.getNumRows() + ",1:" + src.getNumColumns() + "] "
 					+ "out of overall matrix range [1:" + rlen + ",1:" + clen + "].");
 			}

 			// 3) reblock and write
 			MatrixIndexes indexes = new MatrixIndexes();

 			if(rlen <= blen && clen <= blen && rl == 0) { // opt for single block
 				// directly write single block
 				indexes.setIndexes(1, 1);
 				writer.append(indexes, src);
 			}
 			else {
 				// general case
 				// initialize blocks for reuse (at most 4 different blocks required)
 				MatrixBlock[] blocks = createMatrixBlocksForReuse(rlen, clen, blen, sparse, src.getNonZeros());

 				// create and write sub-blocks of matrix
 				for(int blockRow = rl / blen; blockRow < (int) Math.ceil(ru / (double) blen); blockRow++) {
 					for(int blockCol = 0; blockCol < (int) Math.ceil(src.getNumColumns() / (double) blen); blockCol++) {
 						int maxRow = (blockRow * blen + blen < src.getNumRows()) ? blen : src.getNumRows() - blockRow * blen;
 						int maxCol = (blockCol * blen + blen < src.getNumColumns()) ? blen : src.getNumColumns() -
 							blockCol * blen;

 						int row_offset = blockRow * blen;
 						int col_offset = blockCol * blen;

 						// get reuse matrix block
 						MatrixBlock block = getMatrixBlockForReuse(blocks, maxRow, maxCol, blen);

 						// copy submatrix to block
 						src.slice(row_offset, row_offset + maxRow - 1, col_offset, col_offset + maxCol - 1, block);

 						// append block to sequence file
 						indexes.setIndexes(blockRow + 1, blockCol + 1);
 						writer.append(indexes, block);

 						// reset block for later reuse
 						block.reset();
 					}
 				}
 			}
 		}
 		finally {
 			IOUtilFunctions.closeSilently(writer);
 		}
 	}

 	protected final void writeDiagBinaryBlockMatrixToHDFS(Path path, JobConf job, FileSystem fs, MatrixBlock src,
 		long rlen, long clen, int blen) throws IOException, DMLRuntimeException {
 		boolean sparse = src.isInSparseFormat();

 		final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);

 		try {
 			// 2) bound check for src block
 			if(src.getNumRows() > rlen || src.getNumColumns() > clen) {
 				throw new IOException("Matrix block [1:" + src.getNumRows() + ",1:" + src.getNumColumns() + "] "
 					+ "out of overall matrix range [1:" + rlen + ",1:" + clen + "].");
 			}

 			// 3) reblock and write
 			MatrixIndexes indexes = new MatrixIndexes();

 			if(rlen <= blen && clen <= blen) { // opt for single block
 				// directly write single block
 				indexes.setIndexes(1, 1);
 				writer.append(indexes, src);
 			}
 			else { // general case
 				// initialize blocks for reuse (at most 4 different blocks required)
 				MatrixBlock[] blocks = createMatrixBlocksForReuse(rlen, clen, blen, sparse, src.getNonZeros());
 				MatrixBlock emptyBlock = new MatrixBlock();

 				// create and write subblocks of matrix
 				for(int blockRow = 0; blockRow < (int) Math.ceil(src.getNumRows() / (double) blen); blockRow++) {

 					for(int blockCol = 0; blockCol < (int) Math.ceil(src.getNumColumns() / (double) blen); blockCol++) {
 						int maxRow = (blockRow * blen + blen < src.getNumRows()) ? blen : src.getNumRows() - blockRow * blen;
 						int maxCol = (blockCol * blen + blen < src.getNumColumns()) ? blen : src.getNumColumns() -
 							blockCol * blen;
 						MatrixBlock block = null;

 						if(blockRow == blockCol) { // block on diagonal
 							int row_offset = blockRow * blen;
 							int col_offset = blockCol * blen;

 							// get reuse matrix block
 							block = getMatrixBlockForReuse(blocks, maxRow, maxCol, blen);

 							// copy submatrix to block
 							src.slice(row_offset, row_offset + maxRow - 1, col_offset, col_offset + maxCol - 1, block);
 						}
 						else { // empty block (not on diagonal)
 							block = emptyBlock;
 							block.reset(maxRow, maxCol);
 						}

 						// append block to sequence file
 						indexes.setIndexes(blockRow + 1, blockCol + 1);
 						writer.append(indexes, block);

 						// reset block for later reuse
 						if(blockRow != blockCol)
 							block.reset();
 					}
 				}
 			}
 		}
 		finally {
 			IOUtilFunctions.closeSilently(writer);
 		}
 	}
 }
	/*
	* 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.sysds.runtime.io;

	import java.io.IOException;

	import org.apache.hadoop.fs.FileSystem;
	import org.apache.hadoop.fs.Path;
	import org.apache.hadoop.io.SequenceFile.Writer;
	import org.apache.hadoop.mapred.JobConf;
	import org.apache.sysds.conf.ConfigurationManager;
	import org.apache.sysds.runtime.DMLRuntimeException;
	import org.apache.sysds.runtime.compress.CompressedMatrixBlock;
	import org.apache.sysds.runtime.matrix.data.MatrixBlock;
	import org.apache.sysds.runtime.matrix.data.MatrixIndexes;
	import org.apache.sysds.runtime.util.HDFSTool;

	public class WriterBinaryBlock extends MatrixWriter {
	protected int _replication = -1;

	public WriterBinaryBlock(int replication) {
	_replication = replication;
	}

	@Override
	public final void writeMatrixToHDFS(MatrixBlock src, String fname, long rlen, long clen, int blen, long nnz,
	boolean diag) throws IOException, DMLRuntimeException {
	// prepare file access
	JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
	Path path = new Path(fname);
	FileSystem fs = IOUtilFunctions.getFileSystem(path, job);

	// if the file already exists on HDFS, remove it.
	HDFSTool.deleteFileIfExistOnHDFS(fname);

	// set up preferred custom serialization framework for binary block format
	if(HDFSTool.USE_BINARYBLOCK_SERIALIZATION)
	HDFSTool.addBinaryBlockSerializationFramework(job);

	if(src instanceof CompressedMatrixBlock)
	src = CompressedMatrixBlock.getUncompressed(src, "Decompressing for binary write");

	// core write sequential/parallel
	if(diag)
	writeDiagBinaryBlockMatrixToHDFS(path, job, fs, src, rlen, clen, blen);
	else
	writeBinaryBlockMatrixToHDFS(path, job, fs, src, rlen, clen, blen);

	IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
	}

	@Override
	public final void writeEmptyMatrixToHDFS(String fname, long rlen, long clen, int blen)
	throws IOException, DMLRuntimeException {
	JobConf job = new JobConf(ConfigurationManager.getCachedJobConf());
	Path path = new Path(fname);
	FileSystem fs = IOUtilFunctions.getFileSystem(path, job);
	final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);
	try {
	MatrixIndexes index = new MatrixIndexes(1, 1);
	MatrixBlock block = new MatrixBlock((int) Math.max(Math.min(rlen, blen), 1),
	(int) Math.max(Math.min(clen, blen), 1), true);
	writer.append(index, block);
	}
	finally {
	IOUtilFunctions.closeSilently(writer);
	}

	IOUtilFunctions.deleteCrcFilesFromLocalFileSystem(fs, path);
	}

	protected void writeBinaryBlockMatrixToHDFS(Path path, JobConf job, FileSystem fs, MatrixBlock src, long rlen,
	long clen, int blen) throws IOException, DMLRuntimeException {
	// sequential write
	writeBinaryBlockMatrixToSequenceFile(path, job, fs, src, blen, 0, (int) rlen);
	}

	protected final void writeBinaryBlockMatrixToSequenceFile(Path path, JobConf job, FileSystem fs, MatrixBlock src,
	int blen, int rl, int ru) throws IOException {
	boolean sparse = src.isInSparseFormat();
	int rlen = src.getNumRows();
	int clen = src.getNumColumns();

	final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);

	try { // 2) bound check for src block
	if(src.getNumRows() > rlen \|\| src.getNumColumns() > clen) {
	throw new IOException("Matrix block [1:" + src.getNumRows() + ",1:" + src.getNumColumns() + "] "
	+ "out of overall matrix range [1:" + rlen + ",1:" + clen + "].");
	}

	// 3) reblock and write
	MatrixIndexes indexes = new MatrixIndexes();

	if(rlen <= blen && clen <= blen && rl == 0) { // opt for single block
	// directly write single block
	indexes.setIndexes(1, 1);
	writer.append(indexes, src);
	}
	else {
	// general case
	// initialize blocks for reuse (at most 4 different blocks required)
	MatrixBlock[] blocks = createMatrixBlocksForReuse(rlen, clen, blen, sparse, src.getNonZeros());

	// create and write sub-blocks of matrix
	for(int blockRow = rl / blen; blockRow < (int) Math.ceil(ru / (double) blen); blockRow++) {
	for(int blockCol = 0; blockCol < (int) Math.ceil(src.getNumColumns() / (double) blen); blockCol++) {
	int maxRow = (blockRow * blen + blen < src.getNumRows()) ? blen : src.getNumRows() - blockRow * blen;
	int maxCol = (blockCol * blen + blen < src.getNumColumns()) ? blen : src.getNumColumns() -
	blockCol * blen;

	int row_offset = blockRow * blen;
	int col_offset = blockCol * blen;

	// get reuse matrix block
	MatrixBlock block = getMatrixBlockForReuse(blocks, maxRow, maxCol, blen);

	// copy submatrix to block
	src.slice(row_offset, row_offset + maxRow - 1, col_offset, col_offset + maxCol - 1, block);

	// append block to sequence file
	indexes.setIndexes(blockRow + 1, blockCol + 1);
	writer.append(indexes, block);

	// reset block for later reuse
	block.reset();
	}
	}
	}
	}
	finally {
	IOUtilFunctions.closeSilently(writer);
	}
	}

	protected final void writeDiagBinaryBlockMatrixToHDFS(Path path, JobConf job, FileSystem fs, MatrixBlock src,
	long rlen, long clen, int blen) throws IOException, DMLRuntimeException {
	boolean sparse = src.isInSparseFormat();

	final Writer writer = IOUtilFunctions.getSeqWriter(path, job, _replication);

	try {
	// 2) bound check for src block
	if(src.getNumRows() > rlen \|\| src.getNumColumns() > clen) {
	throw new IOException("Matrix block [1:" + src.getNumRows() + ",1:" + src.getNumColumns() + "] "
	+ "out of overall matrix range [1:" + rlen + ",1:" + clen + "].");
	}

	// 3) reblock and write
	MatrixIndexes indexes = new MatrixIndexes();

	if(rlen <= blen && clen <= blen) { // opt for single block
	// directly write single block
	indexes.setIndexes(1, 1);
	writer.append(indexes, src);
	}
	else { // general case
	// initialize blocks for reuse (at most 4 different blocks required)
	MatrixBlock[] blocks = createMatrixBlocksForReuse(rlen, clen, blen, sparse, src.getNonZeros());
	MatrixBlock emptyBlock = new MatrixBlock();

	// create and write subblocks of matrix
	for(int blockRow = 0; blockRow < (int) Math.ceil(src.getNumRows() / (double) blen); blockRow++) {

	for(int blockCol = 0; blockCol < (int) Math.ceil(src.getNumColumns() / (double) blen); blockCol++) {
	int maxRow = (blockRow * blen + blen < src.getNumRows()) ? blen : src.getNumRows() - blockRow * blen;
	int maxCol = (blockCol * blen + blen < src.getNumColumns()) ? blen : src.getNumColumns() -
	blockCol * blen;
	MatrixBlock block = null;

	if(blockRow == blockCol) { // block on diagonal
	int row_offset = blockRow * blen;
	int col_offset = blockCol * blen;

	// get reuse matrix block
	block = getMatrixBlockForReuse(blocks, maxRow, maxCol, blen);

	// copy submatrix to block
	src.slice(row_offset, row_offset + maxRow - 1, col_offset, col_offset + maxCol - 1, block);
	}
	else { // empty block (not on diagonal)
	block = emptyBlock;
	block.reset(maxRow, maxCol);
	}

	// append block to sequence file
	indexes.setIndexes(blockRow + 1, blockCol + 1);
	writer.append(indexes, block);

	// reset block for later reuse
	if(blockRow != blockCol)
	block.reset();
	}
	}
	}
	}
	finally {
	IOUtilFunctions.closeSilently(writer);
	}
	}
	}