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From edwardy...@apache.org
Subject svn commit: r747265 - in /incubator/hama/trunk/src: java/org/apache/hama/ java/org/apache/hama/algebra/ test/org/apache/hama/
Date Tue, 24 Feb 2009 02:52:49 GMT
Author: edwardyoon
Date: Tue Feb 24 02:52:48 2009
New Revision: 747265

URL: http://svn.apache.org/viewvc?rev=747265&view=rev
Log:
Add SparseMatrix/Vector classes

Added:
    incubator/hama/trunk/src/java/org/apache/hama/SparseMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/SparseVector.java
    incubator/hama/trunk/src/test/org/apache/hama/TestSparseMatrix.java
    incubator/hama/trunk/src/test/org/apache/hama/TestSparseVector.java
Modified:
    incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/AbstractVector.java
    incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java
    incubator/hama/trunk/src/java/org/apache/hama/SubMatrix.java
    incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyMap.java
    incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java
    incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java

Modified: incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/AbstractMatrix.java Tue Feb 24 02:52:48 2009
@@ -1,360 +1,384 @@
-/**
- * Copyright 2007 The Apache Software Foundation
- *
- * 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.hama;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.hadoop.hbase.HColumnDescriptor;
-import org.apache.hadoop.hbase.HConstants;
-import org.apache.hadoop.hbase.HTableDescriptor;
-import org.apache.hadoop.hbase.MasterNotRunningException;
-import org.apache.hadoop.hbase.RegionException;
-import org.apache.hadoop.hbase.HColumnDescriptor.CompressionType;
-import org.apache.hadoop.hbase.client.HBaseAdmin;
-import org.apache.hadoop.hbase.client.HTable;
-import org.apache.hadoop.hbase.io.BatchUpdate;
-import org.apache.hadoop.hbase.io.Cell;
-import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
-import org.apache.hadoop.hbase.io.RowResult;
-import org.apache.hadoop.hbase.mapred.IdentityTableReduce;
-import org.apache.hadoop.hbase.mapred.TableMap;
-import org.apache.hadoop.hbase.mapred.TableMapReduceUtil;
-import org.apache.hadoop.hbase.util.Bytes;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reporter;
-import org.apache.hama.io.VectorUpdate;
-import org.apache.hama.util.BytesUtil;
-import org.apache.hama.util.JobManager;
-import org.apache.log4j.Logger;
-
-/**
- * Methods of the matrix classes
- */
-public abstract class AbstractMatrix implements Matrix {
-  static final Logger LOG = Logger.getLogger(AbstractMatrix.class);
-
-  protected HamaConfiguration config;
-  protected HBaseAdmin admin;
-  // a matrix just need a table path to point to the table which stores matrix.
-  // let HamaAdmin manage Matrix Name space.
-  protected String matrixPath;
-  protected HTable table;
-  protected HTableDescriptor tableDesc;
-  protected HamaAdmin hamaAdmin;
-
-  protected boolean closed = true;
-
-  /**
-   * Sets the job configuration
-   * 
-   * @param conf configuration object
-   * @throws MasterNotRunningException
-   */
-  public void setConfiguration(HamaConfiguration conf)
-      throws MasterNotRunningException {
-    this.config = conf;
-    this.admin = new HBaseAdmin(config);
-
-    hamaAdmin = new HamaAdminImpl(conf, admin);
-  }
-
-  /**
-   * Create matrix space
-   */
-  protected void create() throws IOException {
-    // It should run only when table doesn't exist.
-    if (!admin.tableExists(matrixPath)) {
-      this.tableDesc.addFamily(new HColumnDescriptor(Bytes
-          .toBytes(Constants.COLUMN), 3, CompressionType.NONE, false, false,
-          Integer.MAX_VALUE, HConstants.FOREVER, false));
-      this.tableDesc.addFamily(new HColumnDescriptor(Constants.ATTRIBUTE));
-      this.tableDesc.addFamily(new HColumnDescriptor(Constants.ALIASEFAMILY));
-      // It's a temporary data.
-      this.tableDesc.addFamily(new HColumnDescriptor(Bytes
-          .toBytes(Constants.BLOCK), 1, CompressionType.NONE, false, false,
-          Integer.MAX_VALUE, HConstants.FOREVER, false));
-
-      LOG.info("Initializing the matrix storage.");
-      this.admin.createTable(this.tableDesc);
-      LOG.info("Create Matrix " + matrixPath);
-
-      // connect to the table.
-      table = new HTable(config, matrixPath);
-      table.setAutoFlush(true);
-
-      // Record the matrix type in METADATA_TYPE
-      BatchUpdate update = new BatchUpdate(Constants.METADATA);
-      update.put(Constants.METADATA_TYPE, Bytes.toBytes(this.getClass()
-          .getSimpleName()));
-
-      table.commit(update);
-
-      // the new matrix's reference is 1.
-      setReference(1);
-    }
-  }
-
-  public HTable getHTable() {
-    return this.table;
-  }
-
-  /** {@inheritDoc} */
-  public int getRows() throws IOException {
-    Cell rows = null;
-    rows = table.get(Constants.METADATA, Constants.METADATA_ROWS);
-    return (rows != null) ? BytesUtil.bytesToInt(rows.getValue()) : 0;
-  }
-
-  /** {@inheritDoc} */
-  public int getColumns() throws IOException {
-    Cell columns = table.get(Constants.METADATA, Constants.METADATA_COLUMNS);
-    return BytesUtil.bytesToInt(columns.getValue());
-  }
-
-  /** {@inheritDoc} */
-  public String getRowLabel(int row) throws IOException {
-    Cell rows = null;
-    rows = table.get(BytesUtil.getRowIndex(row), Bytes
-        .toBytes(Constants.ATTRIBUTE + "string"));
-
-    return (rows != null) ? Bytes.toString(rows.getValue()) : null;
-  }
-
-  /** {@inheritDoc} */
-  public String getColumnLabel(int column) throws IOException {
-    Cell rows = null;
-    rows = table.get(Constants.CINDEX, (Constants.ATTRIBUTE + column));
-    return (rows != null) ? Bytes.toString(rows.getValue()) : null;
-  }
-
-  /** {@inheritDoc} */
-  public void setRowLabel(int row, String name) throws IOException {
-    VectorUpdate update = new VectorUpdate(row);
-    update.put(Constants.ATTRIBUTE + "string", name);
-    table.commit(update.getBatchUpdate());
-  }
-  
-  /** {@inheritDoc} */
-  public void set(int i, int j, double value) throws IOException {
-    VectorUpdate update = new VectorUpdate(i);
-    update.put(j, value);
-    table.commit(update.getBatchUpdate());
-
-  }
-
-  /** {@inheritDoc} */
-  public void setDimension(int rows, int columns) throws IOException {
-    VectorUpdate update = new VectorUpdate(Constants.METADATA);
-    update.put(Constants.METADATA_ROWS, rows);
-    update.put(Constants.METADATA_COLUMNS, columns);
-
-    table.commit(update.getBatchUpdate());
-  }
-  
-  public void increaseRows() throws IOException {
-    int nValue = this.getRows() + 1;
-    try {
-      this.setDimension(nValue, this.getColumns());
-    } catch (NullPointerException ne) {
-      // If there is no metadata of dimension, nothing to do.
-    }
-  }
-  
-  public void increaseColumns() throws IOException {
-    int nValue = this.getColumns() + 1;
-    try {
-      this.setDimension(this.getRows(), nValue);
-    } catch (NullPointerException ne) {
-      // If there is no metadata of dimension, nothing to do.
-    }
-  }
-  
-  /** {@inheritDoc} */
-  public void add(int i, int j, double value) throws IOException {
-    VectorUpdate update = new VectorUpdate(i);
-    update.put(j, value + this.get(i, j));
-    table.commit(update.getBatchUpdate());
-
-  }
-  
-  /**
-   * Just full scan a table.
-   */
-  public static class TableReadMapper extends MapReduceBase implements
-      TableMap<ImmutableBytesWritable, BatchUpdate> {
-    private static List<Double> alpha = new ArrayList<Double>();
-
-    @SuppressWarnings("unchecked")
-    public void map(ImmutableBytesWritable key, RowResult value,
-        OutputCollector<ImmutableBytesWritable, BatchUpdate> output,
-        @SuppressWarnings("unused")
-        Reporter reporter) throws IOException {
-
-      BatchUpdate update = new BatchUpdate(key.get());
-      for (Map.Entry<byte[], Cell> e : value.entrySet()) {
-        if (alpha.size() == 0) {
-          update.put(e.getKey(), e.getValue().getValue());
-        } else {
-          String column = new String(e.getKey());
-          if(column.startsWith(Constants.COLUMN)) {
-            double currValue = BytesUtil.bytesToDouble(e.getValue().getValue());
-            update.put(e.getKey(), (BytesUtil.doubleToBytes(currValue * alpha.get(0))));
-          } else {
-            update.put(e.getKey(), e.getValue().getValue());
-          }
-        }
-      }
-      output.collect(key, update);
-    }
-
-    public static void setAlpha(double a) {
-      if(alpha.size() > 0) 
-        alpha = new ArrayList<Double>();
-      alpha.add(a);
-    }
-  }
-
-  /** {@inheritDoc} */
-  public Matrix set(Matrix B) throws IOException {
-    JobConf jobConf = new JobConf(config);
-    jobConf.setJobName("set MR job : " + this.getPath());
-
-    jobConf.setNumMapTasks(config.getNumMapTasks());
-    jobConf.setNumReduceTasks(config.getNumReduceTasks());
-
-    TableMapReduceUtil.initTableMapJob(B.getPath(), Constants.COLUMN + " "
-        + Constants.ATTRIBUTE + " " + Constants.ALIASEFAMILY + " "
-        + Constants.BLOCK, TableReadMapper.class, ImmutableBytesWritable.class,
-        BatchUpdate.class, jobConf);
-    TableMapReduceUtil.initTableReduceJob(this.getPath(),
-        IdentityTableReduce.class, jobConf);
-
-    JobManager.execute(jobConf);
-    return this;
-  }
-
-  /** {@inheritDoc} */
-  public Matrix set(double alpha, Matrix B) throws IOException {
-    JobConf jobConf = new JobConf(config);
-    jobConf.setJobName("set MR job : " + this.getPath());
-
-    jobConf.setNumMapTasks(config.getNumMapTasks());
-    jobConf.setNumReduceTasks(config.getNumReduceTasks());
-
-    TableReadMapper.setAlpha(alpha);
-    TableMapReduceUtil.initTableMapJob(B.getPath(), Constants.COLUMN + " "
-        + Constants.ATTRIBUTE + " " + Constants.ALIASEFAMILY + " "
-        + Constants.BLOCK, TableReadMapper.class, ImmutableBytesWritable.class,
-        BatchUpdate.class, jobConf);
-    TableMapReduceUtil.initTableReduceJob(this.getPath(),
-        IdentityTableReduce.class, jobConf);
-
-    JobManager.execute(jobConf);
-    return this;
-  }
-
-  /** {@inheritDoc} */
-  public void setColumnLabel(int column, String name) throws IOException {
-    VectorUpdate update = new VectorUpdate(Constants.CINDEX);
-    update.put(column, name);
-    table.commit(update.getBatchUpdate());
-  }
-
-  /** {@inheritDoc} */
-  public String getPath() {
-    return matrixPath;
-  }
-
-  protected void setReference(int reference) throws IOException {
-    BatchUpdate update = new BatchUpdate(Constants.METADATA);
-    update.put(Constants.METADATA_REFERENCE, Bytes.toBytes(reference));
-    table.commit(update);
-
-  }
-
-  protected int incrementAndGetRef() throws IOException {
-    int reference = 1;
-    Cell rows = null;
-    rows = table.get(Constants.METADATA, Constants.METADATA_REFERENCE);
-    if (rows != null) {
-      reference = Bytes.toInt(rows.getValue());
-      reference++;
-    }
-    setReference(reference);
-    return reference;
-  }
-
-  protected int decrementAndGetRef() throws IOException {
-    int reference = 0;
-    Cell rows = null;
-    rows = table.get(Constants.METADATA, Constants.METADATA_REFERENCE);
-    if (rows != null) {
-      reference = Bytes.toInt(rows.getValue());
-      if (reference > 0) // reference==0, we need not to decrement it.
-        reference--;
-    }
-    setReference(reference);
-    return reference;
-  }
-
-  protected boolean hasAliaseName() throws IOException {
-    Cell rows = null;
-    rows = table.get(Constants.METADATA, Constants.ALIASENAME);
-    return (rows != null) ? true : false;
-  }
-
-  public void close() throws IOException {
-    if (closed) // have been closed
-      return;
-    int reference = decrementAndGetRef();
-    if (reference <= 0) { // no reference again.
-      if (!hasAliaseName()) { // the table has not been aliased, we delete the
-        // table.
-        if (admin.isTableEnabled(matrixPath)) {
-          while (admin.isTableEnabled(matrixPath)) {
-            try {
-              admin.disableTable(matrixPath);
-            } catch (RegionException e) {
-              LOG.warn(e);
-            }
-          }
-
-          admin.deleteTable(matrixPath);
-        }
-      }
-    }
-    closed = true;
-  }
-
-  public boolean save(String aliasename) throws IOException {
-    // mark & update the aliase name in "alise:name" meta column.
-    // ! one matrix has only one aliasename now.
-    BatchUpdate update = new BatchUpdate(Constants.METADATA);
-    update.put(Constants.ALIASENAME, Bytes.toBytes(aliasename));
-    table.commit(update);
-
-    return hamaAdmin.save(this, aliasename);
-  }
-}
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.HColumnDescriptor;
+import org.apache.hadoop.hbase.HConstants;
+import org.apache.hadoop.hbase.HTableDescriptor;
+import org.apache.hadoop.hbase.MasterNotRunningException;
+import org.apache.hadoop.hbase.RegionException;
+import org.apache.hadoop.hbase.HColumnDescriptor.CompressionType;
+import org.apache.hadoop.hbase.client.HBaseAdmin;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.BatchUpdate;
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
+import org.apache.hadoop.hbase.io.RowResult;
+import org.apache.hadoop.hbase.mapred.IdentityTableReduce;
+import org.apache.hadoop.hbase.mapred.TableMap;
+import org.apache.hadoop.hbase.mapred.TableMapReduceUtil;
+import org.apache.hadoop.hbase.util.Bytes;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.OutputCollector;
+import org.apache.hadoop.mapred.Reporter;
+import org.apache.hama.io.VectorUpdate;
+import org.apache.hama.util.BytesUtil;
+import org.apache.hama.util.JobManager;
+import org.apache.hama.util.RandomVariable;
+import org.apache.log4j.Logger;
+
+/**
+ * Methods of the matrix classes
+ */
+public abstract class AbstractMatrix implements Matrix {
+  static int tryPathLength = Constants.DEFAULT_PATH_LENGTH;
+  static final String TABLE_PREFIX = DenseMatrix.class.getSimpleName() + "_";
+  static final Logger LOG = Logger.getLogger(AbstractMatrix.class);
+
+  protected HamaConfiguration config;
+  protected HBaseAdmin admin;
+  // a matrix just need a table path to point to the table which stores matrix.
+  // let HamaAdmin manage Matrix Name space.
+  protected String matrixPath;
+  protected HTable table;
+  protected HTableDescriptor tableDesc;
+  protected HamaAdmin hamaAdmin;
+
+  protected boolean closed = true;
+
+  /**
+   * Sets the job configuration
+   * 
+   * @param conf configuration object
+   * @throws MasterNotRunningException
+   */
+  public void setConfiguration(HamaConfiguration conf)
+      throws MasterNotRunningException {
+    this.config = conf;
+    this.admin = new HBaseAdmin(config);
+
+    hamaAdmin = new HamaAdminImpl(conf, admin);
+  }
+
+  /**
+   * try to create a new matrix with a new random name. try times will be
+   * (Integer.MAX_VALUE - 4) * DEFAULT_TRY_TIMES;
+   * 
+   * @throws IOException
+   */
+  protected void tryToCreateTable() throws IOException {
+    int tryTimes = Constants.DEFAULT_TRY_TIMES;
+    do {
+      matrixPath = TABLE_PREFIX + RandomVariable.randMatrixPath(tryPathLength);
+
+      if (!admin.tableExists(matrixPath)) { // no table 'matrixPath' in hbase.
+        tableDesc = new HTableDescriptor(matrixPath);
+        create();
+        return;
+      }
+
+      tryTimes--;
+      if (tryTimes <= 0) { // this loop has exhausted DEFAULT_TRY_TIMES.
+        tryPathLength++;
+        tryTimes = Constants.DEFAULT_TRY_TIMES;
+      }
+
+    } while (tryPathLength <= Constants.DEFAULT_MAXPATHLEN);
+    // exhaustes the try times.
+    // throw out an IOException to let the user know what happened.
+    throw new IOException("Try too many times to create a table in hbase.");
+  }
+  
+  /**
+   * Create matrix space
+   */
+  protected void create() throws IOException {
+    // It should run only when table doesn't exist.
+    if (!admin.tableExists(matrixPath)) {
+      this.tableDesc.addFamily(new HColumnDescriptor(Bytes
+          .toBytes(Constants.COLUMN), 3, CompressionType.NONE, false, false,
+          Integer.MAX_VALUE, HConstants.FOREVER, false));
+      this.tableDesc.addFamily(new HColumnDescriptor(Constants.ATTRIBUTE));
+      this.tableDesc.addFamily(new HColumnDescriptor(Constants.ALIASEFAMILY));
+      // It's a temporary data.
+      this.tableDesc.addFamily(new HColumnDescriptor(Bytes
+          .toBytes(Constants.BLOCK), 1, CompressionType.NONE, false, false,
+          Integer.MAX_VALUE, HConstants.FOREVER, false));
+
+      LOG.info("Initializing the matrix storage.");
+      this.admin.createTable(this.tableDesc);
+      LOG.info("Create Matrix " + matrixPath);
+
+      // connect to the table.
+      table = new HTable(config, matrixPath);
+      table.setAutoFlush(true);
+
+      // Record the matrix type in METADATA_TYPE
+      BatchUpdate update = new BatchUpdate(Constants.METADATA);
+      update.put(Constants.METADATA_TYPE, Bytes.toBytes(this.getClass()
+          .getSimpleName()));
+
+      table.commit(update);
+
+      // the new matrix's reference is 1.
+      setReference(1);
+    }
+  }
+
+  public HTable getHTable() {
+    return this.table;
+  }
+
+  /** {@inheritDoc} */
+  public int getRows() throws IOException {
+    Cell rows = null;
+    rows = table.get(Constants.METADATA, Constants.METADATA_ROWS);
+    return (rows != null) ? BytesUtil.bytesToInt(rows.getValue()) : 0;
+  }
+
+  /** {@inheritDoc} */
+  public int getColumns() throws IOException {
+    Cell columns = table.get(Constants.METADATA, Constants.METADATA_COLUMNS);
+    return BytesUtil.bytesToInt(columns.getValue());
+  }
+
+  /** {@inheritDoc} */
+  public String getRowLabel(int row) throws IOException {
+    Cell rows = null;
+    rows = table.get(BytesUtil.getRowIndex(row), Bytes
+        .toBytes(Constants.ATTRIBUTE + "string"));
+
+    return (rows != null) ? Bytes.toString(rows.getValue()) : null;
+  }
+
+  /** {@inheritDoc} */
+  public String getColumnLabel(int column) throws IOException {
+    Cell rows = null;
+    rows = table.get(Constants.CINDEX, (Constants.ATTRIBUTE + column));
+    return (rows != null) ? Bytes.toString(rows.getValue()) : null;
+  }
+
+  /** {@inheritDoc} */
+  public void setRowLabel(int row, String name) throws IOException {
+    VectorUpdate update = new VectorUpdate(row);
+    update.put(Constants.ATTRIBUTE + "string", name);
+    table.commit(update.getBatchUpdate());
+  }
+  
+  /** {@inheritDoc} */
+  public void setDimension(int rows, int columns) throws IOException {
+    VectorUpdate update = new VectorUpdate(Constants.METADATA);
+    update.put(Constants.METADATA_ROWS, rows);
+    update.put(Constants.METADATA_COLUMNS, columns);
+
+    table.commit(update.getBatchUpdate());
+  }
+  
+  public void increaseRows() throws IOException {
+    int nValue = this.getRows() + 1;
+    try {
+      this.setDimension(nValue, this.getColumns());
+    } catch (NullPointerException ne) {
+      // If there is no metadata of dimension, nothing to do.
+    }
+  }
+  
+  public void increaseColumns() throws IOException {
+    int nValue = this.getColumns() + 1;
+    try {
+      this.setDimension(this.getRows(), nValue);
+    } catch (NullPointerException ne) {
+      // If there is no metadata of dimension, nothing to do.
+    }
+  }
+  
+  /** {@inheritDoc} */
+  public void add(int i, int j, double value) throws IOException {
+    VectorUpdate update = new VectorUpdate(i);
+    update.put(j, value + this.get(i, j));
+    table.commit(update.getBatchUpdate());
+
+  }
+  
+  /**
+   * Just full scan a table.
+   */
+  public static class TableReadMapper extends MapReduceBase implements
+      TableMap<ImmutableBytesWritable, BatchUpdate> {
+    private static List<Double> alpha = new ArrayList<Double>();
+
+    @SuppressWarnings("unchecked")
+    public void map(ImmutableBytesWritable key, RowResult value,
+        OutputCollector<ImmutableBytesWritable, BatchUpdate> output,
+        @SuppressWarnings("unused")
+        Reporter reporter) throws IOException {
+
+      BatchUpdate update = new BatchUpdate(key.get());
+      for (Map.Entry<byte[], Cell> e : value.entrySet()) {
+        if (alpha.size() == 0) {
+          update.put(e.getKey(), e.getValue().getValue());
+        } else {
+          String column = new String(e.getKey());
+          if(column.startsWith(Constants.COLUMN)) {
+            double currValue = BytesUtil.bytesToDouble(e.getValue().getValue());
+            update.put(e.getKey(), (BytesUtil.doubleToBytes(currValue * alpha.get(0))));
+          } else {
+            update.put(e.getKey(), e.getValue().getValue());
+          }
+        }
+      }
+      output.collect(key, update);
+    }
+
+    public static void setAlpha(double a) {
+      if(alpha.size() > 0) 
+        alpha = new ArrayList<Double>();
+      alpha.add(a);
+    }
+  }
+
+  /** {@inheritDoc} */
+  public Matrix set(Matrix B) throws IOException {
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("set MR job : " + this.getPath());
+
+    jobConf.setNumMapTasks(config.getNumMapTasks());
+    jobConf.setNumReduceTasks(config.getNumReduceTasks());
+
+    TableMapReduceUtil.initTableMapJob(B.getPath(), Constants.COLUMN + " "
+        + Constants.ATTRIBUTE + " " + Constants.ALIASEFAMILY + " "
+        + Constants.BLOCK, TableReadMapper.class, ImmutableBytesWritable.class,
+        BatchUpdate.class, jobConf);
+    TableMapReduceUtil.initTableReduceJob(this.getPath(),
+        IdentityTableReduce.class, jobConf);
+
+    JobManager.execute(jobConf);
+    return this;
+  }
+
+  /** {@inheritDoc} */
+  public Matrix set(double alpha, Matrix B) throws IOException {
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("set MR job : " + this.getPath());
+
+    jobConf.setNumMapTasks(config.getNumMapTasks());
+    jobConf.setNumReduceTasks(config.getNumReduceTasks());
+
+    TableReadMapper.setAlpha(alpha);
+    TableMapReduceUtil.initTableMapJob(B.getPath(), Constants.COLUMN + " "
+        + Constants.ATTRIBUTE + " " + Constants.ALIASEFAMILY + " "
+        + Constants.BLOCK, TableReadMapper.class, ImmutableBytesWritable.class,
+        BatchUpdate.class, jobConf);
+    TableMapReduceUtil.initTableReduceJob(this.getPath(),
+        IdentityTableReduce.class, jobConf);
+
+    JobManager.execute(jobConf);
+    return this;
+  }
+
+  /** {@inheritDoc} */
+  public void setColumnLabel(int column, String name) throws IOException {
+    VectorUpdate update = new VectorUpdate(Constants.CINDEX);
+    update.put(column, name);
+    table.commit(update.getBatchUpdate());
+  }
+
+  /** {@inheritDoc} */
+  public String getPath() {
+    return matrixPath;
+  }
+
+  protected void setReference(int reference) throws IOException {
+    BatchUpdate update = new BatchUpdate(Constants.METADATA);
+    update.put(Constants.METADATA_REFERENCE, Bytes.toBytes(reference));
+    table.commit(update);
+
+  }
+
+  protected int incrementAndGetRef() throws IOException {
+    int reference = 1;
+    Cell rows = null;
+    rows = table.get(Constants.METADATA, Constants.METADATA_REFERENCE);
+    if (rows != null) {
+      reference = Bytes.toInt(rows.getValue());
+      reference++;
+    }
+    setReference(reference);
+    return reference;
+  }
+
+  protected int decrementAndGetRef() throws IOException {
+    int reference = 0;
+    Cell rows = null;
+    rows = table.get(Constants.METADATA, Constants.METADATA_REFERENCE);
+    if (rows != null) {
+      reference = Bytes.toInt(rows.getValue());
+      if (reference > 0) // reference==0, we need not to decrement it.
+        reference--;
+    }
+    setReference(reference);
+    return reference;
+  }
+
+  protected boolean hasAliaseName() throws IOException {
+    Cell rows = null;
+    rows = table.get(Constants.METADATA, Constants.ALIASENAME);
+    return (rows != null) ? true : false;
+  }
+
+  public void close() throws IOException {
+    if (closed) // have been closed
+      return;
+    int reference = decrementAndGetRef();
+    if (reference <= 0) { // no reference again.
+      if (!hasAliaseName()) { // the table has not been aliased, we delete the
+        // table.
+        if (admin.isTableEnabled(matrixPath)) {
+          while (admin.isTableEnabled(matrixPath)) {
+            try {
+              admin.disableTable(matrixPath);
+            } catch (RegionException e) {
+              LOG.warn(e);
+            }
+          }
+
+          admin.deleteTable(matrixPath);
+        }
+      }
+    }
+    closed = true;
+  }
+
+  public boolean save(String aliasename) throws IOException {
+    // mark & update the aliase name in "alise:name" meta column.
+    // ! one matrix has only one aliasename now.
+    BatchUpdate update = new BatchUpdate(Constants.METADATA);
+    update.put(Constants.ALIASENAME, Bytes.toBytes(aliasename));
+    table.commit(update);
+
+    return hamaAdmin.save(this, aliasename);
+  }
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/AbstractVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/AbstractVector.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/AbstractVector.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/AbstractVector.java Tue Feb 24 02:52:48 2009
@@ -21,11 +21,9 @@
 
 import java.util.Iterator;
 
-import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.MapWritable;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.Writable;
-import org.apache.hama.io.DoubleEntry;
 
 /**
  * Methods of the vector classes
@@ -34,48 +32,6 @@
   protected MapWritable entries;
   
   /**
-   * Gets the value of index
-   * 
-   * @param index
-   * @return the value of v(index)
-   */
-  public double get(int index) {
-    double value;
-    try {
-      value = ((DoubleEntry) this.entries.get(new IntWritable(index))).getValue();
-    } catch (NullPointerException e) {
-      throw new ArrayIndexOutOfBoundsException(index);
-    }
-    
-    return value;
-  }
-  
-  /**
-   * Sets the value of index
-   * 
-   * @param index
-   * @param value
-   */
-  public void set(int index, double value) {
-    // If entries are null, create new object 
-    if(this.entries == null) {
-      this.entries = new MapWritable();
-    }
-    
-    this.entries.put(new IntWritable(index), new DoubleEntry(value));
-  }
-  
-  /**
-   * Adds the value to v(index)
-   * 
-   * @param index
-   * @param value
-   */
-  public void add(int index, double value) {
-    set(index, get(index) + value);
-  }
-  
-  /**
    * Returns an Iterator.
    * 
    * @return iterator
@@ -105,4 +61,11 @@
   public MapWritable getEntries() {
     return this.entries;
   }
+  
+  /**
+   * Clears the entries.
+   */
+  public void clear() {
+    this.entries = null;
+  }
 }

Modified: incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/DenseMatrix.java Tue Feb 24 02:52:48 2009
@@ -25,7 +25,6 @@
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.HConstants;
-import org.apache.hadoop.hbase.HTableDescriptor;
 import org.apache.hadoop.hbase.client.HTable;
 import org.apache.hadoop.hbase.client.Scanner;
 import org.apache.hadoop.hbase.io.Cell;
@@ -60,8 +59,6 @@
  * This class represents a dense matrix.
  */
 public class DenseMatrix extends AbstractMatrix implements Matrix {
-  static int tryPathLength = Constants.DEFAULT_PATH_LENGTH;
-  static final String TABLE_PREFIX = DenseMatrix.class.getSimpleName() + "_";
   static private final Path TMP_DIR = new Path(DenseMatrix.class
       .getSimpleName()
       + "_TMP_dir");
@@ -183,35 +180,6 @@
   }
 
   /**
-   * try to create a new matrix with a new random name. try times will be
-   * (Integer.MAX_VALUE - 4) * DEFAULT_TRY_TIMES;
-   * 
-   * @throws IOException
-   */
-  private void tryToCreateTable() throws IOException {
-    int tryTimes = Constants.DEFAULT_TRY_TIMES;
-    do {
-      matrixPath = TABLE_PREFIX + RandomVariable.randMatrixPath(tryPathLength);
-
-      if (!admin.tableExists(matrixPath)) { // no table 'matrixPath' in hbase.
-        tableDesc = new HTableDescriptor(matrixPath);
-        create();
-        return;
-      }
-
-      tryTimes--;
-      if (tryTimes <= 0) { // this loop has exhausted DEFAULT_TRY_TIMES.
-        tryPathLength++;
-        tryTimes = Constants.DEFAULT_TRY_TIMES;
-      }
-
-    } while (tryPathLength <= Constants.DEFAULT_MAXPATHLEN);
-    // exhaustes the try times.
-    // throw out an IOException to let the user know what happened.
-    throw new IOException("Try too many times to create a table in hbase.");
-  }
-
-  /**
    * Generate matrix with random elements
    * 
    * @param conf configuration object
@@ -310,9 +278,9 @@
    * @return an m-by-n matrix with ones on the diagonal and zeros elsewhere.
    * @throws IOException
    */
-  public static Matrix identity(HamaConfiguration conf, int m, int n)
+  public static DenseMatrix identity(HamaConfiguration conf, int m, int n)
       throws IOException {
-    Matrix identity = new DenseMatrix(conf);
+    DenseMatrix identity = new DenseMatrix(conf);
     LOG.info("Create the " + m + " * " + n + " identity matrix : "
         + identity.getPath());
 
@@ -341,7 +309,10 @@
       throw new ArrayIndexOutOfBoundsException(i +", "+ j);
     
     Cell c = table.get(BytesUtil.getRowIndex(i), BytesUtil.getColumnIndex(j));
-    return (c != null) ? BytesUtil.bytesToDouble(c.getValue()) : 0;
+    if(c == null)
+      throw new NullPointerException("Unexpected null");
+    
+    return BytesUtil.bytesToDouble(c.getValue());
   }
 
   /**
@@ -377,6 +348,13 @@
     return new DenseVector(trunk);
   }
 
+  /** {@inheritDoc} */
+  public void set(int i, int j, double value) throws IOException {
+    VectorUpdate update = new VectorUpdate(i);
+    update.put(j, value);
+    table.commit(update.getBatchUpdate());
+  }
+  
   /**
    * Set the row of a matrix to a given vector
    * 
@@ -418,10 +396,10 @@
    * @return C
    * @throws IOException
    */
-  public Matrix add(Matrix B) throws IOException {
+  public DenseMatrix add(Matrix B) throws IOException {
     ensureForAddition(B);
     
-    Matrix result = new DenseMatrix(config);
+    DenseMatrix result = new DenseMatrix(config);
     JobConf jobConf = new JobConf(config);
     jobConf.setJobName("addition MR job" + result.getPath());
 
@@ -446,12 +424,12 @@
    * @return C
    * @throws IOException
    */
-  public Matrix add(double alpha, Matrix B) throws IOException {
+  public DenseMatrix add(double alpha, Matrix B) throws IOException {
     ensureForAddition(B);
     
-    Matrix temp = new DenseMatrix(config);
+    DenseMatrix temp = new DenseMatrix(config);
     temp.set(alpha, B);
-    Matrix result = this.add(temp);
+    DenseMatrix result = this.add(temp);
     return result;
   }
   
@@ -468,10 +446,10 @@
    * @return C
    * @throws IOException
    */
-  public Matrix mult(Matrix B) throws IOException {
+  public DenseMatrix mult(Matrix B) throws IOException {
     ensureForMultiplication(B);
     
-    Matrix result = new DenseMatrix(config);
+    DenseMatrix result = new DenseMatrix(config);
 
     JobConf jobConf = new JobConf(config);
     jobConf.setJobName("multiplication MR job : " + result.getPath());
@@ -479,7 +457,7 @@
     jobConf.setNumMapTasks(config.getNumMapTasks());
     jobConf.setNumReduceTasks(config.getNumReduceTasks());
 
-    SIMDMultiplyMap.initJob(this.getPath(), B.getPath(), SIMDMultiplyMap.class,
+    SIMDMultiplyMap.initJob(this.getPath(), B.getPath(), this.getType(), SIMDMultiplyMap.class,
         IntWritable.class, MapWritable.class, jobConf);
     SIMDMultiplyReduce.initJob(result.getPath(), SIMDMultiplyReduce.class,
         jobConf);
@@ -495,16 +473,16 @@
    * @return C
    * @throws IOException
    */
-  public Matrix mult(Matrix B, int blocks) throws IOException {
+  public DenseMatrix mult(Matrix B, int blocks) throws IOException {
     ensureForMultiplication(B);
     
-    Matrix collectionTable = new DenseMatrix(config);
+    DenseMatrix collectionTable = new DenseMatrix(config);
     LOG.info("Collect Blocks");
 
     collectBlocksMapRed(this.getPath(), collectionTable, blocks, true);
     collectBlocksMapRed(B.getPath(), collectionTable, blocks, false);
     
-    Matrix result = new DenseMatrix(config);
+    DenseMatrix result = new DenseMatrix(config);
 
     JobConf jobConf = new JobConf(config);
     jobConf.setJobName("multiplication MR job : " + result.getPath());

Modified: incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/DenseVector.java Tue Feb 24 02:52:48 2009
@@ -19,6 +19,7 @@
  */
 package org.apache.hama;
 
+import java.io.IOException;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
@@ -97,12 +98,11 @@
       return this;
     }
 
-    for (int i = 0; i < this.size(); i++) {
-      double value = (this.get(i) + v2.get(i));
-
-      this.entries.put(new IntWritable(i), new DoubleEntry(value));
+    for(Map.Entry<Writable, Writable> e : this.getEntries().entrySet()) {
+      double value = ((DoubleEntry) e.getValue()).getValue() + v2.get(((IntWritable) e.getKey()).get());
+      this.entries.put(e.getKey(), new DoubleEntry(value));
     }
-
+    
     return this;
   }
 
@@ -129,7 +129,7 @@
    * @param alpha
    * @return v = alpha*v
    */
-  public Vector scale(double alpha) {
+  public DenseVector scale(double alpha) {
     for(Map.Entry<Writable, Writable> e : this.entries.entrySet()) {
       this.entries.put(e.getKey(), new DoubleEntry(((DoubleEntry) e.getValue()).getValue() * alpha));
     }
@@ -190,6 +190,49 @@
     return Math.sqrt(square_sum);
   }
 
+  /**
+   * Gets the value of index
+   * 
+   * @param index
+   * @return the value of v(index)
+   * @throws IOException 
+   */
+  public double get(int index) {
+    double value;
+    try {
+      value = ((DoubleEntry) this.entries.get(new IntWritable(index))).getValue();
+    } catch (NullPointerException e) {
+      throw new NullPointerException("Unexpected null value : " + e.toString());
+    }
+    
+    return value;
+  }
+  
+  /**
+   * Sets the value of index
+   * 
+   * @param index
+   * @param value
+   */
+  public void set(int index, double value) {
+    // If entries are null, create new object 
+    if(this.entries == null) {
+      this.entries = new MapWritable();
+    }
+    
+    this.entries.put(new IntWritable(index), new DoubleEntry(value));
+  }
+  
+  /**
+   * Adds the value to v(index)
+   * 
+   * @param index
+   * @param value
+   */
+  public void add(int index, double value) {
+    set(index, get(index) + value);
+  }
+  
   public double getNorm2Robust() {
     // TODO Auto-generated method stub
     return 0;
@@ -218,11 +261,4 @@
 
     return res;
   }
-
-  /**
-   * Clears the entries.
-   */
-  public void clear() {
-    this.entries = null;
-  }
 }

Added: incubator/hama/trunk/src/java/org/apache/hama/SparseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/SparseMatrix.java?rev=747265&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/SparseMatrix.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/SparseMatrix.java Tue Feb 24 02:52:48 2009
@@ -0,0 +1,208 @@
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.IOException;
+import java.util.Random;
+
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hama.algebra.SIMDMultiplyMap;
+import org.apache.hama.algebra.SIMDMultiplyReduce;
+import org.apache.hama.io.VectorUpdate;
+import org.apache.hama.util.BytesUtil;
+import org.apache.hama.util.JobManager;
+import org.apache.hama.util.RandomVariable;
+
+public class SparseMatrix extends AbstractMatrix implements Matrix {
+
+  public SparseMatrix(HamaConfiguration conf) throws IOException {
+    setConfiguration(conf);
+
+    tryToCreateTable();
+
+    closed = false;
+  }
+
+  /**
+   * Load a matrix from an existed matrix table whose tablename is 'matrixpath' !!
+   * It is an internal used for map/reduce.
+   * 
+   * @param conf configuration object
+   * @param matrixpath
+   * @throws IOException
+   * @throws IOException
+   */
+  public SparseMatrix(HamaConfiguration conf, String matrixpath)
+      throws IOException {
+    setConfiguration(conf);
+    matrixPath = matrixpath;
+    // load the matrix
+    table = new HTable(conf, matrixPath);
+    // TODO: now we don't increment the reference of the table
+    // for it's an internal use for map/reduce.
+    // if we want to increment the reference of the table,
+    // we don't know where to call Matrix.close in Add & Mul map/reduce
+    // process to decrement the reference. It seems difficulty.
+  }
+  /**
+   * Generate matrix with random elements
+   * 
+   * @param conf configuration object
+   * @param m the number of rows.
+   * @param n the number of columns.
+   * @return an m-by-n matrix with uniformly distributed random elements.
+   * @throws IOException
+   */
+  public static SparseMatrix random(HamaConfiguration conf, int m, int n)
+      throws IOException {
+    SparseMatrix rand = new SparseMatrix(conf);
+    SparseVector vector = new SparseVector();
+    LOG.info("Create the " + m + " * " + n + " random matrix : "
+        + rand.getPath());
+
+    for (int i = 0; i < m; i++) {
+      vector.clear();
+      for (int j = 0; j < n; j++) {
+        Random r = new Random(); 
+        if(r.nextInt(2) != 0)
+          vector.set(j, RandomVariable.rand());
+      }
+      rand.setRow(i, vector);
+    }
+
+    rand.setDimension(m, n);
+    return rand;
+  }
+  
+  @Override
+  public Matrix add(Matrix B) throws IOException {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public Matrix add(double alpha, Matrix B) throws IOException {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public double get(int i, int j) throws IOException {
+    if(this.getRows() < i || this.getColumns() < j)
+      throw new ArrayIndexOutOfBoundsException(i +", "+ j);
+    
+    Cell c = table.get(BytesUtil.getRowIndex(i), BytesUtil.getColumnIndex(j));
+    return (c != null) ? BytesUtil.bytesToDouble(c.getValue()) : 0.0;
+  }
+
+  @Override
+  public Vector getColumn(int j) throws IOException {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  /**
+   * Gets the vector of row
+   * 
+   * @param i the row index of the matrix
+   * @return the vector of row
+   * @throws IOException
+   */
+  public SparseVector getRow(int i) throws IOException {
+    // Should returns zero-fill vector.
+    return new SparseVector(table.getRow(BytesUtil.getRowIndex(i)));
+  }
+
+  /** {@inheritDoc} */
+  public void set(int i, int j, double value) throws IOException {
+    if(value != 0) {
+      VectorUpdate update = new VectorUpdate(i);
+      update.put(j, value);
+      table.commit(update.getBatchUpdate());
+    }
+  }
+  
+  /**
+   * Returns type of matrix
+   */
+  public String getType() {
+    return this.getClass().getSimpleName();
+  }
+
+  @Override
+  public SparseMatrix mult(Matrix B) throws IOException {
+    SparseMatrix result = new SparseMatrix(config);
+
+    JobConf jobConf = new JobConf(config);
+    jobConf.setJobName("multiplication MR job : " + result.getPath());
+
+    jobConf.setNumMapTasks(config.getNumMapTasks());
+    jobConf.setNumReduceTasks(config.getNumReduceTasks());
+
+    SIMDMultiplyMap.initJob(this.getPath(), B.getPath(), this.getType(), SIMDMultiplyMap.class,
+        IntWritable.class, MapWritable.class, jobConf);
+    SIMDMultiplyReduce.initJob(result.getPath(), SIMDMultiplyReduce.class,
+        jobConf);
+    JobManager.execute(jobConf);
+    result.setDimension(this.getRows(), this.getColumns());
+    return result;
+  }
+
+  @Override
+  public Matrix multAdd(double alpha, Matrix B, Matrix C) throws IOException {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public double norm(Norm type) throws IOException {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  @Override
+  public void setColumn(int column, Vector vector) throws IOException {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void setRow(int row, Vector vector) throws IOException {
+    if(this.getRows() < row)
+      increaseRows();
+    
+    if(vector.size() > 0) {  // stores if size > 0
+      VectorUpdate update = new VectorUpdate(row);
+      update.putAll(((SparseVector) vector).getEntries());
+      table.commit(update.getBatchUpdate());
+    }
+  }
+
+  @Override
+  public SubMatrix subMatrix(int i0, int i1, int j0, int j1) throws IOException {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+}

Added: incubator/hama/trunk/src/java/org/apache/hama/SparseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/SparseVector.java?rev=747265&view=auto
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/SparseVector.java (added)
+++ incubator/hama/trunk/src/java/org/apache/hama/SparseVector.java Tue Feb 24 02:52:48 2009
@@ -0,0 +1,167 @@
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hadoop.hbase.io.RowResult;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.io.MapWritable;
+import org.apache.hadoop.io.Writable;
+import org.apache.hama.io.DoubleEntry;
+import org.apache.hama.util.BytesUtil;
+import org.apache.log4j.Logger;
+
+public class SparseVector extends AbstractVector implements Vector {
+  static final Logger LOG = Logger.getLogger(SparseVector.class);
+  public SparseVector() {
+    this(new MapWritable());
+  }
+
+  public SparseVector(MapWritable m) {
+    this.entries = m;
+  }
+  
+  public SparseVector(RowResult row) {
+    this.entries = new MapWritable();
+    for (Map.Entry<byte[], Cell> f : row.entrySet()) {
+      this.entries.put(new IntWritable(BytesUtil.getColumnIndex(f.getKey())), 
+          new DoubleEntry(f.getValue()));
+    }
+  }
+
+  @Override
+  public Vector add(double alpha, Vector v) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+  
+  /**
+   * x = v + x
+   * 
+   * @param v2
+   * @return x = v + x
+   */
+  public SparseVector add(Vector v2) {
+    if (this.size() == 0) {
+      SparseVector trunk = (SparseVector) v2;
+      this.entries = trunk.entries;
+      return this;
+    }
+
+    for(Map.Entry<Writable, Writable> e : ((SparseVector )v2).getEntries().entrySet()) {
+      
+      if(this.entries.containsKey(e.getKey())) {
+        // add
+        double value = ((DoubleEntry) e.getValue()).getValue() + this.get(((IntWritable) e.getKey()).get());
+        this.entries.put(e.getKey(), new DoubleEntry(value));
+      } else {
+        //  put
+        this.entries.put(e.getKey(), e.getValue());
+      }
+    }
+
+    return this;
+  }
+
+  @Override
+  public double dot(Vector v) {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  @Override
+  public double norm(Norm type) {
+    // TODO Auto-generated method stub
+    return 0;
+  }
+
+  /**
+   * v = alpha*v 
+   * 
+   * @param alpha
+   * @return v = alpha*v
+   */
+  public SparseVector scale(double alpha) {
+    for(Map.Entry<Writable, Writable> e : this.entries.entrySet()) {
+      this.entries.put(e.getKey(), new DoubleEntry(((DoubleEntry) e.getValue()).getValue() * alpha));
+    }
+    return this;
+  }
+
+  /**
+   * Gets the value of index
+   * 
+   * @param index
+   * @return the value of v(index)
+   * @throws IOException 
+   */
+  public double get(int index) {
+    double value;
+    try {
+      value = ((DoubleEntry) this.entries.get(new IntWritable(index))).getValue();
+    } catch (NullPointerException e) { // returns zero if there is no value
+      return 0;
+    }
+    
+    return value;
+  }
+  
+  /**
+   * Sets the value of index
+   * 
+   * @param index
+   * @param value
+   */
+  public void set(int index, double value) {
+    // If entries are null, create new object 
+    if(this.entries == null) {
+      this.entries = new MapWritable();
+    }
+    
+    if(value != 0) // only stores non-zero element
+      this.entries.put(new IntWritable(index), new DoubleEntry(value));
+  }
+  
+  /**
+   * Adds the value to v(index)
+   * 
+   * @param index
+   * @param value
+   */
+  public void add(int index, double value) {
+    set(index, get(index) + value);
+  }
+  
+  @Override
+  public Vector set(Vector v) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public Vector subVector(int i0, int i1) {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+}

Modified: incubator/hama/trunk/src/java/org/apache/hama/SubMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/SubMatrix.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/SubMatrix.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/SubMatrix.java Tue Feb 24 02:52:48 2009
@@ -1,223 +1,222 @@
-/**
- * Copyright 2007 The Apache Software Foundation
- *
- * 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.hama;
-
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.IOException;
-
-import org.apache.hama.util.BytesUtil;
-import org.apache.log4j.Logger;
-
-/**
- * A sub matrix is a matrix formed by selecting certain rows and columns from a
- * bigger matrix. This is a in-memory operation only.
- */
-public class SubMatrix {
-  static final Logger LOG = Logger.getLogger(SubMatrix.class);
-  private double[][] matrix;
-
-  /**
-   * Constructor
-   * 
-   * @param i the size of rows
-   * @param j the size of columns
-   */
-  public SubMatrix(int i, int j) {
-    this.matrix = new double[i][j];
-  }
-
-  /**
-   * Constructor
-   * 
-   * @param c a two dimensional double array
-   */
-  public SubMatrix(double[][] c) {
-    double[][] matrix = c;
-    this.matrix = matrix;
-  }
-
-  public SubMatrix(byte[] matrix) throws IOException {
-    ByteArrayInputStream bos = new ByteArrayInputStream(matrix);
-    DataInputStream dis = new DataInputStream(bos);
-    
-    int rows = dis.readInt();
-    int columns = dis.readInt();
-    this.matrix = new double[rows][columns];
-    
-    for(int i = 0; i < rows; i++) {
-      for(int j = 0; j < columns; j++) {
-        this.matrix[i][j] = dis.readDouble();        
-      }
-    }
-    
-    dis.close();
-    bos.close();
-  }
-  
-  /**
-   * Sets the value
-   * 
-   * @param row
-   * @param column
-   * @param value
-   */
-  public void set(int row, int column, double value) {
-    matrix[row][column] = value;
-  }
-
-  /**
-   * Sets the value
-   * 
-   * @param row
-   * @param column
-   * @param value
-   */
-  public void set(int row, int column, byte[] value) {
-    matrix[row][column] = BytesUtil.bytesToDouble(value);    
-  }
-  
-  /**
-   * Gets the value
-   * 
-   * @param i
-   * @param j
-   * @return the value of submatrix(i, j)
-   */
-  public double get(int i, int j) {
-    return matrix[i][j];
-  }
-
-  public void add(int row, int column, double value) {
-    matrix[row][column] = matrix[row][column] + value;
-  }
-
-  /**
-   * c = a+b
-   * 
-   * @param b
-   * @return c
-   */
-  public SubMatrix add(SubMatrix b) {
-    SubMatrix c = new SubMatrix(this.getRows(), this.getColumns());
-    
-    for (int i = 0; i < this.getRows(); i++) {
-      for (int j = 0; j < this.getColumns(); j++) {
-        c.set(i, j, (this.get(i, j) + b.get(i, j)));
-      }
-    }
-
-    return c;
-  }
-
-  /**
-   * c = a*b
-   * 
-   * @param b
-   * @return c
-   */
-  public SubMatrix mult(SubMatrix b) {
-    SubMatrix c = new SubMatrix(this.getRows(), b.getColumns());
-    
-    for (int i = 0; i < this.getRows(); i++) {
-      for (int j = 0; j < b.getColumns(); j++) {
-        for (int k = 0; k < this.getColumns(); k++) {
-          c.add(i, j, this.get(i, k) * b.get(k, j));
-        }
-      }
-    }
-
-    return c;
-  }
-
-  /**
-   * Gets the number of rows
-   * 
-   * @return the number of rows
-   */
-  public int getRows() {
-    return this.matrix.length;
-  }
-
-  /**
-   * Gets the number of columns
-   * 
-   * @return the number of columns
-   */
-  public int getColumns() {
-    return this.matrix[0].length;
-  }
-
-  /**
-   * Close
-   */
-  public void close() {
-    matrix = null;
-  }
-
-  /**
-   * @return the 2d double array
-   */
-  public double[][] getDoubleArray() {
-    double[][] result = matrix;
-    return result;
-  }
-
-  /**
-   * Gets the bytes of the sub matrix
-   * 
-   * @return the bytes of the sub matrix
-   * @throws IOException
-   */
-  public byte[] getBytes() throws IOException {
-    ByteArrayOutputStream bos = new ByteArrayOutputStream();
-    DataOutputStream dos = new DataOutputStream(bos);
-    
-    dos.writeInt(this.getRows());
-    dos.writeInt(this.getColumns());
-    
-    for(int i = 0; i < this.getRows(); i++) {
-      for(int j = 0; j < this.getColumns(); j++) {
-        dos.writeDouble(this.get(i, j));
-      }
-    }
-
-    byte[] data = bos.toByteArray();
-    dos.close();
-    bos.close();
-    return data;
-  }
-
-  public String toString() {
-    StringBuilder result = new StringBuilder();
-    for (int i = 0; i < this.getRows(); i++) {
-      for (int j = 0; j < this.getColumns(); j++) {
-        result.append(this.get(i, j));
-        result.append('\t');
-      }
-      result.append('\n');
-    }
-    return result.toString();
-  }
-}
-
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.IOException;
+
+import org.apache.hama.util.BytesUtil;
+import org.apache.log4j.Logger;
+
+/**
+ * A sub matrix is a matrix formed by selecting certain rows and columns from a
+ * bigger matrix. This is a in-memory operation only.
+ */
+public class SubMatrix {
+  static final Logger LOG = Logger.getLogger(SubMatrix.class);
+  private double[][] matrix;
+
+  /**
+   * Constructor
+   * 
+   * @param i the size of rows
+   * @param j the size of columns
+   */
+  public SubMatrix(int i, int j) {
+    this.matrix = new double[i][j];
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param c a two dimensional double array
+   */
+  public SubMatrix(double[][] c) {
+    double[][] matrix = c;
+    this.matrix = matrix;
+  }
+
+  public SubMatrix(byte[] matrix) throws IOException {
+    ByteArrayInputStream bos = new ByteArrayInputStream(matrix);
+    DataInputStream dis = new DataInputStream(bos);
+    
+    int rows = dis.readInt();
+    int columns = dis.readInt();
+    this.matrix = new double[rows][columns];
+    
+    for(int i = 0; i < rows; i++) {
+      for(int j = 0; j < columns; j++) {
+        this.matrix[i][j] = dis.readDouble();        
+      }
+    }
+    
+    dis.close();
+    bos.close();
+  }
+  
+  /**
+   * Sets the value
+   * 
+   * @param row
+   * @param column
+   * @param value
+   */
+  public void set(int row, int column, double value) {
+    matrix[row][column] = value;
+  }
+
+  /**
+   * Sets the value
+   * 
+   * @param row
+   * @param column
+   * @param value
+   */
+  public void set(int row, int column, byte[] value) {
+    matrix[row][column] = BytesUtil.bytesToDouble(value);    
+  }
+  
+  /**
+   * Gets the value
+   * 
+   * @param i
+   * @param j
+   * @return the value of submatrix(i, j)
+   */
+  public double get(int i, int j) {
+    return matrix[i][j];
+  }
+
+  public void add(int row, int column, double value) {
+    matrix[row][column] = matrix[row][column] + value;
+  }
+
+  /**
+   * c = a+b
+   * 
+   * @param b
+   * @return c
+   */
+  public SubMatrix add(SubMatrix b) {
+    SubMatrix c = new SubMatrix(this.getRows(), this.getColumns());
+    
+    for (int i = 0; i < this.getRows(); i++) {
+      for (int j = 0; j < this.getColumns(); j++) {
+        c.set(i, j, (this.get(i, j) + b.get(i, j)));
+      }
+    }
+
+    return c;
+  }
+
+  /**
+   * c = a*b
+   * 
+   * @param b
+   * @return c
+   */
+  public SubMatrix mult(SubMatrix b) {
+    SubMatrix c = new SubMatrix(this.getRows(), b.getColumns());
+    
+    for (int i = 0; i < this.getRows(); i++) {
+      for (int j = 0; j < b.getColumns(); j++) {
+        for (int k = 0; k < this.getColumns(); k++) {
+          c.add(i, j, this.get(i, k) * b.get(k, j));
+        }
+      }
+    }
+
+    return c;
+  }
+
+  /**
+   * Gets the number of rows
+   * 
+   * @return the number of rows
+   */
+  public int getRows() {
+    return this.matrix.length;
+  }
+
+  /**
+   * Gets the number of columns
+   * 
+   * @return the number of columns
+   */
+  public int getColumns() {
+    return this.matrix[0].length;
+  }
+
+  /**
+   * Close
+   */
+  public void close() {
+    matrix = null;
+  }
+
+  /**
+   * @return the 2d double array
+   */
+  public double[][] getDoubleArray() {
+    double[][] result = matrix;
+    return result;
+  }
+
+  /**
+   * Gets the bytes of the sub matrix
+   * 
+   * @return the bytes of the sub matrix
+   * @throws IOException
+   */
+  public byte[] getBytes() throws IOException {
+    ByteArrayOutputStream bos = new ByteArrayOutputStream();
+    DataOutputStream dos = new DataOutputStream(bos);
+    
+    dos.writeInt(this.getRows());
+    dos.writeInt(this.getColumns());
+    
+    for(int i = 0; i < this.getRows(); i++) {
+      for(int j = 0; j < this.getColumns(); j++) {
+        dos.writeDouble(this.get(i, j));
+      }
+    }
+
+    byte[] data = bos.toByteArray();
+    dos.close();
+    bos.close();
+    return data;
+  }
+
+  public String toString() {
+    StringBuilder result = new StringBuilder();
+    for (int i = 0; i < this.getRows(); i++) {
+      for (int j = 0; j < this.getColumns(); j++) {
+        result.append(this.get(i, j));
+        result.append('\t');
+      }
+      result.append('\n');
+    }
+    return result.toString();
+  }
+}
+

Modified: incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyMap.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyMap.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyMap.java (original)
+++ incubator/hama/trunk/src/java/org/apache/hama/algebra/SIMDMultiplyMap.java Tue Feb 24 02:52:48 2009
@@ -34,7 +34,9 @@
 import org.apache.hama.DenseVector;
 import org.apache.hama.HamaConfiguration;
 import org.apache.hama.Matrix;
-import org.apache.hama.io.DoubleEntry;
+import org.apache.hama.SparseMatrix;
+import org.apache.hama.SparseVector;
+import org.apache.hama.Vector;
 import org.apache.hama.mapred.VectorInputFormat;
 import org.apache.log4j.Logger;
 
@@ -45,18 +47,27 @@
 Mapper<IntWritable, MapWritable, IntWritable, MapWritable> {
   static final Logger LOG = Logger.getLogger(SIMDMultiplyMap.class);
   protected Matrix matrix_b;
+  protected Vector sum;
+  protected String type;
   public static final String MATRIX_B = "hama.multiplication.matrix.b";
-  public static final DenseVector sum = new DenseVector();;
+  public static final String MATRIX_TYPE = "hama.multiplication.matrix.type";
   
   public void configure(JobConf job) {
     try {
-      matrix_b = new DenseMatrix(new HamaConfiguration(job), job.get(MATRIX_B, ""));
+      type = job.get(MATRIX_TYPE, "");
+      if(type.equals("SparseMatrix")) {
+        matrix_b = new SparseMatrix(new HamaConfiguration(job), job.get(MATRIX_B, ""));
+        sum = new SparseVector();
+      } else {
+        matrix_b = new DenseMatrix(new HamaConfiguration(job), job.get(MATRIX_B, ""));
+        sum = new DenseVector();
+      }
     } catch (IOException e) {
       LOG.warn("Load matrix_b failed : " + e.getMessage());
     }
   }
 
-  public static void initJob(String matrix_a, String matrix_b,
+  public static void initJob(String matrix_a, String matrix_b, String type, 
       Class<SIMDMultiplyMap> map, Class<IntWritable> outputKeyClass,
       Class<MapWritable> outputValueClass, JobConf jobConf) {
 
@@ -64,6 +75,7 @@
     jobConf.setMapOutputKeyClass(outputKeyClass);
     jobConf.setMapperClass(map);
     jobConf.set(MATRIX_B, matrix_b);
+    jobConf.set(MATRIX_TYPE, type);
 
     jobConf.setInputFormat(VectorInputFormat.class);
     FileInputFormat.addInputPaths(jobConf, matrix_a);
@@ -74,12 +86,26 @@
   public void map(IntWritable key, MapWritable value,
       OutputCollector<IntWritable, MapWritable> output, Reporter reporter)
       throws IOException {
-    sum.clear();
-
-    for(int i = 0; i < value.size(); i++) {
-      sum.add(matrix_b.getRow(i).scale(((DoubleEntry) value.get(new IntWritable(i))).getValue()));
+    if(type.equals("SparseMatrix")) {
+      ((SparseVector) sum).clear();
+      SparseVector currVector = new SparseVector(value);
+      
+      for(int i = 0; i < matrix_b.getColumns(); i++) {
+        ((SparseVector) sum).add(((SparseMatrix) matrix_b).getRow(i).scale(
+            currVector.get(i)));
+      }
+      
+      
+      output.collect(key, ((SparseVector) sum).getEntries());
+    } else {
+      ((DenseVector) sum).clear();
+      DenseVector currVector = new DenseVector(value);
+      for(int i = 0; i < value.size(); i++) {
+        ((DenseVector) sum).add(((DenseMatrix) matrix_b).getRow(i).scale(
+            currVector.get(i)));
+      }
+      output.collect(key, ((DenseVector) sum).getEntries());
     }
     
-    output.collect(key, sum.getEntries());
   }
 }

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestDenseMatrix.java Tue Feb 24 02:52:48 2009
@@ -185,8 +185,9 @@
     a.set(m1);
 
     for (int i = 0; i < 5; i++) {
-      int x = RandomVariable.randInt(0, 10);
-      int y = RandomVariable.randInt(0, 10);
+      // between 0 ~ SIZE -1
+      int x = RandomVariable.randInt(0, SIZE - 1);
+      int y = RandomVariable.randInt(0, SIZE - 1);
       assertEquals(a.get(x, y), m1.get(x, y));
     }
   }
@@ -196,8 +197,8 @@
     a.set(0.5, m1);
     
     for (int i = 0; i < 5; i++) {
-      int x = RandomVariable.randInt(0, 10);
-      int y = RandomVariable.randInt(0, 10);
+      int x = RandomVariable.randInt(0, SIZE - 1);
+      int y = RandomVariable.randInt(0, SIZE - 1);
       assertEquals(a.get(x, y), (m1.get(x, y) * 0.5));
     }
   }
@@ -274,8 +275,8 @@
     // load matrix m1 using aliase1
     DenseMatrix loadTest = new DenseMatrix(conf, aliase1, false);
 
-    for (int i = 0; i < loadTest.getRows(); i++) {
-      for (int j = 0; j < loadTest.getColumns(); j++) {
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
         assertEquals(m1.get(i, j), loadTest.get(i, j));
       }
     }

Modified: incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java?rev=747265&r1=747264&r2=747265&view=diff
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java (original)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestDenseVector.java Tue Feb 24 02:52:48 2009
@@ -39,9 +39,9 @@
   private static final double norm1 = 12.0;
   private static final double norm2 = 6.782329983125268;
   private static double[][] values = { { 2, 5, 1, 4 }, { 4, 1, 3, 3 } };
-  private static Matrix m1;
-  private static Vector v1;
-  private static Vector v2;
+  private static DenseMatrix m1;
+  private static DenseVector v1;
+  private static DenseVector v2;
 
   public static Test suite() {
     TestSetup setup = new TestSetup(new TestSuite(TestDenseVector.class)) {
@@ -122,7 +122,7 @@
     boolean ex = false;
     try {
       v1.get(5);
-    } catch (ArrayIndexOutOfBoundsException e) {
+    } catch (NullPointerException e) {
       ex = true;
     }
     assertTrue(ex);

Added: incubator/hama/trunk/src/test/org/apache/hama/TestSparseMatrix.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestSparseMatrix.java?rev=747265&view=auto
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestSparseMatrix.java (added)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestSparseMatrix.java Tue Feb 24 02:52:48 2009
@@ -0,0 +1,112 @@
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.IOException;
+
+import junit.extensions.TestSetup;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.apache.log4j.Logger;
+
+public class TestSparseMatrix extends TestCase {
+  static final Logger LOG = Logger.getLogger(TestSparseMatrix.class);
+  private static int SIZE = 10;
+  private static SparseMatrix m1;
+  private static SparseMatrix m2;
+
+  public static Test suite() {
+    TestSetup setup = new TestSetup(new TestSuite(TestSparseMatrix.class)) {
+      protected void setUp() throws Exception {
+        HCluster hCluster = new HCluster();
+        hCluster.setUp();
+
+        m1 = SparseMatrix.random(hCluster.getConf(), SIZE, SIZE);
+        m2 = SparseMatrix.random(hCluster.getConf(), SIZE, SIZE);
+      }
+
+      protected void tearDown() {
+        try {
+          closeTest();
+        } catch (IOException e) {
+          e.printStackTrace();
+        }
+      }
+    };
+    return setup;
+  }
+
+  public static void closeTest() throws IOException {
+    m1.close();
+    m2.close();
+  }
+
+  public void testSparsity() throws IOException {
+    boolean appeared = false;
+    for(int i = 0; i < m1.getRows(); i++) {
+      for(int j = 0; j < m1.getColumns(); j++) {
+        if(m1.get(i, j) == 0)
+          appeared = true;
+      }
+    }
+    
+    assertTrue(appeared);
+  }
+  
+  /**
+   * Test matrices multiplication
+   * 
+   * @throws IOException
+   */
+  public void testMatrixMult() throws IOException {
+    SparseMatrix result = m1.mult(m2);
+    verifyMultResult(m1, m2, result);
+  }
+  
+  /**
+   * Verifying multiplication result
+   * 
+   * @param m1
+   * @param m2
+   * @param result
+   * @throws IOException
+   */
+  private void verifyMultResult(SparseMatrix m1, SparseMatrix m2, SparseMatrix result)
+      throws IOException {
+    double[][] c = new double[SIZE][SIZE];
+
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
+        for (int k = 0; k < SIZE; k++) {
+          c[i][k] += m1.get(i, j) * m2.get(j, k);
+        }
+      }
+    }
+
+    for (int i = 0; i < SIZE; i++) {
+      for (int j = 0; j < SIZE; j++) {
+        double gap = (c[i][j] - result.get(i, j));
+        assertTrue(gap < 0.000001 || gap < -0.000001);
+      }
+    }
+  }
+}

Added: incubator/hama/trunk/src/test/org/apache/hama/TestSparseVector.java
URL: http://svn.apache.org/viewvc/incubator/hama/trunk/src/test/org/apache/hama/TestSparseVector.java?rev=747265&view=auto
==============================================================================
--- incubator/hama/trunk/src/test/org/apache/hama/TestSparseVector.java (added)
+++ incubator/hama/trunk/src/test/org/apache/hama/TestSparseVector.java Tue Feb 24 02:52:48 2009
@@ -0,0 +1,77 @@
+/**
+ * Copyright 2007 The Apache Software Foundation
+ *
+ * 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.hama;
+
+import java.io.IOException;
+
+import junit.extensions.TestSetup;
+import junit.framework.Test;
+import junit.framework.TestCase;
+import junit.framework.TestSuite;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.hbase.client.HTable;
+import org.apache.hadoop.hbase.io.Cell;
+import org.apache.hama.util.BytesUtil;
+
+public class TestSparseVector extends TestCase {
+  final static Log LOG = LogFactory.getLog(TestSparseVector.class.getName());
+  private static SparseMatrix m1;
+  private static SparseVector v1;
+  private static SparseVector v2;
+  private static double[][] values = { { 2, 0, 0, 4 }, { 0, 0, 3, 3 } };
+
+  public static Test suite() {
+    TestSetup setup = new TestSetup(new TestSuite(TestSparseVector.class)) {
+      protected void setUp() throws Exception {
+        HCluster hCluster = new HCluster();
+        hCluster.setUp();
+
+        m1 = new SparseMatrix(hCluster.getConf());
+
+        for (int i = 0; i < 2; i++)
+          for (int j = 0; j < 4; j++)
+            m1.set(i, j, values[i][j]);
+
+        v1 = m1.getRow(0);
+        v2 = m1.getRow(1);
+      }
+
+      protected void tearDown() {
+        LOG.info("tearDown()");
+      }
+    };
+    return setup;
+  }
+
+  /**
+   * Test get/set methods
+   * @throws IOException 
+   */
+  public void testGetSet() throws IOException {
+    assertEquals(v1.get(1), 0.0);
+    assertEquals(v2.get(1), 0.0);
+    
+    HTable table = m1.getHTable();
+    Cell c = table.get(BytesUtil.getRowIndex(0), BytesUtil.getColumnIndex(1));
+    assertTrue(c == null);
+  }
+}



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