HBASE-13082 Coarsen StoreScanner locks to RegionScanner (Ram)

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/DefaultStoreFileManager.java

@@ -54,6 +54,13 @@ class DefaultStoreFileManager implements StoreFileManager {
    * is atomically replaced when its contents change.
    */
   private volatile ImmutableList<StoreFile> storefiles = null;
+  /**
+   * List of compacted files inside this store that needs to be excluded in reads
+   * because further new reads will be using only the newly created files out of compaction.
+   * These compacted files will be deleted/cleared once all the existing readers on these
+   * compacted files are done.
+   */
+  private volatile List<StoreFile> compactedfiles = null;
 
   public DefaultStoreFileManager(CellComparator kvComparator, Configuration conf,
       CompactionConfiguration comConf) {
@@ -74,6 +81,11 @@ class DefaultStoreFileManager implements StoreFileManager {
     return storefiles;
   }
 
+  @Override
+  public Collection<StoreFile> getCompactedfiles() {
+    return compactedfiles;
+  }
+
   @Override
   public void insertNewFiles(Collection<StoreFile> sfs) throws IOException {
     ArrayList<StoreFile> newFiles = new ArrayList<StoreFile>(storefiles);
@@ -88,6 +100,13 @@ class DefaultStoreFileManager implements StoreFileManager {
     return result;
   }
 
+  @Override
+  public Collection<StoreFile> clearCompactedFiles() {
+    List<StoreFile> result = compactedfiles;
+    compactedfiles = new ArrayList<StoreFile>();
+    return result;
+  }
+
   @Override
   public final int getStorefileCount() {
     return storefiles.size();
@@ -95,13 +114,42 @@ class DefaultStoreFileManager implements StoreFileManager {
 
   @Override
   public void addCompactionResults(
-    Collection<StoreFile> compactedFiles, Collection<StoreFile> results) {
+    Collection<StoreFile> newCompactedfiles, Collection<StoreFile> results) {
     ArrayList<StoreFile> newStoreFiles = Lists.newArrayList(storefiles);
-    newStoreFiles.removeAll(compactedFiles);
+    newStoreFiles.removeAll(newCompactedfiles);
     if (!results.isEmpty()) {
       newStoreFiles.addAll(results);
     }
     sortAndSetStoreFiles(newStoreFiles);
+    ArrayList<StoreFile> updatedCompactedfiles = null;
+    if (this.compactedfiles != null) {
+      updatedCompactedfiles = new ArrayList<StoreFile>(this.compactedfiles);
+      updatedCompactedfiles.addAll(newCompactedfiles);
+    } else {
+      updatedCompactedfiles = new ArrayList<StoreFile>(newCompactedfiles);
+    }
+    markCompactedAway(newCompactedfiles);
+    this.compactedfiles = sortCompactedfiles(updatedCompactedfiles);
+  }
+
+  // Mark the files as compactedAway once the storefiles and compactedfiles list is finalised
+  // Let a background thread close the actual reader on these compacted files and also
+  // ensure to evict the blocks from block cache so that they are no longer in
+  // cache
+  private void markCompactedAway(Collection<StoreFile> compactedFiles) {
+    for (StoreFile file : compactedFiles) {
+      file.markCompactedAway();
+    }
+  }
+
+  @Override
+  public void removeCompactedFiles(Collection<StoreFile> removedCompactedfiles) throws IOException {
+    ArrayList<StoreFile> updatedCompactedfiles = null;
+    if (this.compactedfiles != null) {
+      updatedCompactedfiles = new ArrayList<StoreFile>(this.compactedfiles);
+      updatedCompactedfiles.removeAll(removedCompactedfiles);
+      this.compactedfiles = sortCompactedfiles(updatedCompactedfiles);
+    }
   }
 
   @Override
@@ -166,6 +214,12 @@ class DefaultStoreFileManager implements StoreFileManager {
     storefiles = ImmutableList.copyOf(storeFiles);
   }
 
+  private List<StoreFile> sortCompactedfiles(List<StoreFile> storefiles) {
+    // Sorting may not be really needed here for the compacted files?
+    Collections.sort(storefiles, StoreFile.Comparators.SEQ_ID);
+    return new ArrayList<StoreFile>(storefiles);
+  }
+
   @Override
   public double getCompactionPressure() {
     int storefileCount = getStorefileCount();

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HRegion.java

@@ -73,6 +73,7 @@ import org.apache.hadoop.hbase.Cell;
 import org.apache.hadoop.hbase.CellComparator;
 import org.apache.hadoop.hbase.CellScanner;
 import org.apache.hadoop.hbase.CellUtil;
+import org.apache.hadoop.hbase.ChoreService;
 import org.apache.hadoop.hbase.CompoundConfiguration;
 import org.apache.hadoop.hbase.DoNotRetryIOException;
 import org.apache.hadoop.hbase.DroppedSnapshotException;
@@ -148,6 +149,7 @@ import org.apache.hadoop.hbase.protobuf.generated.WALProtos.RegionEventDescripto
 import org.apache.hadoop.hbase.protobuf.generated.WALProtos.StoreDescriptor;
 import org.apache.hadoop.hbase.regionserver.ScannerContext.LimitScope;
 import org.apache.hadoop.hbase.regionserver.ScannerContext.NextState;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionContext;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionThroughputController;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionThroughputControllerFactory;
@@ -297,6 +299,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
   protected final Configuration conf;
   private final Configuration baseConf;
   private final int rowLockWaitDuration;
+  private CompactedHFilesDischarger compactedFileDischarger;
   static final int DEFAULT_ROWLOCK_WAIT_DURATION = 30000;
 
   // The internal wait duration to acquire a lock before read/update
@@ -809,6 +812,20 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
     // Initialize all the HStores
     status.setStatus("Initializing all the Stores");
     long maxSeqId = initializeStores(reporter, status);
+    // Start the CompactedHFilesDischarger here. This chore helps to remove the compacted files
+    // that will no longer be used in reads.
+    if (this.getRegionServerServices() != null) {
+      ChoreService choreService = this.getRegionServerServices().getChoreService();
+      if (choreService != null) {
+        // Default is 2 mins. The default value for TTLCleaner is 5 mins so we set this to
+        // 2 mins so that compacted files can be archived before the TTLCleaner runs
+        int cleanerInterval =
+            conf.getInt("hbase.hfile.compactions.cleaner.interval", 2 * 60 * 1000);
+        this.compactedFileDischarger =
+            new CompactedHFilesDischarger(cleanerInterval, this.getRegionServerServices(), this);
+        choreService.scheduleChore(compactedFileDischarger);
+      }
+    }
     this.mvcc.advanceTo(maxSeqId);
     if (ServerRegionReplicaUtil.shouldReplayRecoveredEdits(this)) {
       // Recover any edits if available.
@@ -1513,6 +1530,9 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
       if (this.metricsRegionWrapper != null) {
         Closeables.closeQuietly(this.metricsRegionWrapper);
       }
+      // stop the Compacted hfile discharger
+      if (this.compactedFileDischarger != null) this.compactedFileDischarger.cancel(true);
+
       status.markComplete("Closed");
       LOG.info("Closed " + this);
       return result;
@@ -6658,6 +6678,10 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
       dstRegion.getRegionFileSystem().logFileSystemState(LOG);
     }
 
+    // clear the compacted files if any
+    for (Store s : dstRegion.getStores()) {
+      s.closeAndArchiveCompactedFiles();
+    }
     if (dstRegion.getRegionFileSystem().hasReferences(dstRegion.getTableDesc())) {
       throw new IOException("Merged region " + dstRegion
           + " still has references after the compaction, is compaction canceled?");
@@ -7527,7 +7551,7 @@ public class HRegion implements HeapSize, PropagatingConfigurationObserver, Regi
   public static final long FIXED_OVERHEAD = ClassSize.align(
       ClassSize.OBJECT +
       ClassSize.ARRAY +
-      43 * ClassSize.REFERENCE + 3 * Bytes.SIZEOF_INT +
+      44 * ClassSize.REFERENCE + 3 * Bytes.SIZEOF_INT +
       (14 * Bytes.SIZEOF_LONG) +
       5 * Bytes.SIZEOF_BOOLEAN);
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java

@@ -39,7 +39,9 @@ import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorCompletionService;
 import java.util.concurrent.Future;
+import java.util.concurrent.ThreadFactory;
 import java.util.concurrent.ThreadPoolExecutor;
+import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
 
@@ -76,6 +78,7 @@ import org.apache.hadoop.hbase.io.hfile.InvalidHFileException;
 import org.apache.hadoop.hbase.monitoring.MonitoredTask;
 import org.apache.hadoop.hbase.protobuf.ProtobufUtil;
 import org.apache.hadoop.hbase.protobuf.generated.WALProtos.CompactionDescriptor;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactionConfiguration;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionContext;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionProgress;
 import org.apache.hadoop.hbase.regionserver.compactions.CompactionRequest;
@@ -90,7 +93,7 @@ import org.apache.hadoop.hbase.util.ChecksumType;
 import org.apache.hadoop.hbase.util.ClassSize;
 import org.apache.hadoop.hbase.util.EnvironmentEdgeManager;
 import org.apache.hadoop.hbase.util.ReflectionUtils;
-import org.apache.hadoop.ipc.RemoteException;
+import org.apache.hadoop.hbase.util.Threads;
 import org.apache.hadoop.util.StringUtils;
 import org.apache.hadoop.util.StringUtils.TraditionalBinaryPrefix;
 
@@ -138,6 +141,8 @@ public class HStore implements Store {
   static int closeCheckInterval = 0;
   private volatile long storeSize = 0L;
   private volatile long totalUncompressedBytes = 0L;
+  private ThreadPoolExecutor compactionCleanerthreadPoolExecutor = null;
+  private CompletionService<StoreFile> completionService = null;
 
   /**
    * RWLock for store operations.
@@ -181,7 +186,6 @@ public class HStore implements Store {
 
   private long blockingFileCount;
   private int compactionCheckMultiplier;
-
   protected Encryption.Context cryptoContext = Encryption.Context.NONE;
 
   private volatile long flushedCellsCount = 0;
@@ -272,7 +276,10 @@ public class HStore implements Store {
           "hbase.hstore.flush.retries.number must be > 0, not "
               + flushRetriesNumber);
     }
-
+    compactionCleanerthreadPoolExecutor = getThreadPoolExecutor(
+      conf.getInt(CompactionConfiguration.HBASE_HSTORE_COMPACTION_MAX_KEY, 10));
+    completionService =
+        new ExecutorCompletionService<StoreFile>(compactionCleanerthreadPoolExecutor);
     // Crypto context for new store files
     String cipherName = family.getEncryptionType();
     if (cipherName != null) {
@@ -551,14 +558,15 @@ public class HStore implements Store {
         try {
           Future<StoreFile> future = completionService.take();
           StoreFile storeFile = future.get();
+          if (storeFile != null) {
             long length = storeFile.getReader().length();
             this.storeSize += length;
-          this.totalUncompressedBytes +=
+            this.totalUncompressedBytes += storeFile.getReader().getTotalUncompressedBytes();
-              storeFile.getReader().getTotalUncompressedBytes();
             if (LOG.isDebugEnabled()) {
               LOG.debug("loaded " + storeFile.toStringDetailed());
             }
             results.add(storeFile);
+          }
         } catch (InterruptedException e) {
           if (ioe == null) ioe = new InterruptedIOException(e.getMessage());
         } catch (ExecutionException e) {
@@ -656,8 +664,7 @@ public class HStore implements Store {
       region.getMVCC().advanceTo(this.getMaxSequenceId());
     }
 
-    // notify scanners, close file readers, and recompute store size
+    completeCompaction(toBeRemovedStoreFiles);
-    completeCompaction(toBeRemovedStoreFiles, false);
   }
 
   private StoreFile createStoreFileAndReader(final Path p) throws IOException {
@@ -834,7 +841,6 @@ public class HStore implements Store {
       // the lock.
       this.lock.writeLock().unlock();
     }
-    notifyChangedReadersObservers();
     LOG.info("Loaded HFile " + sf.getFileInfo() + " into store '" + getColumnFamilyName());
     if (LOG.isTraceEnabled()) {
       String traceMessage = "BULK LOAD time,size,store size,store files ["
@@ -850,7 +856,10 @@ public class HStore implements Store {
     try {
       // Clear so metrics doesn't find them.
       ImmutableCollection<StoreFile> result = storeEngine.getStoreFileManager().clearFiles();
-
+      Collection<StoreFile> compactedfiles =
+          storeEngine.getStoreFileManager().clearCompactedFiles();
+      // clear the compacted files
+      removeCompactedFiles(compactedfiles);
       if (!result.isEmpty()) {
         // initialize the thread pool for closing store files in parallel.
         ThreadPoolExecutor storeFileCloserThreadPool = this.region
@@ -892,6 +901,9 @@ public class HStore implements Store {
         }
         if (ioe != null) throw ioe;
       }
+      if (compactionCleanerthreadPoolExecutor != null) {
+        compactionCleanerthreadPoolExecutor.shutdownNow();
+      }
       LOG.info("Closed " + this);
       return result;
     } finally {
@@ -1087,10 +1099,8 @@ public class HStore implements Store {
       // the lock.
       this.lock.writeLock().unlock();
     }
-
+    // notify to be called here - only in case of flushes
-    // Tell listeners of the change in readers.
     notifyChangedReadersObservers();
-
     if (LOG.isTraceEnabled()) {
       long totalSize = 0;
       for (StoreFile sf : sfs) {
@@ -1268,7 +1278,7 @@ public class HStore implements Store {
         compactedCellsSize += getCompactionProgress().totalCompactedSize;
       }
       // At this point the store will use new files for all new scanners.
-      completeCompaction(filesToCompact, true); // Archive old files & update store size.
+      completeCompaction(filesToCompact); // update store size.
 
       logCompactionEndMessage(cr, sfs, compactionStartTime);
       return sfs;
@@ -1456,7 +1466,7 @@ public class HStore implements Store {
       LOG.info("Replaying compaction marker, replacing input files: " +
           inputStoreFiles + " with output files : " + outputStoreFiles);
       this.replaceStoreFiles(inputStoreFiles, outputStoreFiles);
-      this.completeCompaction(inputStoreFiles, removeFiles);
+      this.completeCompaction(inputStoreFiles);
     }
   }
 
@@ -1508,7 +1518,7 @@ public class HStore implements Store {
           this.getCoprocessorHost().postCompact(this, sf, null);
         }
         replaceStoreFiles(filesToCompact, Lists.newArrayList(sf));
-        completeCompaction(filesToCompact, true);
+        completeCompaction(filesToCompact);
       }
     } finally {
       synchronized (filesCompacting) {
@@ -1770,54 +1780,7 @@ public class HStore implements Store {
   @VisibleForTesting
   protected void completeCompaction(final Collection<StoreFile> compactedFiles)
     throws IOException {
-    completeCompaction(compactedFiles, true);
+    LOG.debug("Completing compaction...");
-  }
-
-
-  /**
-   * <p>It works by processing a compaction that's been written to disk.
-   *
-   * <p>It is usually invoked at the end of a compaction, but might also be
-   * invoked at HStore startup, if the prior execution died midway through.
-   *
-   * <p>Moving the compacted TreeMap into place means:
-   * <pre>
-   * 1) Unload all replaced StoreFile, close and collect list to delete.
-   * 2) Compute new store size
-   * </pre>
-   *
-   * @param compactedFiles list of files that were compacted
-   */
-  @VisibleForTesting
-  protected void completeCompaction(final Collection<StoreFile> compactedFiles, boolean removeFiles)
-      throws IOException {
-    try {
-      // Do not delete old store files until we have sent out notification of
-      // change in case old files are still being accessed by outstanding scanners.
-      // Don't do this under writeLock; see HBASE-4485 for a possible deadlock
-      // scenario that could have happened if continue to hold the lock.
-      notifyChangedReadersObservers();
-      // At this point the store will use new files for all scanners.
-
-      // let the archive util decide if we should archive or delete the files
-      LOG.debug("Removing store files after compaction...");
-      boolean evictOnClose = 
-          cacheConf != null? cacheConf.shouldEvictOnClose(): true; 
-      for (StoreFile compactedFile : compactedFiles) {
-        compactedFile.closeReader(evictOnClose);
-      }
-      if (removeFiles) {
-        this.fs.removeStoreFiles(this.getColumnFamilyName(), compactedFiles);
-      }
-    } catch (IOException e) {
-      e = e instanceof RemoteException ?
-                ((RemoteException)e).unwrapRemoteException() : e;
-      LOG.error("Failed removing compacted files in " + this +
-        ". Files we were trying to remove are " + compactedFiles.toString() +
-        "; some of them may have been already removed", e);
-    }
-
-    // 4. Compute new store size
     this.storeSize = 0L;
     this.totalUncompressedBytes = 0L;
     for (StoreFile hsf : this.storeEngine.getStoreFileManager().getStorefiles()) {
@@ -2248,7 +2211,7 @@ public class HStore implements Store {
   }
 
   public static final long FIXED_OVERHEAD =
-      ClassSize.align(ClassSize.OBJECT + (16 * ClassSize.REFERENCE) + (10 * Bytes.SIZEOF_LONG)
+      ClassSize.align(ClassSize.OBJECT + (18 * ClassSize.REFERENCE) + (10 * Bytes.SIZEOF_LONG)
               + (5 * Bytes.SIZEOF_INT) + (2 * Bytes.SIZEOF_BOOLEAN));
 
   public static final long DEEP_OVERHEAD = ClassSize.align(FIXED_OVERHEAD
@@ -2365,4 +2328,112 @@ public class HStore implements Store {
   public boolean isPrimaryReplicaStore() {
 	   return getRegionInfo().getReplicaId() == HRegionInfo.DEFAULT_REPLICA_ID;
   }
+
+  @Override
+  public void closeAndArchiveCompactedFiles() throws IOException {
+    lock.readLock().lock();
+    Collection<StoreFile> copyCompactedfiles = null;
+    try {
+      Collection<StoreFile> compactedfiles =
+          this.getStoreEngine().getStoreFileManager().getCompactedfiles();
+      if (compactedfiles != null && compactedfiles.size() != 0) {
+        // Do a copy under read lock
+        copyCompactedfiles = new ArrayList<StoreFile>(compactedfiles);
+      } else {
+        if (LOG.isTraceEnabled()) {
+          LOG.trace("No compacted files to archive");
+          return;
+        }
+      }
+    } finally {
+      lock.readLock().unlock();
+    }
+    removeCompactedFiles(copyCompactedfiles);
+  }
+
+  private ThreadPoolExecutor getThreadPoolExecutor(int maxThreads) {
+    return Threads.getBoundedCachedThreadPool(maxThreads, maxThreads * 3, TimeUnit.SECONDS,
+      new ThreadFactory() {
+        private int count = 1;
+
+        @Override
+        public Thread newThread(Runnable r) {
+          return new Thread(r, "CompactedfilesArchiver-" + count++);
+        }
+      });
+  }
+
+  private void removeCompactedFiles(Collection<StoreFile> compactedfiles) throws IOException {
+    if (compactedfiles != null && !compactedfiles.isEmpty()) {
+      if (LOG.isDebugEnabled()) {
+        LOG.debug("Removing the compacted store files " + compactedfiles);
+      }
+      for (final StoreFile file : compactedfiles) {
+        completionService.submit(new Callable<StoreFile>() {
+          @Override
+          public StoreFile call() throws IOException {
+            synchronized (file) {
+              try {
+                StoreFile.Reader r = file.getReader();
+                if (r == null) {
+                  if (LOG.isDebugEnabled()) {
+                    LOG.debug("The file " + file + " was closed but still not archived.");
+                  }
+                  return file;
+                }
+                if (r != null && r.isCompactedAway() && !r.isReferencedInReads()) {
+                  // Even if deleting fails we need not bother as any new scanners won't be
+                  // able to use the compacted file as the status is already compactedAway
+                  if (LOG.isTraceEnabled()) {
+                    LOG.trace("Closing and archiving the file " + file.getPath());
+                  }
+                  r.close(true);
+                  // Just close and return
+                  return file;
+                }
+              } catch (Exception e) {
+                LOG.error("Exception while trying to close the compacted store file "
+                    + file.getPath().getName());
+              }
+            }
+            return null;
+          }
+        });
+      }
+      final List<StoreFile> filesToRemove = new ArrayList<StoreFile>(compactedfiles.size());
+      try {
+        for (final StoreFile file : compactedfiles) {
+          Future<StoreFile> future = completionService.take();
+          StoreFile closedFile = future.get();
+          if (closedFile != null) {
+            filesToRemove.add(closedFile);
+          }
+        }
+      } catch (InterruptedException ie) {
+        LOG.error("Interrupted exception while closing the compacted files", ie);
+      } catch (Exception e) {
+        LOG.error("Exception occured while closing the compacted files", e);
+      }
+      if (isPrimaryReplicaStore()) {
+        archiveAndRemoveCompactedFiles(filesToRemove);
+      }
+
+    }
+  }
+
+  private void archiveAndRemoveCompactedFiles(List<StoreFile> filesToArchive) throws IOException {
+    if (!filesToArchive.isEmpty()) {
+      if (LOG.isTraceEnabled()) {
+        LOG.trace("Moving the files " + filesToArchive + " to archive");
+      }
+      // Only if this is successful it has to be removed
+      this.fs.removeStoreFiles(this.getFamily().getNameAsString(), filesToArchive);
+      try {
+        lock.writeLock().lock();
+        this.getStoreEngine().getStoreFileManager().removeCompactedFiles(filesToArchive);
+      } finally {
+        lock.writeLock().unlock();
+      }
+    }
+  }
 }

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/ReversedStoreScanner.java

@@ -123,24 +123,13 @@ class ReversedStoreScanner extends StoreScanner implements KeyValueScanner {
 
   @Override
   public boolean seekToPreviousRow(Cell key) throws IOException {
-    lock.lock();
-    try {
     checkReseek();
     return this.heap.seekToPreviousRow(key);
-    } finally {
-      lock.unlock();
-    }
-
   }
   
   @Override
   public boolean backwardSeek(Cell key) throws IOException {
-    lock.lock();
-    try {
     checkReseek();
     return this.heap.backwardSeek(key);
-    } finally {
-      lock.unlock();
-    }
   }
 }

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/Store.java

@@ -466,4 +466,9 @@ public interface Store extends HeapSize, StoreConfigInformation, PropagatingConf
   void bulkLoadHFile(StoreFileInfo fileInfo) throws IOException;
 
   boolean isPrimaryReplicaStore();
+
+  /**
+   * Closes and archives the compacted files under this store
+   */
+  void closeAndArchiveCompactedFiles() throws IOException;
 }

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreFile.java

@@ -29,6 +29,8 @@ import java.util.Map;
 import java.util.SortedSet;
 import java.util.UUID;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.locks.ReentrantReadWriteLock;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -61,6 +63,7 @@ import org.apache.hadoop.hbase.util.Writables;
 import org.apache.hadoop.io.WritableUtils;
 import org.apache.hadoop.hbase.io.hfile.HFileBlock;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Function;
 import com.google.common.base.Preconditions;
 import com.google.common.collect.ImmutableList;
@@ -378,6 +381,19 @@ public class StoreFile {
     return bulkLoadedHFile || metadataMap.containsKey(BULKLOAD_TIME_KEY);
   }
 
+  @VisibleForTesting
+  public boolean isCompactedAway() {
+    if (this.reader != null) {
+      return this.reader.isCompactedAway();
+    }
+    return true;
+  }
+
+  @VisibleForTesting
+  public int getRefCount() {
+    return this.reader.refCount.get();
+  }
+
   /**
    * Return the timestamp at which this bulk load file was generated.
    */
@@ -552,6 +568,15 @@ public class StoreFile {
     }
   }
 
+  /**
+   * Marks the status of the file as compactedAway.
+   */
+  public void markCompactedAway() {
+    if (this.reader != null) {
+      this.reader.markCompactedAway();
+    }
+  }
+
   /**
    * Delete this file
    * @throws IOException
@@ -1137,6 +1162,12 @@ public class StoreFile {
     private boolean bulkLoadResult = false;
     private KeyValue.KeyOnlyKeyValue lastBloomKeyOnlyKV = null;
     private boolean skipResetSeqId = true;
+    // Counter that is incremented every time a scanner is created on the
+    // store file.  It is decremented when the scan on the store file is
+    // done.
+    private AtomicInteger refCount = new AtomicInteger(0);
+    // Indicates if the file got compacted
+    private volatile boolean compactedAway = false;
 
     public Reader(FileSystem fs, Path path, CacheConfig cacheConf, Configuration conf)
         throws IOException {
@@ -1144,6 +1175,10 @@ public class StoreFile {
       bloomFilterType = BloomType.NONE;
     }
 
+    void markCompactedAway() {
+      this.compactedAway = true;
+    }
+
     public Reader(FileSystem fs, Path path, FSDataInputStreamWrapper in, long size,
         CacheConfig cacheConf, Configuration conf) throws IOException {
       reader = HFile.createReader(fs, path, in, size, cacheConf, conf);
@@ -1195,11 +1230,35 @@ public class StoreFile {
     public StoreFileScanner getStoreFileScanner(boolean cacheBlocks,
                                                boolean pread,
                                                boolean isCompaction, long readPt) {
+      // Increment the ref count
+      refCount.incrementAndGet();
       return new StoreFileScanner(this,
                                  getScanner(cacheBlocks, pread, isCompaction),
                                  !isCompaction, reader.hasMVCCInfo(), readPt);
     }
 
+    /**
+     * Decrement the ref count associated with the reader when ever a scanner associated
+     * with the reader is closed
+     */
+    void decrementRefCount() {
+      refCount.decrementAndGet();
+    }
+
+    /**
+     * @return true if the file is still used in reads
+     */
+    public boolean isReferencedInReads() {
+      return refCount.get() != 0;
+    }
+ 
+    /**
+     * @return true if the file is compacted
+     */
+    public boolean isCompactedAway() {
+      return this.compactedAway;
+    }
+
     /**
      * Warning: Do not write further code which depends on this call. Instead
      * use getStoreFileScanner() which uses the StoreFileScanner class/interface
@@ -1710,7 +1769,13 @@ public class StoreFile {
     private static class GetFileSize implements Function<StoreFile, Long> {
       @Override
       public Long apply(StoreFile sf) {
+        if (sf.getReader() != null) {
           return sf.getReader().length();
+        } else {
+          // the reader may be null for the compacted files and if the archiving
+          // had failed.
+          return -1L;
+        }
       }
     }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreFileManager.java

@@ -53,19 +53,33 @@ public interface StoreFileManager {
   void insertNewFiles(Collection<StoreFile> sfs) throws IOException;
 
   /**
-   * Adds compaction results into the structure.
+   * Adds only the new compaction results into the structure.
    * @param compactedFiles The input files for the compaction.
    * @param results The resulting files for the compaction.
    */
   void addCompactionResults(
       Collection<StoreFile> compactedFiles, Collection<StoreFile> results) throws IOException;
 
+  /**
+   * Remove the compacted files
+   * @param compactedFiles the list of compacted files
+   * @throws IOException
+   */
+  void removeCompactedFiles(Collection<StoreFile> compactedFiles) throws IOException;
+
   /**
    * Clears all the files currently in use and returns them.
    * @return The files previously in use.
    */
   ImmutableCollection<StoreFile> clearFiles();
 
+  /**
+   * Clears all the compacted files and returns them. This method is expected to be
+   * accessed single threaded.
+   * @return The files compacted previously.
+   */
+  Collection<StoreFile> clearCompactedFiles();
+
   /**
    * Gets the snapshot of the store files currently in use. Can be used for things like metrics
    * and checks; should not assume anything about relations between store files in the list.
@@ -73,6 +87,15 @@ public interface StoreFileManager {
    */
   Collection<StoreFile> getStorefiles();
 
+  /**
+   * List of compacted files inside this store that needs to be excluded in reads
+   * because further new reads will be using only the newly created files out of compaction.
+   * These compacted files will be deleted/cleared once all the existing readers on these
+   * compacted files are done.
+   * @return the list of compacted files
+   */
+  Collection<StoreFile> getCompactedfiles();
+
   /**
    * Returns the number of files currently in use.
    * @return The number of files.

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreFileScanner.java

@@ -248,6 +248,9 @@ public class StoreFileScanner implements KeyValueScanner {
   public void close() {
     cur = null;
     this.hfs.close();
+    if (this.reader != null) {
+      this.reader.decrementRefCount();
+    }
   }
 
   /**

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StoreScanner.java

@@ -27,7 +27,6 @@ import java.util.List;
 import java.util.NavigableSet;
 import java.util.Set;
 import java.util.concurrent.CountDownLatch;
-import java.util.concurrent.locks.ReentrantLock;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -125,7 +124,8 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
 
   // A flag whether use pread for scan
   private boolean scanUsePread = false;
-  protected ReentrantLock lock = new ReentrantLock();
+  // Indicates whether there was flush during the course of the scan
+  protected volatile boolean flushed = false;
   
   protected final long readPt;
 
@@ -403,15 +403,11 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
 
   @Override
   public Cell peek() {
-    lock.lock();
+    checkResetHeap();
-    try {
     if (this.heap == null) {
       return this.lastTop;
     }
     return this.heap.peek();
-    } finally {
-      lock.unlock();
-    }
   }
 
   @Override
@@ -426,8 +422,6 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
   }
 
   private void close(boolean withHeapClose) {
-    lock.lock();
-    try {
     if (this.closing) {
       return;
     }
@@ -450,21 +444,14 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
       }
     }
     this.lastTop = null; // If both are null, we are closed.
-    } finally {
-      lock.unlock();
-    }
   }
 
   @Override
   public boolean seek(Cell key) throws IOException {
-    lock.lock();
+    checkResetHeap();
-    try {
     // reset matcher state, in case that underlying store changed
     checkReseek();
     return this.heap.seek(key);
-    } finally {
-      lock.unlock();
-    }
   }
 
   @Override
@@ -480,11 +467,10 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
    */
   @Override
   public boolean next(List<Cell> outResult, ScannerContext scannerContext) throws IOException {
-    lock.lock();
-    try {
     if (scannerContext == null) {
       throw new IllegalArgumentException("Scanner context cannot be null");
     }
+    checkResetHeap();
     if (checkReseek()) {
       return scannerContext.setScannerState(NextState.MORE_VALUES).hasMoreValues();
     }
@@ -509,8 +495,8 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
     // If no limits exists in the scope LimitScope.Between_Cells then we are sure we are changing
     // rows. Else it is possible we are still traversing the same row so we must perform the row
     // comparison.
-      if (!scannerContext.hasAnyLimit(LimitScope.BETWEEN_CELLS) || matcher.curCell == null ||
+    if (!scannerContext.hasAnyLimit(LimitScope.BETWEEN_CELLS) || matcher.curCell == null
-          !CellUtil.matchingRow(cell, matcher.curCell)) {
+        || !CellUtil.matchingRow(cell, matcher.curCell)) {
       this.countPerRow = 0;
       matcher.setToNewRow(cell);
     }
@@ -550,8 +536,7 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
         }
 
         this.countPerRow++;
-          if (storeLimit > -1 &&
+        if (storeLimit > -1 && this.countPerRow > (storeLimit + storeOffset)) {
-              this.countPerRow > (storeLimit + storeOffset)) {
           // do what SEEK_NEXT_ROW does.
           if (!matcher.moreRowsMayExistAfter(cell)) {
             return scannerContext.setScannerState(NextState.NO_MORE_VALUES).hasMoreValues();
@@ -574,8 +559,8 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
           scannerContext.incrementBatchProgress(1);
 
           if (totalBytesRead > maxRowSize) {
-              throw new RowTooBigException("Max row size allowed: " + maxRowSize
+            throw new RowTooBigException(
-                  + ", but the row is bigger than that.");
+                "Max row size allowed: " + maxRowSize + ", but the row is bigger than that.");
           }
         }
 
@@ -644,9 +629,6 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
     // No more keys
     close(false);// Do all cleanup except heap.close()
     return scannerContext.setScannerState(NextState.NO_MORE_VALUES).hasMoreValues();
-    } finally {
-      lock.unlock();
-    }
   }
 
   /*
@@ -684,30 +666,26 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
   // Implementation of ChangedReadersObserver
   @Override
   public void updateReaders() throws IOException {
-    lock.lock();
+    flushed = true;
-    try {
+    // Let the next() call handle re-creating and seeking
-    if (this.closing) return;
+  }
 
+  protected void nullifyCurrentHeap() {
+    if (this.closing) return;
     // All public synchronized API calls will call 'checkReseek' which will cause
     // the scanner stack to reseek if this.heap==null && this.lastTop != null.
     // But if two calls to updateReaders() happen without a 'next' or 'peek' then we
     // will end up calling this.peek() which would cause a reseek in the middle of a updateReaders
     // which is NOT what we want, not to mention could cause an NPE. So we early out here.
     if (this.heap == null) return;
-
     // this could be null.
-    this.lastTop = this.peek();
+    this.lastTop = this.heap.peek();
 
     //DebugPrint.println("SS updateReaders, topKey = " + lastTop);
 
     // close scanners to old obsolete Store files
     this.heapsForDelayedClose.add(this.heap);// Don't close now. Delay it till StoreScanner#close
     this.heap = null; // the re-seeks could be slow (access HDFS) free up memory ASAP
-
-    // Let the next() call handle re-creating and seeking
-    } finally {
-      lock.unlock();
-    }
   }
 
   /**
@@ -793,8 +771,7 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
 
   @Override
   public boolean reseek(Cell kv) throws IOException {
-    lock.lock();
+    checkResetHeap();
-    try {
     // Heap will not be null, if this is called from next() which.
     // If called from RegionScanner.reseek(...) make sure the scanner
     // stack is reset if needed.
@@ -803,8 +780,24 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
       return heap.requestSeek(kv, true, useRowColBloom);
     }
     return heap.reseek(kv);
-    } finally {
+  }
-      lock.unlock();
+
+  protected void checkResetHeap() {
+    // check the var without any lock. Suppose even if we see the old
+    // value here still it is ok to continue because we will not be resetting
+    // the heap but will continue with the referenced memstore's snapshot. For compactions
+    // any way we don't need the updateReaders at all to happen as we still continue with 
+    // the older files
+    if (flushed) {
+      // If the 'flushed' is found to be true then there is a need to ensure
+      // that the current scanner updates the heap that it has and then proceed
+      // with the scan and ensure to reset the flushed inside the lock
+      // One thing can be sure that the same store scanner cannot be in reseek and
+      // next at the same time ie. within the same store scanner it is always single
+      // threaded
+      nullifyCurrentHeap();
+      // reset the flag
+      flushed = false;
     }
   }
 
@@ -883,8 +876,6 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
 
   @Override
   public void shipped() throws IOException {
-    lock.lock();
-    try {
     for (KeyValueHeap h : this.heapsForDelayedClose) {
       h.close();// There wont be further fetch of Cells from these scanners. Just close.
     }
@@ -892,9 +883,6 @@ public class StoreScanner extends NonReversedNonLazyKeyValueScanner
     if (this.heap != null) {
       this.heap.shipped();
     }
-    } finally {
-      lock.unlock();
-    }
   }
 }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/StripeStoreFileManager.java

@@ -106,6 +106,7 @@ public class StripeStoreFileManager
 
     /** Cached list of all files in the structure, to return from some calls */
     public ImmutableList<StoreFile> allFilesCached = ImmutableList.<StoreFile>of();
+    private ImmutableList<StoreFile> allCompactedFilesCached = ImmutableList.<StoreFile>of();
   }
   private State state = null;
 
@@ -140,9 +141,15 @@ public class StripeStoreFileManager
     return state.allFilesCached;
   }
 
+  @Override
+  public Collection<StoreFile> getCompactedfiles() {
+    return state.allCompactedFilesCached;
+  }
+
   @Override
   public void insertNewFiles(Collection<StoreFile> sfs) throws IOException {
     CompactionOrFlushMergeCopy cmc = new CompactionOrFlushMergeCopy(true);
+    // Passing null does not cause NPE??
     cmc.mergeResults(null, sfs);
     debugDumpState("Added new files");
   }
@@ -156,6 +163,13 @@ public class StripeStoreFileManager
     return result;
   }
 
+  @Override
+  public ImmutableCollection<StoreFile> clearCompactedFiles() {
+    ImmutableCollection<StoreFile> result = state.allCompactedFilesCached;
+    this.state = new State();
+    return result;
+  }
+
   @Override
   public int getStorefileCount() {
     return state.allFilesCached.size();
@@ -306,9 +320,31 @@ public class StripeStoreFileManager
     // copies and apply the result at the end.
     CompactionOrFlushMergeCopy cmc = new CompactionOrFlushMergeCopy(false);
     cmc.mergeResults(compactedFiles, results);
+    markCompactedAway(compactedFiles);
     debugDumpState("Merged compaction results");
   }
 
+  // Mark the files as compactedAway once the storefiles and compactedfiles list is finalised
+  // Let a background thread close the actual reader on these compacted files and also
+  // ensure to evict the blocks from block cache so that they are no longer in
+  // cache
+  private void markCompactedAway(Collection<StoreFile> compactedFiles) {
+    for (StoreFile file : compactedFiles) {
+      file.markCompactedAway();
+    }
+  }
+
+  @Override
+  public void removeCompactedFiles(Collection<StoreFile> compactedFiles) throws IOException {
+    // See class comment for the assumptions we make here.
+    LOG.debug("Attempting to delete compaction results: " + compactedFiles.size());
+    // In order to be able to fail in the middle of the operation, we'll operate on lazy
+    // copies and apply the result at the end.
+    CompactionOrFlushMergeCopy cmc = new CompactionOrFlushMergeCopy(false);
+    cmc.deleteResults(compactedFiles);
+    debugDumpState("Deleted compaction results");
+  }
+
   @Override
   public int getStoreCompactionPriority() {
     // If there's only L0, do what the default store does.
@@ -684,7 +720,7 @@ public class StripeStoreFileManager
       this.isFlush = isFlush;
     }
 
-    public void mergeResults(Collection<StoreFile> compactedFiles, Collection<StoreFile> results)
+    private void mergeResults(Collection<StoreFile> compactedFiles, Collection<StoreFile> results)
         throws IOException {
       assert this.compactedFiles == null && this.results == null;
       this.compactedFiles = compactedFiles;
@@ -696,12 +732,20 @@ public class StripeStoreFileManager
         processNewCandidateStripes(newStripes);
       }
       // Create new state and update parent.
-      State state = createNewState();
+      State state = createNewState(false);
       StripeStoreFileManager.this.state = state;
       updateMetadataMaps();
     }
 
-    private State createNewState() {
+    private void deleteResults(Collection<StoreFile> compactedFiles) throws IOException {
+      this.compactedFiles = compactedFiles;
+      // Create new state and update parent.
+      State state = createNewState(true);
+      StripeStoreFileManager.this.state = state;
+      updateMetadataMaps();
+    }
+
+    private State createNewState(boolean delCompactedFiles) {
       State oldState = StripeStoreFileManager.this.state;
       // Stripe count should be the same unless the end rows changed.
       assert oldState.stripeFiles.size() == this.stripeFiles.size() || this.stripeEndRows != null;
@@ -717,9 +761,21 @@ public class StripeStoreFileManager
       }
 
       List<StoreFile> newAllFiles = new ArrayList<StoreFile>(oldState.allFilesCached);
-      if (!isFlush) newAllFiles.removeAll(compactedFiles);
+      List<StoreFile> newAllCompactedFiles =
+          new ArrayList<StoreFile>(oldState.allCompactedFilesCached);
+      if (!isFlush) {
+        newAllFiles.removeAll(compactedFiles);
+        if (delCompactedFiles) {
+          newAllCompactedFiles.removeAll(compactedFiles);
+        } else {
+          newAllCompactedFiles.addAll(compactedFiles);
+        }
+      }
+      if (results != null) {
         newAllFiles.addAll(results);
+      }
       newState.allFilesCached = ImmutableList.copyOf(newAllFiles);
+      newState.allCompactedFilesCached = ImmutableList.copyOf(newAllCompactedFiles);
       return newState;
     }
 
@@ -970,16 +1026,18 @@ public class StripeStoreFileManager
     // Order by seqnum is reversed.
     for (int i = 1; i < stripe.size(); ++i) {
       StoreFile sf = stripe.get(i);
+      synchronized (sf) {
         long fileTs = sf.getReader().getMaxTimestamp();
         if (fileTs < maxTs && !filesCompacting.contains(sf)) {
-        LOG.info("Found an expired store file: " + sf.getPath()
+          LOG.info("Found an expired store file: " + sf.getPath() + " whose maxTimeStamp is "
-            + " whose maxTimeStamp is " + fileTs + ", which is below " + maxTs);
+              + fileTs + ", which is below " + maxTs);
           if (expiredStoreFiles == null) {
             expiredStoreFiles = new ArrayList<StoreFile>();
           }
           expiredStoreFiles.add(sf);
         }
       }
+    }
     return expiredStoreFiles;
   }
 

hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/compactions/CompactedHFilesDischarger.java

@@ -0,0 +1,74 @@
+/**
+ * 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.hadoop.hbase.regionserver.compactions;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.hadoop.hbase.ScheduledChore;
+import org.apache.hadoop.hbase.Stoppable;
+import org.apache.hadoop.hbase.classification.InterfaceAudience;
+import org.apache.hadoop.hbase.regionserver.Region;
+import org.apache.hadoop.hbase.regionserver.Store;
+
+/**
+ * A chore service that periodically cleans up the compacted files when there are no active readers
+ * using those compacted files and also helps in clearing the block cache with these compacted
+ * file entries
+ */
+@InterfaceAudience.Private
+public class CompactedHFilesDischarger extends ScheduledChore {
+  private static final Log LOG = LogFactory.getLog(CompactedHFilesDischarger.class);
+  private Region region;
+
+  /**
+   * @param period the period of time to sleep between each run
+   * @param stopper the stopper
+   * @param region the store to identify the family name
+   */
+  public CompactedHFilesDischarger(final int period, final Stoppable stopper, final Region region) {
+    // Need to add the config classes
+    super("CompactedHFilesCleaner", stopper, period);
+    this.region = region;
+  }
+
+  @Override
+  public void chore() {
+    if (LOG.isTraceEnabled()) {
+      LOG.trace(
+        "Started the compacted hfiles cleaner for the region " + this.region.getRegionInfo());
+    }
+    for (Store store : region.getStores()) {
+      try {
+        store.closeAndArchiveCompactedFiles();
+        if (LOG.isTraceEnabled()) {
+          LOG.trace("Completed archiving the compacted files for the region "
+              + this.region.getRegionInfo() + " under the store " + store.getColumnFamilyName());
+        }
+      } catch (Exception e) {
+        LOG.error(
+          "Exception while trying to close and archive the comapcted store files of the store  "
+              + store.getColumnFamilyName() + " in the region " + this.region.getRegionInfo(),
+          e);
+      }
+    }
+    if (LOG.isTraceEnabled()) {
+      LOG.trace(
+        "Completed the compacted hfiles cleaner for the region " + this.region.getRegionInfo());
+    }
+  }
+}

hbase-server/src/test/java/org/apache/hadoop/hbase/TestIOFencing.java

@@ -197,17 +197,6 @@ public class TestIOFencing {
       r = (CompactionBlockerRegion) region;
     }
 
-    @Override
-    protected void completeCompaction(final Collection<StoreFile> compactedFiles,
-        boolean removeFiles) throws IOException {
-      try {
-        r.compactionsWaiting.countDown();
-        r.compactionsBlocked.await();
-      } catch (InterruptedException ex) {
-        throw new IOException(ex);
-      }
-      super.completeCompaction(compactedFiles, removeFiles);
-    }
     @Override
     protected void completeCompaction(Collection<StoreFile> compactedFiles) throws IOException {
       try {

hbase-server/src/test/java/org/apache/hadoop/hbase/backup/example/TestZooKeeperTableArchiveClient.java

@@ -42,8 +42,10 @@ import org.apache.hadoop.hbase.client.ConnectionFactory;
 import org.apache.hadoop.hbase.client.Put;
 import org.apache.hadoop.hbase.master.cleaner.BaseHFileCleanerDelegate;
 import org.apache.hadoop.hbase.master.cleaner.HFileCleaner;
+import org.apache.hadoop.hbase.regionserver.HRegion;
 import org.apache.hadoop.hbase.regionserver.Region;
 import org.apache.hadoop.hbase.regionserver.Store;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.testclassification.MediumTests;
 import org.apache.hadoop.hbase.testclassification.MiscTests;
 import org.apache.hadoop.hbase.util.Bytes;
@@ -170,10 +172,11 @@ public class TestZooKeeperTableArchiveClient {
 
     // create the region
     HColumnDescriptor hcd = new HColumnDescriptor(TEST_FAM);
-    Region region = UTIL.createTestRegion(STRING_TABLE_NAME, hcd);
+    HRegion region = UTIL.createTestRegion(STRING_TABLE_NAME, hcd);
-
+    final CompactedHFilesDischarger compactionCleaner =
+        new CompactedHFilesDischarger(100, stop, region);
     loadFlushAndCompact(region, TEST_FAM);
-
+    compactionCleaner.chore();
     // get the current hfiles in the archive directory
     List<Path> files = getAllFiles(fs, archiveDir);
     if (files == null) {
@@ -217,18 +220,22 @@ public class TestZooKeeperTableArchiveClient {
     HFileCleaner cleaner = setupAndCreateCleaner(conf, fs, archiveDir, stop);
     List<BaseHFileCleanerDelegate> cleaners = turnOnArchiving(STRING_TABLE_NAME, cleaner);
     final LongTermArchivingHFileCleaner delegate = (LongTermArchivingHFileCleaner) cleaners.get(0);
-
     // create the region
     HColumnDescriptor hcd = new HColumnDescriptor(TEST_FAM);
-    Region region = UTIL.createTestRegion(STRING_TABLE_NAME, hcd);
+    HRegion region = UTIL.createTestRegion(STRING_TABLE_NAME, hcd);
+    final CompactedHFilesDischarger compactionCleaner =
+        new CompactedHFilesDischarger(100, stop, region);
     loadFlushAndCompact(region, TEST_FAM);
-
+    compactionCleaner.chore();
     // create the another table that we don't archive
     hcd = new HColumnDescriptor(TEST_FAM);
-    Region otherRegion = UTIL.createTestRegion(otherTable, hcd);
+    HRegion otherRegion = UTIL.createTestRegion(otherTable, hcd);
+    final CompactedHFilesDischarger compactionCleaner1 =
+        new CompactedHFilesDischarger(100, stop, otherRegion);
     loadFlushAndCompact(otherRegion, TEST_FAM);
-
+    compactionCleaner1.chore();
     // get the current hfiles in the archive directory
+    // Should  be archived
     List<Path> files = getAllFiles(fs, archiveDir);
     if (files == null) {
       FSUtils.logFileSystemState(fs, archiveDir, LOG);

hbase-server/src/test/java/org/apache/hadoop/hbase/mapreduce/TestHFileOutputFormat2.java

@@ -29,6 +29,7 @@ import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Random;
@@ -74,6 +75,7 @@ import org.apache.hadoop.hbase.io.hfile.HFile;
 import org.apache.hadoop.hbase.io.hfile.HFile.Reader;
 import org.apache.hadoop.hbase.regionserver.BloomType;
 import org.apache.hadoop.hbase.regionserver.HRegion;
+import org.apache.hadoop.hbase.regionserver.Store;
 import org.apache.hadoop.hbase.regionserver.StoreFile;
 import org.apache.hadoop.hbase.regionserver.TimeRangeTracker;
 import org.apache.hadoop.hbase.testclassification.LargeTests;
@@ -95,6 +97,8 @@ import org.junit.experimental.categories.Category;
 import org.junit.rules.TestRule;
 import org.mockito.Mockito;
 
+import com.google.common.collect.Lists;
+
 /**
  * Simple test for {@link CellSortReducer} and {@link HFileOutputFormat2}.
  * Sets up and runs a mapreduce job that writes hfile output.
@@ -1002,6 +1006,12 @@ public class TestHFileOutputFormat2  {
         quickPoll(new Callable<Boolean>() {
           @Override
           public Boolean call() throws Exception {
+            List<HRegion> regions = util.getMiniHBaseCluster().getRegions(TABLE_NAME);
+            for (HRegion region : regions) {
+              for (Store store : region.getStores()) {
+                store.closeAndArchiveCompactedFiles();
+              }
+            }
             return fs.listStatus(storePath).length == 1;
           }
         }, 5000);
@@ -1015,6 +1025,12 @@ public class TestHFileOutputFormat2  {
       quickPoll(new Callable<Boolean>() {
         @Override
         public Boolean call() throws Exception {
+          List<HRegion> regions = util.getMiniHBaseCluster().getRegions(TABLE_NAME);
+          for (HRegion region : regions) {
+            for (Store store : region.getStores()) {
+              store.closeAndArchiveCompactedFiles();
+            }
+          }
           return fs.listStatus(storePath).length == 1;
         }
       }, 5000);

hbase-server/src/test/java/org/apache/hadoop/hbase/master/cleaner/TestSnapshotFromMaster.java

@@ -48,6 +48,9 @@ import org.apache.hadoop.hbase.protobuf.generated.MasterProtos.IsSnapshotDoneReq
 import org.apache.hadoop.hbase.protobuf.generated.MasterProtos.IsSnapshotDoneResponse;
 import org.apache.hadoop.hbase.regionserver.ConstantSizeRegionSplitPolicy;
 import org.apache.hadoop.hbase.regionserver.HRegion;
+import org.apache.hadoop.hbase.regionserver.HStore;
+import org.apache.hadoop.hbase.regionserver.Store;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.snapshot.SnapshotDescriptionUtils;
 import org.apache.hadoop.hbase.snapshot.SnapshotReferenceUtil;
 import org.apache.hadoop.hbase.snapshot.SnapshotTestingUtils;
@@ -121,6 +124,7 @@ public class TestSnapshotFromMaster {
     conf.setLong(SnapshotHFileCleaner.HFILE_CACHE_REFRESH_PERIOD_CONF_KEY, cacheRefreshPeriod);
     conf.set(HConstants.HBASE_REGION_SPLIT_POLICY_KEY,
       ConstantSizeRegionSplitPolicy.class.getName());
+    conf.setInt("hbase.hfile.compactions.cleaner.interval", 20 * 1000);
 
   }
 
@@ -320,6 +324,10 @@ public class TestSnapshotFromMaster {
       region.waitForFlushesAndCompactions(); // enable can trigger a compaction, wait for it.
       region.compactStores(); // min is 2 so will compact and archive
     }
+    for (HRegion region : regions) {
+      CompactedHFilesDischarger cleaner = new CompactedHFilesDischarger(100, null, region);
+      cleaner.chore();
+    }
     LOG.info("After compaction File-System state");
     FSUtils.logFileSystemState(fs, rootDir, LOG);
 

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/MockStoreFile.java

@@ -78,6 +78,11 @@ public class MockStoreFile extends StoreFile {
     return false;
   }
 
+  @Override
+  public boolean isCompactedAway() {
+    return false;
+  }
+
   @Override
   public byte[] getMetadataValue(byte[] key) {
     return this.metadata.get(key);

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestEncryptionKeyRotation.java

@@ -19,9 +19,11 @@ package org.apache.hadoop.hbase.regionserver;
 
 import static org.junit.Assert.*;
 
+import java.io.IOException;
 import java.security.Key;
 import java.security.SecureRandom;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 
 import javax.crypto.spec.SecretKeySpec;
@@ -123,13 +125,14 @@ public class TestEncryptionKeyRotation {
 
     // And major compact
     TEST_UTIL.getHBaseAdmin().majorCompact(htd.getTableName());
+    final List<Path> updatePaths = findCompactedStorefilePaths(htd.getTableName());
     TEST_UTIL.waitFor(30000, 1000, true, new Predicate<Exception>() {
       @Override
       public boolean evaluate() throws Exception {
         // When compaction has finished, all of the original files will be
         // gone
         boolean found = false;
-        for (Path path: initialPaths) {
+        for (Path path: updatePaths) {
           found = TEST_UTIL.getTestFileSystem().exists(path);
           if (found) {
             LOG.info("Found " + path);
@@ -141,14 +144,20 @@ public class TestEncryptionKeyRotation {
     });
 
     // Verify we have store file(s) with only the new key
+    Thread.sleep(1000);
+    waitForCompaction(htd.getTableName());
     List<Path> pathsAfterCompaction = findStorefilePaths(htd.getTableName());
     assertTrue(pathsAfterCompaction.size() > 0);
     for (Path path: pathsAfterCompaction) {
-      assertFalse("Store file " + path + " retains initial key",
-        Bytes.equals(initialCFKey.getEncoded(), extractHFileKey(path)));
       assertTrue("Store file " + path + " has incorrect key",
         Bytes.equals(secondCFKey.getEncoded(), extractHFileKey(path)));
     }
+    List<Path> compactedPaths = findCompactedStorefilePaths(htd.getTableName());
+    assertTrue(compactedPaths.size() > 0);
+    for (Path path: compactedPaths) {
+      assertTrue("Store file " + path + " retains initial key",
+        Bytes.equals(initialCFKey.getEncoded(), extractHFileKey(path)));
+    }
   }
 
   @Test
@@ -194,6 +203,33 @@ public class TestEncryptionKeyRotation {
     }
   }
 
+  private static void waitForCompaction(TableName tableName)
+      throws IOException, InterruptedException {
+    boolean compacted = false;
+    for (Region region : TEST_UTIL.getRSForFirstRegionInTable(tableName)
+        .getOnlineRegions(tableName)) {
+      for (Store store : region.getStores()) {
+        compacted = false;
+        while (!compacted) {
+          if (store.getStorefiles() != null) {
+            while (store.getStorefilesCount() != 1) {
+              Thread.sleep(100);
+            }
+            for (StoreFile storefile : store.getStorefiles()) {
+              if (!storefile.isCompactedAway()) {
+                compacted = true;
+                break;
+              }
+              Thread.sleep(100);
+            }
+          } else {
+            break;
+          }
+        }
+      }
+    }
+  }
+  
   private static List<Path> findStorefilePaths(TableName tableName) throws Exception {
     List<Path> paths = new ArrayList<Path>();
     for (Region region:
@@ -207,6 +243,23 @@ public class TestEncryptionKeyRotation {
     return paths;
   }
 
+  private static List<Path> findCompactedStorefilePaths(TableName tableName) throws Exception {
+    List<Path> paths = new ArrayList<Path>();
+    for (Region region:
+        TEST_UTIL.getRSForFirstRegionInTable(tableName).getOnlineRegions(tableName)) {
+      for (Store store : region.getStores()) {
+        Collection<StoreFile> compactedfiles =
+            ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+        if (compactedfiles != null) {
+          for (StoreFile storefile : compactedfiles) {
+            paths.add(storefile.getPath());
+          }
+        }
+      }
+    }
+    return paths;
+  }
+
   private void createTableAndFlush(HTableDescriptor htd) throws Exception {
     HColumnDescriptor hcd = htd.getFamilies().iterator().next();
     // Create the test table

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestHRegionReplayEvents.java

@@ -69,6 +69,7 @@ import org.apache.hadoop.hbase.protobuf.generated.WALProtos.RegionEventDescripto
 import org.apache.hadoop.hbase.protobuf.generated.WALProtos.StoreDescriptor;
 import org.apache.hadoop.hbase.regionserver.HRegion.FlushResultImpl;
 import org.apache.hadoop.hbase.regionserver.HRegion.PrepareFlushResult;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.regionserver.compactions.NoLimitCompactionThroughputController;
 import org.apache.hadoop.hbase.regionserver.wal.WALEdit;
 import org.apache.hadoop.hbase.testclassification.MediumTests;
@@ -1369,6 +1370,8 @@ public class TestHRegionReplayEvents {
 
     // Test case 3: compact primary files
     primaryRegion.compactStores();
+    CompactedHFilesDischarger cleaner = new CompactedHFilesDischarger(100, null, primaryRegion);
+    cleaner.chore();
     secondaryRegion.refreshStoreFiles();
     assertPathListsEqual(primaryRegion.getStoreFileList(families),
       secondaryRegion.getStoreFileList(families));

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestRegionMergeTransactionOnCluster.java

@@ -36,6 +36,7 @@ import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.hbase.CoordinatedStateManager;
 import org.apache.hadoop.hbase.HBaseTestingUtility;
+import org.apache.hadoop.hbase.HColumnDescriptor;
 import org.apache.hadoop.hbase.HConstants;
 import org.apache.hadoop.hbase.HRegionInfo;
 import org.apache.hadoop.hbase.HTableDescriptor;
@@ -61,6 +62,7 @@ import org.apache.hadoop.hbase.master.RegionStates;
 import org.apache.hadoop.hbase.protobuf.generated.RegionServerStatusProtos.RegionStateTransition.TransitionCode;
 import org.apache.hadoop.hbase.protobuf.generated.RegionServerStatusProtos.ReportRegionStateTransitionRequest;
 import org.apache.hadoop.hbase.protobuf.generated.RegionServerStatusProtos.ReportRegionStateTransitionResponse;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.testclassification.LargeTests;
 import org.apache.hadoop.hbase.testclassification.RegionServerTests;
 import org.apache.hadoop.hbase.util.Bytes;
@@ -212,7 +214,7 @@ public class TestRegionMergeTransactionOnCluster {
       List<Pair<HRegionInfo, ServerName>> tableRegions = MetaTableAccessor
           .getTableRegionsAndLocations(master.getConnection(), tableName);
       HRegionInfo mergedRegionInfo = tableRegions.get(0).getFirst();
-      HTableDescriptor tableDescritor = master.getTableDescriptors().get(
+      HTableDescriptor tableDescriptor = master.getTableDescriptors().get(
           tableName);
       Result mergedRegionResult = MetaTableAccessor.getRegionResult(
         master.getConnection(), mergedRegionInfo.getRegionName());
@@ -236,19 +238,34 @@ public class TestRegionMergeTransactionOnCluster {
       assertTrue(fs.exists(regionAdir));
       assertTrue(fs.exists(regionBdir));
 
+      HColumnDescriptor[] columnFamilies = tableDescriptor.getColumnFamilies();
+      HRegionFileSystem hrfs = new HRegionFileSystem(
+        TEST_UTIL.getConfiguration(), fs, tabledir, mergedRegionInfo);
+      int count = 0;
+      for(HColumnDescriptor colFamily : columnFamilies) {
+        count += hrfs.getStoreFiles(colFamily.getName()).size();
+      }
       admin.compactRegion(mergedRegionInfo.getRegionName());
       // wait until merged region doesn't have reference file
       long timeout = System.currentTimeMillis() + waitTime;
-      HRegionFileSystem hrfs = new HRegionFileSystem(
-          TEST_UTIL.getConfiguration(), fs, tabledir, mergedRegionInfo);
       while (System.currentTimeMillis() < timeout) {
-        if (!hrfs.hasReferences(tableDescritor)) {
+        if (!hrfs.hasReferences(tableDescriptor)) {
           break;
         }
         Thread.sleep(50);
       }
-      assertFalse(hrfs.hasReferences(tableDescritor));
+      int newcount = 0;
-
+      for(HColumnDescriptor colFamily : columnFamilies) {
+        newcount += hrfs.getStoreFiles(colFamily.getName()).size();
+      }
+      assertTrue(newcount > count);
+      // clean up the merged region store files
+      List<HRegion> regions = 
+          TEST_UTIL.getHBaseCluster().getRegions(tableDescriptor.getName());
+      for (HRegion region : regions) {
+        CompactedHFilesDischarger cleaner = new CompactedHFilesDischarger(100, null, region);
+        cleaner.chore();
+      }
       // run CatalogJanitor to clean merge references in hbase:meta and archive the
       // files of merging regions
       int cleaned = admin.runCatalogScan();

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestRegionReplicas.java

@@ -47,6 +47,7 @@ import org.apache.hadoop.hbase.io.hfile.HFileScanner;
 import org.apache.hadoop.hbase.protobuf.ProtobufUtil;
 import org.apache.hadoop.hbase.protobuf.RequestConverter;
 import org.apache.hadoop.hbase.protobuf.generated.ClientProtos;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactedHFilesDischarger;
 import org.apache.hadoop.hbase.util.Bytes;
 import org.apache.hadoop.hbase.util.Threads;
 import org.apache.hadoop.hdfs.DFSConfigKeys;
@@ -248,6 +249,7 @@ public class TestRegionReplicas {
       LOG.info("Flushing primary region");
       Region region = getRS().getRegionByEncodedName(hriPrimary.getEncodedName());
       region.flush(true);
+      HRegion primaryRegion = (HRegion) region;
 
       // ensure that chore is run
       LOG.info("Sleeping for " + (4 * refreshPeriod));
@@ -277,7 +279,7 @@ public class TestRegionReplicas {
       assertGetRpc(hriSecondary, 1042, true);
       assertGetRpc(hriSecondary, 2042, true);
 
-      // ensure that we are see the 3 store files
+      // ensure that we see the 3 store files
       Assert.assertEquals(3, secondaryRegion.getStore(f).getStorefilesCount());
 
       // force compaction
@@ -292,7 +294,8 @@ public class TestRegionReplicas {
       }
 
       // ensure that we see the compacted file only
-      Assert.assertEquals(1, secondaryRegion.getStore(f).getStorefilesCount());
+      // This will be 4 until the cleaner chore runs
+      Assert.assertEquals(4, secondaryRegion.getStore(f).getStorefilesCount());
 
     } finally {
       HTU.deleteNumericRows(table, HConstants.CATALOG_FAMILY, 0, 1000);
@@ -451,7 +454,9 @@ public class TestRegionReplicas {
       LOG.info("Force Major compaction on primary region " + hriPrimary);
       primaryRegion.compact(true);
       Assert.assertEquals(1, primaryRegion.getStore(f).getStorefilesCount());
-
+      CompactedHFilesDischarger cleaner =
+          new CompactedHFilesDischarger(100, null, (HRegion) primaryRegion);
+      cleaner.chore();
       // scan all the hfiles on the secondary.
       // since there are no read on the secondary when we ask locations to
       // the NN a FileNotFound exception will be returned and the FileLink

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestStore.java

@@ -1030,6 +1030,18 @@ public class TestStore {
     store.getRegionFileSystem().removeStoreFiles(store.getColumnFamilyName(), Lists.newArrayList(sf));
   }
 
+  private void closeCompactedFile(int index) throws IOException {
+    Collection<StoreFile> files =
+        this.store.getStoreEngine().getStoreFileManager().getCompactedfiles();
+    StoreFile sf = null;
+    Iterator<StoreFile> it = files.iterator();
+    for (int i = 0; i <= index; i++) {
+      sf = it.next();
+    }
+    sf.closeReader(true);
+    store.getStoreEngine().getStoreFileManager().removeCompactedFiles(Lists.newArrayList(sf));
+  }
+
   @Test
   public void testRefreshStoreFiles() throws Exception {
     init(name.getMethodName());
@@ -1057,6 +1069,7 @@ public class TestStore {
     store.refreshStoreFiles();
     assertEquals(5, this.store.getStorefilesCount());
 
+    closeCompactedFile(0);
     archiveStoreFile(0);
 
     assertEquals(5, this.store.getStorefilesCount());

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/TestStripeStoreFileManager.java

@@ -137,6 +137,7 @@ public class TestStripeStoreFileManager {
     MockStoreFile stripe0a = createFile(0, 100, OPEN_KEY, KEY_B),
         stripe1 = createFile(KEY_B, OPEN_KEY);
     manager.addCompactionResults(al(l0File), al(stripe0a, stripe1));
+    manager.removeCompactedFiles(al(l0File));
     // If we want a key <= KEY_A, we should get everything except stripe1.
     ArrayList<StoreFile> sfsDump = dumpIterator(manager.getCandidateFilesForRowKeyBefore(KV_A));
     assertEquals(2, sfsDump.size());
@@ -162,6 +163,7 @@ public class TestStripeStoreFileManager {
     // a candidate from the first file, the old one should not be removed.
     StoreFile stripe0b = createFile(0, 101, OPEN_KEY, KEY_B);
     manager.addCompactionResults(al(l0File2), al(stripe0b));
+    manager.removeCompactedFiles(al(l0File2));
     sfs = manager.getCandidateFilesForRowKeyBefore(KV_A);
     assertEquals(stripe0b, sfs.next());
     sfs.remove();
@@ -350,10 +352,12 @@ public class TestStripeStoreFileManager {
     // Here, [B, C] is logically [B, inf), so we should be able to compact it to that only.
     verifyInvalidCompactionScenario(manager, al(sf), al(createFile(KEY_B, KEY_C)));
     manager.addCompactionResults(al(sf), al(createFile(KEY_B, OPEN_KEY)));
+    manager.removeCompactedFiles(al(sf));
     // Do the same for other variants.
     manager = createManager(al(sf, createFile(KEY_C, OPEN_KEY)));
     verifyInvalidCompactionScenario(manager, al(sf), al(createFile(KEY_B, KEY_C)));
     manager.addCompactionResults(al(sf), al(createFile(OPEN_KEY, KEY_C)));
+    manager.removeCompactedFiles(al(sf));
     manager = createManager(al(sf));
     verifyInvalidCompactionScenario(manager, al(sf), al(createFile(KEY_B, KEY_C)));
     manager.addCompactionResults(al(sf), al(createFile(OPEN_KEY, OPEN_KEY)));
@@ -379,6 +383,7 @@ public class TestStripeStoreFileManager {
     StoreFile sf_B2C_0 = createFile(KEY_B, KEY_C);
     StoreFile sf_C2i_0 = createFile(KEY_C, OPEN_KEY);
     manager.addCompactionResults(al(sf_L0_0a), al(sf_i2B_0, sf_B2C_0, sf_C2i_0));
+    manager.removeCompactedFiles(al(sf_L0_0a));
     verifyAllFiles(manager, al(sf_L0_0b, sf_i2B_0, sf_B2C_0, sf_C2i_0));
 
     // Add another l0 file, "compact" both L0 into two stripes
@@ -387,51 +392,61 @@ public class TestStripeStoreFileManager {
     StoreFile sf_B2C_1 = createFile(KEY_B, KEY_C);
     manager.insertNewFiles(al(sf_L0_1));
     manager.addCompactionResults(al(sf_L0_0b, sf_L0_1), al(sf_i2B_1, sf_B2C_1));
+    manager.removeCompactedFiles(al(sf_L0_0b, sf_L0_1));
     verifyAllFiles(manager, al(sf_i2B_0, sf_B2C_0, sf_C2i_0, sf_i2B_1, sf_B2C_1));
 
     // Try compacting with invalid file (no metadata) - should add files to L0.
     StoreFile sf_L0_2 = createFile(null, null);
     manager.addCompactionResults(al(), al(sf_L0_2));
+    manager.removeCompactedFiles(al());
     verifyAllFiles(manager, al(sf_i2B_0, sf_B2C_0, sf_C2i_0, sf_i2B_1, sf_B2C_1, sf_L0_2));
     // Remove it...
     manager.addCompactionResults(al(sf_L0_2), al());
+    manager.removeCompactedFiles(al(sf_L0_2));
 
     // Do regular compaction in the first stripe.
     StoreFile sf_i2B_3 = createFile(OPEN_KEY, KEY_B);
     manager.addCompactionResults(al(sf_i2B_0, sf_i2B_1), al(sf_i2B_3));
+    manager.removeCompactedFiles(al(sf_i2B_0, sf_i2B_1));
     verifyAllFiles(manager, al(sf_B2C_0, sf_C2i_0, sf_B2C_1, sf_i2B_3));
 
     // Rebalance two stripes.
     StoreFile sf_B2D_4 = createFile(KEY_B, KEY_D);
     StoreFile sf_D2i_4 = createFile(KEY_D, OPEN_KEY);
     manager.addCompactionResults(al(sf_B2C_0, sf_C2i_0, sf_B2C_1), al(sf_B2D_4, sf_D2i_4));
+    manager.removeCompactedFiles(al(sf_B2C_0, sf_C2i_0, sf_B2C_1));
     verifyAllFiles(manager, al(sf_i2B_3, sf_B2D_4, sf_D2i_4));
 
     // Split the first stripe.
     StoreFile sf_i2A_5 = createFile(OPEN_KEY, KEY_A);
     StoreFile sf_A2B_5 = createFile(KEY_A, KEY_B);
     manager.addCompactionResults(al(sf_i2B_3), al(sf_i2A_5, sf_A2B_5));
+    manager.removeCompactedFiles(al(sf_i2B_3));
     verifyAllFiles(manager, al(sf_B2D_4, sf_D2i_4, sf_i2A_5, sf_A2B_5));
 
     // Split the middle stripe.
     StoreFile sf_B2C_6 = createFile(KEY_B, KEY_C);
     StoreFile sf_C2D_6 = createFile(KEY_C, KEY_D);
     manager.addCompactionResults(al(sf_B2D_4), al(sf_B2C_6, sf_C2D_6));
+    manager.removeCompactedFiles(al(sf_B2D_4));
     verifyAllFiles(manager, al(sf_D2i_4, sf_i2A_5, sf_A2B_5, sf_B2C_6, sf_C2D_6));
 
     // Merge two different middle stripes.
     StoreFile sf_A2C_7 = createFile(KEY_A, KEY_C);
     manager.addCompactionResults(al(sf_A2B_5, sf_B2C_6), al(sf_A2C_7));
+    manager.removeCompactedFiles(al(sf_A2B_5, sf_B2C_6));
     verifyAllFiles(manager, al(sf_D2i_4, sf_i2A_5, sf_C2D_6, sf_A2C_7));
 
     // Merge lower half.
     StoreFile sf_i2C_8 = createFile(OPEN_KEY, KEY_C);
     manager.addCompactionResults(al(sf_i2A_5, sf_A2C_7), al(sf_i2C_8));
+    manager.removeCompactedFiles(al(sf_i2A_5, sf_A2C_7));
     verifyAllFiles(manager, al(sf_D2i_4, sf_C2D_6, sf_i2C_8));
 
     // Merge all.
     StoreFile sf_i2i_9 = createFile(OPEN_KEY, OPEN_KEY);
     manager.addCompactionResults(al(sf_D2i_4, sf_C2D_6, sf_i2C_8), al(sf_i2i_9));
+    manager.removeCompactedFiles(al(sf_D2i_4, sf_C2D_6, sf_i2C_8));
     verifyAllFiles(manager, al(sf_i2i_9));
   }
 
@@ -451,12 +466,14 @@ public class TestStripeStoreFileManager {
     verifyGetAndScanScenario(sfm, KEY_C, KEY_C, sf_i2d, sf_d2i, sf_c2i);
     // Remove these files.
     sfm.addCompactionResults(al(sf_i2d, sf_d2i), al());
+    sfm.removeCompactedFiles(al(sf_i2d, sf_d2i));
     assertEquals(0, sfm.getLevel0Files().size());
     // Add another file to stripe; then "rebalance" stripes w/o it - the file, which was
     // presumably flushed during compaction, should go to L0.
     StoreFile sf_i2c_2 = createFile(OPEN_KEY, KEY_C);
     sfm.insertNewFiles(al(sf_i2c_2));
     sfm.addCompactionResults(al(sf_i2c, sf_c2i), al(sf_i2d, sf_d2i));
+    sfm.removeCompactedFiles(al(sf_i2c, sf_c2i));
     assertEquals(1, sfm.getLevel0Files().size());
     verifyGetAndScanScenario(sfm, KEY_C, KEY_C, sf_i2d, sf_i2c_2);
   }
@@ -472,9 +489,11 @@ public class TestStripeStoreFileManager {
     ArrayList<StoreFile> compacted = al(createFile(OPEN_KEY, KEY_B),
         createFile(KEY_B, KEY_C), createFile(KEY_C, OPEN_KEY));
     manager.addCompactionResults(al(sf0a), compacted);
+    manager.removeCompactedFiles(al(sf0a));
     // Next L0 compaction only produces file for the first and last stripe.
     ArrayList<StoreFile> compacted2 = al(createFile(OPEN_KEY, KEY_B), createFile(KEY_C, OPEN_KEY));
     manager.addCompactionResults(al(sf0b), compacted2);
+    manager.removeCompactedFiles(al(sf0b));
     compacted.addAll(compacted2);
     verifyAllFiles(manager, compacted);
   }

hbase-server/src/test/java/org/apache/hadoop/hbase/regionserver/compactions/TestCompactedHFilesDischarger.java

@@ -0,0 +1,389 @@
+/*
+ * 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.hadoop.hbase.regionserver.compactions;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.concurrent.CountDownLatch;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.hbase.Cell;
+import org.apache.hadoop.hbase.HBaseTestingUtility;
+import org.apache.hadoop.hbase.HColumnDescriptor;
+import org.apache.hadoop.hbase.HRegionInfo;
+import org.apache.hadoop.hbase.HTableDescriptor;
+import org.apache.hadoop.hbase.Stoppable;
+import org.apache.hadoop.hbase.TableName;
+import org.apache.hadoop.hbase.client.Put;
+import org.apache.hadoop.hbase.client.Scan;
+import org.apache.hadoop.hbase.regionserver.HRegion;
+import org.apache.hadoop.hbase.regionserver.HStore;
+import org.apache.hadoop.hbase.regionserver.Region;
+import org.apache.hadoop.hbase.regionserver.RegionScanner;
+import org.apache.hadoop.hbase.regionserver.Store;
+import org.apache.hadoop.hbase.regionserver.StoreFile;
+import org.apache.hadoop.hbase.testclassification.MediumTests;
+import org.apache.hadoop.hbase.testclassification.RegionServerTests;
+import org.apache.hadoop.hbase.util.Bytes;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+@Category({ MediumTests.class, RegionServerTests.class })
+public class TestCompactedHFilesDischarger {
+  private final HBaseTestingUtility testUtil = new HBaseTestingUtility();
+  private Region region;
+  private final static byte[] fam = Bytes.toBytes("cf_1");
+  private final static byte[] qual1 = Bytes.toBytes("qf_1");
+  private final static byte[] val = Bytes.toBytes("val");
+  private static CountDownLatch latch = new CountDownLatch(3);
+  private static AtomicInteger counter = new AtomicInteger(0);
+  private static AtomicInteger scanCompletedCounter = new AtomicInteger(0);
+
+  @Before
+  public void setUp() throws Exception {
+    TableName tableName = TableName.valueOf(getClass().getSimpleName());
+    HTableDescriptor htd = new HTableDescriptor(tableName);
+    htd.addFamily(new HColumnDescriptor(fam));
+    HRegionInfo info = new HRegionInfo(tableName, null, null, false);
+    Path path = testUtil.getDataTestDir(getClass().getSimpleName());
+    region = HBaseTestingUtility.createRegionAndWAL(info, path, testUtil.getConfiguration(), htd);
+  }
+
+  @After
+  public void tearDown() throws IOException {
+    counter.set(0);
+    scanCompletedCounter.set(0);
+    latch = new CountDownLatch(3);
+    HBaseTestingUtility.closeRegionAndWAL(region);
+    testUtil.cleanupTestDir();
+  }
+
+  @Test
+  public void testCompactedHFilesCleaner() throws Exception {
+    // Create the cleaner object
+    CompactedHFilesDischarger cleaner =
+        new CompactedHFilesDischarger(1000, (Stoppable) null, (HRegion) region);
+    // Add some data to the region and do some flushes
+    for (int i = 1; i < 10; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 11; i < 20; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 21; i < 30; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+
+    Store store = region.getStore(fam);
+    assertEquals(3, store.getStorefilesCount());
+
+    Collection<StoreFile> storefiles = store.getStorefiles();
+    Collection<StoreFile> compactedfiles =
+        ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    // None of the files should be in compacted state.
+    for (StoreFile file : storefiles) {
+      assertFalse(file.isCompactedAway());
+    }
+    // Try to run the cleaner without compaction. there should not be any change
+    cleaner.chore();
+    storefiles = store.getStorefiles();
+    // None of the files should be in compacted state.
+    for (StoreFile file : storefiles) {
+      assertFalse(file.isCompactedAway());
+    }
+    // now do some compaction
+    region.compact(true);
+    // Still the flushed files should be present until the cleaner runs. But the state of it should
+    // be in COMPACTED state
+    assertEquals(1, store.getStorefilesCount());
+    assertEquals(3,
+      ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles().size());
+
+    // Run the cleaner
+    cleaner.chore();
+    assertEquals(1, store.getStorefilesCount());
+    storefiles = store.getStorefiles();
+    for (StoreFile file : storefiles) {
+      // Should not be in compacted state
+      assertFalse(file.isCompactedAway());
+    }
+    compactedfiles = ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    assertTrue(compactedfiles.size() == 0);
+    
+  }
+
+  @Test
+  public void testCleanerWithParallelScannersAfterCompaction() throws Exception {
+    // Create the cleaner object
+    CompactedHFilesDischarger cleaner =
+        new CompactedHFilesDischarger(1000, (Stoppable) null, (HRegion) region);
+    // Add some data to the region and do some flushes
+    for (int i = 1; i < 10; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 11; i < 20; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 21; i < 30; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+
+    Store store = region.getStore(fam);
+    assertEquals(3, store.getStorefilesCount());
+
+    Collection<StoreFile> storefiles = store.getStorefiles();
+    Collection<StoreFile> compactedfiles =
+        ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    // None of the files should be in compacted state.
+    for (StoreFile file : storefiles) {
+      assertFalse(file.isCompactedAway());
+    }
+    // Do compaction
+    region.compact(true);
+    startScannerThreads();
+
+    storefiles = store.getStorefiles();
+    int usedReaderCount = 0;
+    int unusedReaderCount = 0;
+    for (StoreFile file : storefiles) {
+      if (file.getRefCount() == 3) {
+        usedReaderCount++;
+      }
+    }
+    compactedfiles = ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    for(StoreFile file : compactedfiles) {
+      assertEquals("Refcount should be 3", 0, file.getRefCount());
+      unusedReaderCount++;
+    }
+    // Though there are files we are not using them for reads
+    assertEquals("unused reader count should be 3", 3, unusedReaderCount);
+    assertEquals("used reader count should be 1", 1, usedReaderCount);
+    // now run the cleaner
+    cleaner.chore();
+    countDown();
+    assertEquals(1, store.getStorefilesCount());
+    storefiles = store.getStorefiles();
+    for (StoreFile file : storefiles) {
+      // Should not be in compacted state
+      assertFalse(file.isCompactedAway());
+    }
+    compactedfiles = ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    assertTrue(compactedfiles.size() == 0);
+  }
+
+  @Test
+  public void testCleanerWithParallelScanners() throws Exception {
+    // Create the cleaner object
+    CompactedHFilesDischarger cleaner =
+        new CompactedHFilesDischarger(1000, (Stoppable) null, (HRegion) region);
+    // Add some data to the region and do some flushes
+    for (int i = 1; i < 10; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 11; i < 20; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+    for (int i = 21; i < 30; i++) {
+      Put p = new Put(Bytes.toBytes("row" + i));
+      p.addColumn(fam, qual1, val);
+      region.put(p);
+    }
+    // flush them
+    region.flush(true);
+
+    Store store = region.getStore(fam);
+    assertEquals(3, store.getStorefilesCount());
+
+    Collection<StoreFile> storefiles = store.getStorefiles();
+    Collection<StoreFile> compactedfiles =
+        ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    // None of the files should be in compacted state.
+    for (StoreFile file : storefiles) {
+      assertFalse(file.isCompactedAway());
+    }
+    startScannerThreads();
+    // Do compaction
+    region.compact(true);
+
+    storefiles = store.getStorefiles();
+    int usedReaderCount = 0;
+    int unusedReaderCount = 0;
+    for (StoreFile file : storefiles) {
+      if (file.getRefCount() == 0) {
+        unusedReaderCount++;
+      }
+    }
+    compactedfiles =
+        ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    for(StoreFile file : compactedfiles) {
+      assertEquals("Refcount should be 3", 3, file.getRefCount());
+      usedReaderCount++;
+    }
+    // The newly compacted file will not be used by any scanner
+    assertEquals("unused reader count should be 1", 1, unusedReaderCount);
+    assertEquals("used reader count should be 3", 3, usedReaderCount);
+    // now run the cleaner
+    cleaner.chore();
+    countDown();
+    // No change in the number of store files as none of the compacted files could be cleaned up
+    assertEquals(1, store.getStorefilesCount());
+    assertEquals(3,
+      ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles().size());
+    while (scanCompletedCounter.get() != 3) {
+      Thread.sleep(100);
+    }
+    // reset
+    latch = new CountDownLatch(3);
+    scanCompletedCounter.set(0);
+    counter.set(0);
+    // Try creating a new scanner and it should use only the new file created after compaction
+    startScannerThreads();
+    storefiles = store.getStorefiles();
+    usedReaderCount = 0;
+    unusedReaderCount = 0;
+    for (StoreFile file : storefiles) {
+      if (file.getRefCount() == 3) {
+        usedReaderCount++;
+      }
+    }
+    compactedfiles = ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    for(StoreFile file : compactedfiles) {
+      assertEquals("Refcount should be 0", 0, file.getRefCount());
+      unusedReaderCount++;
+    }
+    // Though there are files we are not using them for reads
+    assertEquals("unused reader count should be 3", 3, unusedReaderCount);
+    assertEquals("used reader count should be 1", 1, usedReaderCount);
+    countDown();
+    while (scanCompletedCounter.get() != 3) {
+      Thread.sleep(100);
+    }
+    // Run the cleaner again
+    cleaner.chore();
+    // Now the cleaner should be able to clear it up because there are no active readers
+    assertEquals(1, store.getStorefilesCount());
+    storefiles = store.getStorefiles();
+    for (StoreFile file : storefiles) {
+      // Should not be in compacted state
+      assertFalse(file.isCompactedAway());
+    }
+    compactedfiles = ((HStore) store).getStoreEngine().getStoreFileManager().getCompactedfiles();
+    assertTrue(compactedfiles.size() == 0);
+  }
+
+  protected void countDown() {
+    // count down 3 times
+    latch.countDown();
+    latch.countDown();
+    latch.countDown();
+  }
+
+  protected void startScannerThreads() throws InterruptedException {
+    // Start parallel scan threads
+    ScanThread[] scanThreads = new ScanThread[3];
+    for (int i = 0; i < 3; i++) {
+      scanThreads[i] = new ScanThread((HRegion) region);
+    }
+    for (ScanThread thread : scanThreads) {
+      thread.start();
+    }
+    while (counter.get() != 3) {
+      Thread.sleep(100);
+    }
+  }
+
+  private static class ScanThread extends Thread {
+    private final HRegion region;
+
+    public ScanThread(HRegion region) {
+      this.region = region;
+    }
+
+    @Override
+    public void run() {
+      try {
+        initiateScan(region);
+      } catch (IOException e) {
+        // do nothing
+      }
+    }
+
+    private void initiateScan(HRegion region) throws IOException {
+      Scan scan = new Scan();
+      scan.setCaching(1);
+      RegionScanner resScanner = null;
+      try {
+        resScanner = region.getScanner(scan);
+        List<Cell> results = new ArrayList<Cell>();
+        boolean next = resScanner.next(results);
+        try {
+          counter.incrementAndGet();
+          latch.await();
+        } catch (InterruptedException e) {
+        }
+        while (!next) {
+          resScanner.next(results);
+        }
+      } finally {
+        scanCompletedCounter.incrementAndGet();
+        resScanner.close();
+      }
+    }
+  }
+}