HBASE-20704 Sometimes some compacted storefiles are not archived on region close

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

@@ -924,7 +924,7 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
           storeEngine.getStoreFileManager().clearCompactedFiles();
       // clear the compacted files
       if (CollectionUtils.isNotEmpty(compactedfiles)) {
-        removeCompactedfiles(compactedfiles);
+        removeCompactedfiles(compactedfiles, true);
       }
       if (!result.isEmpty()) {
         // initialize the thread pool for closing store files in parallel.
@@ -2533,6 +2533,11 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
    * Closes and archives the compacted files under this store
    */
   public synchronized void closeAndArchiveCompactedFiles() throws IOException {
+    closeAndArchiveCompactedFiles(false);
+  }
+
+  @VisibleForTesting
+  public synchronized void closeAndArchiveCompactedFiles(boolean storeClosing) throws IOException {
     // ensure other threads do not attempt to archive the same files on close()
     archiveLock.lock();
     try {
@@ -2551,7 +2556,7 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
         lock.readLock().unlock();
       }
       if (CollectionUtils.isNotEmpty(copyCompactedfiles)) {
-        removeCompactedfiles(copyCompactedfiles);
+        removeCompactedfiles(copyCompactedfiles, storeClosing);
       }
     } finally {
       archiveLock.unlock();
@@ -2563,7 +2568,7 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
    * @param compactedfiles The compacted files in this store that are not active in reads
    * @throws IOException
    */
-  private void removeCompactedfiles(Collection<HStoreFile> compactedfiles)
+  private void removeCompactedfiles(Collection<HStoreFile> compactedfiles, boolean storeClosing)
       throws IOException {
     final List<HStoreFile> filesToRemove = new ArrayList<>(compactedfiles.size());
     for (final HStoreFile file : compactedfiles) {
@@ -2575,11 +2580,29 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
             filesToRemove.add(file);
             continue;
           }
-          if (file.isCompactedAway() && !file.isReferencedInReads()) {
+
+          //Compacted files in the list should always be marked compacted away. In the event
+          //they're contradicting in order to guarantee data consistency
+          //should we choose one and ignore the other?
+          if (storeClosing && !file.isCompactedAway()) {
+            String msg =
+                "Region closing but StoreFile is in compacted list but not compacted away: " +
+                file.getPath().getName();
+            throw new IllegalStateException(msg);
+          }
+
+          //If store is closing we're ignoring any references to keep things consistent
+          //and remove compacted storefiles from the region directory
+          if (file.isCompactedAway() && (!file.isReferencedInReads() || storeClosing)) {
+            if (storeClosing && file.isReferencedInReads()) {
+              LOG.debug("Region closing but StoreFile still has references: {}",
+                  file.getPath().getName());
+            }
             // 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
             LOG.trace("Closing and archiving the file {}", file);
             r.close(true);
+            file.closeStreamReaders(true);
             // Just close and return
             filesToRemove.add(file);
           } else {
@@ -2589,8 +2612,16 @@ public class HStore implements Store, HeapSize, StoreConfigInformation, Propagat
                 + ", skipping for now.");
           }
         } catch (Exception e) {
-          LOG.error("Exception while trying to close the compacted store file {}",
+          String msg = "Exception while trying to close the compacted store file " +
-            file.getPath(), e);
+              file.getPath().getName();
+          if (storeClosing) {
+            msg = "Store is closing. " + msg;
+          }
+          LOG.error(msg, e);
+          //if we get an exception let caller know so it can abort the server
+          if (storeClosing) {
+            throw new IOException(msg, e);
+          }
         }
       }
     }

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

@@ -23,6 +23,8 @@ import java.util.Collections;
 import java.util.Map;
 import java.util.Optional;
 import java.util.OptionalLong;
+import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.concurrent.atomic.AtomicInteger;
 
@@ -38,10 +40,14 @@ import org.apache.hadoop.hbase.io.hfile.CacheConfig;
 import org.apache.hadoop.hbase.io.hfile.HFile;
 import org.apache.hadoop.hbase.util.BloomFilterFactory;
 import org.apache.hadoop.hbase.util.Bytes;
+
 import org.apache.yetus.audience.InterfaceAudience;
+
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.apache.hbase.thirdparty.com.google.common.annotations.VisibleForTesting;
+import org.apache.hbase.thirdparty.com.google.common.base.Preconditions;
+
 
 /**
  * A Store data file.  Stores usually have one or more of these files.  They
@@ -57,7 +63,7 @@ import org.apache.hbase.thirdparty.com.google.common.annotations.VisibleForTesti
  * writer and a reader is that we write once but read a lot more.
  */
 @InterfaceAudience.Private
-public class HStoreFile implements StoreFile {
+public class HStoreFile implements StoreFile, StoreFileReader.Listener {
 
   private static final Logger LOG = LoggerFactory.getLogger(HStoreFile.class.getName());
 
@@ -116,6 +122,9 @@ public class HStoreFile implements StoreFile {
   // done.
   private final AtomicInteger refCount = new AtomicInteger(0);
 
+  // Set implementation must be of concurrent type
+  private final Set<StoreFileReader> streamReaders;
+
   private final boolean noReadahead;
 
   private final boolean primaryReplica;
@@ -219,6 +228,7 @@ public class HStoreFile implements StoreFile {
    */
   public HStoreFile(FileSystem fs, StoreFileInfo fileInfo, Configuration conf, CacheConfig cacheConf,
       BloomType cfBloomType, boolean primaryReplica) {
+    this.streamReaders = ConcurrentHashMap.newKeySet();
     this.fs = fs;
     this.fileInfo = fileInfo;
     this.cacheConf = cacheConf;
@@ -502,8 +512,13 @@ public class HStoreFile implements StoreFile {
   public StoreFileScanner getStreamScanner(boolean canUseDropBehind, boolean cacheBlocks,
       boolean isCompaction, long readPt, long scannerOrder, boolean canOptimizeForNonNullColumn)
       throws IOException {
-    return createStreamReader(canUseDropBehind).getStoreFileScanner(cacheBlocks, false,
+    StoreFileReader reader = createStreamReader(canUseDropBehind);
+    reader.setListener(this);
+    StoreFileScanner sfScanner = reader.getStoreFileScanner(cacheBlocks, false,
       isCompaction, readPt, scannerOrder, canOptimizeForNonNullColumn);
+    //Add reader once the scanner is created
+    streamReaders.add(reader);
+    return sfScanner;
   }
 
   /**
@@ -523,6 +538,19 @@ public class HStoreFile implements StoreFile {
       this.reader.close(evictOnClose);
       this.reader = null;
     }
+    closeStreamReaders(evictOnClose);
+  }
+
+  public void closeStreamReaders(boolean evictOnClose) throws IOException {
+    synchronized (this) {
+      for (StoreFileReader entry : streamReaders) {
+        //closing the reader will remove itself from streamReaders thanks to the Listener
+        entry.close(evictOnClose);
+      }
+      int size = streamReaders.size();
+      Preconditions.checkState(size == 0,
+          "There are still streamReaders post close: " + size);
+    }
   }
 
   /**
@@ -589,4 +617,9 @@ public class HStoreFile implements StoreFile {
     TimeRange tr = getReader().timeRange;
     return tr != null ? OptionalLong.of(tr.getMax()) : OptionalLong.empty();
   }
+
+  @Override
+  public void storeFileReaderClosed(StoreFileReader reader) {
+    streamReaders.remove(reader);
+  }
 }

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

@@ -85,6 +85,10 @@ public class StoreFileReader {
   @VisibleForTesting
   final boolean shared;
 
+  private volatile Listener listener;
+
+  private boolean closed = false;
+
   private StoreFileReader(HFile.Reader reader, AtomicInteger refCount, boolean shared) {
     this.reader = reader;
     bloomFilterType = BloomType.NONE;
@@ -209,7 +213,16 @@ public class StoreFileReader {
   }
 
   public void close(boolean evictOnClose) throws IOException {
-    reader.close(evictOnClose);
+    synchronized (this) {
+      if (closed) {
+        return;
+      }
+      reader.close(evictOnClose);
+      closed = true;
+    }
+    if (listener != null) {
+      listener.storeFileReaderClosed(this);
+    }
   }
 
   /**
@@ -644,4 +657,12 @@ public class StoreFileReader {
   void setSkipResetSeqId(boolean skipResetSeqId) {
     this.skipResetSeqId = skipResetSeqId;
   }
+
+  public void setListener(Listener listener) {
+    this.listener = listener;
+  }
+
+  public interface Listener {
+    void storeFileReaderClosed(StoreFileReader reader);
+  }
 }

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

@@ -0,0 +1,210 @@
+/*
+ *
+ * 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;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.util.Collection;
+
+import org.apache.hadoop.hbase.HBaseClassTestRule;
+import org.apache.hadoop.hbase.HBaseTestingUtility;
+import org.apache.hadoop.hbase.KeyValue;
+import org.apache.hadoop.hbase.TableName;
+import org.apache.hadoop.hbase.client.Delete;
+import org.apache.hadoop.hbase.client.Get;
+import org.apache.hadoop.hbase.client.HBaseAdmin;
+import org.apache.hadoop.hbase.client.IsolationLevel;
+import org.apache.hadoop.hbase.client.Put;
+import org.apache.hadoop.hbase.client.Result;
+import org.apache.hadoop.hbase.client.ResultScanner;
+import org.apache.hadoop.hbase.client.Scan;
+import org.apache.hadoop.hbase.client.Table;
+import org.apache.hadoop.hbase.master.cleaner.TimeToLiveHFileCleaner;
+import org.apache.hadoop.hbase.regionserver.compactions.CompactionConfiguration;
+import org.apache.hadoop.hbase.testclassification.MediumTests;
+import org.apache.hadoop.hbase.util.Bytes;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.ClassRule;
+import org.junit.Test;
+import org.junit.experimental.categories.Category;
+
+@Category({MediumTests.class})
+public class TestCleanupCompactedFileOnRegionClose {
+
+  @ClassRule
+  public static final HBaseClassTestRule CLASS_RULE =
+      HBaseClassTestRule.forClass(TestCleanupCompactedFileOnRegionClose.class);
+
+  private static HBaseTestingUtility util;
+
+  @BeforeClass
+  public static void beforeClass() throws Exception {
+    util = new HBaseTestingUtility();
+    util.getConfiguration().setInt(CompactionConfiguration.HBASE_HSTORE_COMPACTION_MIN_KEY,100);
+    util.getConfiguration().set("dfs.blocksize", "64000");
+    util.getConfiguration().set("dfs.namenode.fs-limits.min-block-size", "1024");
+    util.getConfiguration().set(TimeToLiveHFileCleaner.TTL_CONF_KEY,"0");
+    util.startMiniCluster(2);
+  }
+
+  @AfterClass
+  public static void afterclass() throws Exception {
+    util.shutdownMiniCluster();
+  }
+
+  @Test
+  public void testCleanupOnClose() throws Exception {
+    TableName tableName = TableName.valueOf("testCleanupOnClose");
+    String familyName = "f";
+    byte[] familyNameBytes = Bytes.toBytes(familyName);
+    util.createTable(tableName, familyName);
+
+    HBaseAdmin hBaseAdmin = util.getHBaseAdmin();
+    Table table = util.getConnection().getTable(tableName);
+
+    HRegionServer rs = util.getRSForFirstRegionInTable(tableName);
+    Region region = rs.getRegions(tableName).get(0);
+
+    int refSFCount = 4;
+    for (int i = 0; i < refSFCount; i++) {
+      for (int j = 0; j < refSFCount; j++) {
+        Put put = new Put(Bytes.toBytes(j));
+        put.addColumn(familyNameBytes, Bytes.toBytes(i), Bytes.toBytes(j));
+        table.put(put);
+      }
+      util.flush(tableName);
+    }
+    assertEquals(refSFCount, region.getStoreFileList(new byte[][]{familyNameBytes}).size());
+
+    //add a delete, to test wether we end up with an inconsistency post region close
+    Delete delete = new Delete(Bytes.toBytes(refSFCount-1));
+    table.delete(delete);
+    util.flush(tableName);
+    assertFalse(table.exists(new Get(Bytes.toBytes(refSFCount-1))));
+
+    //Create a scanner and keep it open to add references to StoreFileReaders
+    Scan scan = new Scan();
+    scan.setStopRow(Bytes.toBytes(refSFCount-2));
+    scan.setCaching(1);
+    ResultScanner scanner = table.getScanner(scan);
+    Result res = scanner.next();
+    assertNotNull(res);
+    assertEquals(refSFCount, res.getFamilyMap(familyNameBytes).size());
+
+
+    //Verify the references
+    int count = 0;
+    for (HStoreFile sf : (Collection<HStoreFile>)region.getStore(familyNameBytes).getStorefiles()) {
+      synchronized (sf) {
+        if (count < refSFCount) {
+          assertTrue(sf.isReferencedInReads());
+        } else {
+          assertFalse(sf.isReferencedInReads());
+        }
+      }
+      count++;
+    }
+
+    //Major compact to produce compacted storefiles that need to be cleaned up
+    util.compact(tableName, true);
+    assertEquals(1, region.getStoreFileList(new byte[][]{familyNameBytes}).size());
+    assertEquals(refSFCount+1,
+      ((HStore)region.getStore(familyNameBytes)).getStoreEngine().getStoreFileManager()
+          .getCompactedfiles().size());
+
+    //close then open the region to determine wether compacted storefiles get cleaned up on close
+    hBaseAdmin.unassign(region.getRegionInfo().getRegionName(), false);
+    hBaseAdmin.assign(region.getRegionInfo().getRegionName());
+    util.waitUntilNoRegionsInTransition(10000);
+
+
+    assertFalse("Deleted row should not exist",
+        table.exists(new Get(Bytes.toBytes(refSFCount-1))));
+
+    rs = util.getRSForFirstRegionInTable(tableName);
+    region = rs.getRegions(tableName).get(0);
+    assertEquals(1, region.getStoreFileList(new byte[][]{familyNameBytes}).size());
+    assertEquals(0,
+        ((HStore)region.getStore(familyNameBytes)).getStoreEngine().getStoreFileManager()
+            .getCompactedfiles().size());
+  }
+
+  @Test
+  public void testIOExceptionThrownOnClose() throws Exception {
+    byte[] filler = new byte[128000];
+    TableName tableName = TableName.valueOf("testIOExceptionThrownOnClose");
+    String familyName = "f";
+    byte[] familyNameBytes = Bytes.toBytes(familyName);
+    util.createTable(tableName, familyName);
+
+    Table table = util.getConnection().getTable(tableName);
+
+    HRegionServer rs = util.getRSForFirstRegionInTable(tableName);
+    Region region = rs.getRegions(tableName).get(0);
+
+    int refSFCount = 4;
+    for (int i = 0; i < refSFCount; i++) {
+      for (int j = 0; j < refSFCount; j++) {
+        Put put = new Put(Bytes.toBytes(j));
+        put.addColumn(familyNameBytes, Bytes.toBytes(i), filler);
+        table.put(put);
+      }
+      util.flush(tableName);
+    }
+    assertEquals(refSFCount, region.getStoreFileList(new byte[][]{familyNameBytes}).size());
+
+    HStore store = ((HRegion) region).getStore(familyNameBytes);
+    HStoreFile hsf = ((Collection<HStoreFile>)region.getStore(familyNameBytes).getStorefiles())
+        .iterator().next();
+    long readPt = ((HRegion)region).getReadPoint(IsolationLevel.READ_COMMITTED);
+    StoreFileScanner preadScanner = hsf.getPreadScanner(false, readPt, 0, false);
+    StoreFileScanner streamScanner =
+        hsf.getStreamScanner(false, false, false, readPt, 0,  false);
+    preadScanner.seek(KeyValue.LOWESTKEY);
+    streamScanner.seek(KeyValue.LOWESTKEY);
+
+    //Major compact to produce compacted storefiles that need to be cleaned up
+    util.compact(tableName, true);
+    assertNotNull(preadScanner.next());
+    assertNotNull(streamScanner.next());
+    store.closeAndArchiveCompactedFiles(true);
+
+    try {
+      assertNotNull(preadScanner.next());
+      fail("Expected IOException");
+    }catch (IOException ex) {
+      ex.printStackTrace();
+    }
+
+    //Wait a bit for file to be remove from
+    try {
+      assertNotNull(streamScanner.next());
+      fail("Expected IOException");
+    } catch (IOException ex) {
+      ex.printStackTrace();
+    }
+  }
+}