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Posted to commits@accumulo.apache.org by bu...@apache.org on 2014/01/23 08:36:39 UTC
[21/23] Merge branch '1.5.1-SNAPSHOT' into 1.6.0-SNAPSHOT
http://git-wip-us.apache.org/repos/asf/accumulo/blob/e7e5c009/server/tserver/src/main/java/org/apache/accumulo/tserver/Compactor.java
----------------------------------------------------------------------
diff --cc server/tserver/src/main/java/org/apache/accumulo/tserver/Compactor.java
index 0843c13,0000000..df476ec
mode 100644,000000..100644
--- a/server/tserver/src/main/java/org/apache/accumulo/tserver/Compactor.java
+++ b/server/tserver/src/main/java/org/apache/accumulo/tserver/Compactor.java
@@@ -1,546 -1,0 +1,548 @@@
+/*
+ * 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.accumulo.tserver;
+
+import java.io.IOException;
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicLong;
+
+import org.apache.accumulo.core.client.IteratorSetting;
+import org.apache.accumulo.core.conf.AccumuloConfiguration;
+import org.apache.accumulo.core.data.ByteSequence;
+import org.apache.accumulo.core.data.Key;
+import org.apache.accumulo.core.data.KeyExtent;
+import org.apache.accumulo.core.data.Value;
+import org.apache.accumulo.core.data.thrift.IterInfo;
+import org.apache.accumulo.core.file.FileOperations;
+import org.apache.accumulo.core.file.FileSKVIterator;
+import org.apache.accumulo.core.file.FileSKVWriter;
+import org.apache.accumulo.core.iterators.IteratorEnvironment;
+import org.apache.accumulo.core.iterators.IteratorUtil;
+import org.apache.accumulo.core.iterators.IteratorUtil.IteratorScope;
+import org.apache.accumulo.core.iterators.SortedKeyValueIterator;
+import org.apache.accumulo.core.iterators.WrappingIterator;
+import org.apache.accumulo.core.iterators.system.ColumnFamilySkippingIterator;
+import org.apache.accumulo.core.iterators.system.DeletingIterator;
+import org.apache.accumulo.core.iterators.system.MultiIterator;
+import org.apache.accumulo.core.iterators.system.TimeSettingIterator;
+import org.apache.accumulo.core.metadata.schema.DataFileValue;
+import org.apache.accumulo.core.tabletserver.thrift.ActiveCompaction;
+import org.apache.accumulo.core.tabletserver.thrift.CompactionReason;
+import org.apache.accumulo.core.tabletserver.thrift.CompactionType;
+import org.apache.accumulo.core.util.LocalityGroupUtil;
+import org.apache.accumulo.core.util.LocalityGroupUtil.LocalityGroupConfigurationError;
+import org.apache.accumulo.server.fs.FileRef;
+import org.apache.accumulo.server.fs.VolumeManager;
+import org.apache.accumulo.server.problems.ProblemReport;
+import org.apache.accumulo.server.problems.ProblemReportingIterator;
+import org.apache.accumulo.server.problems.ProblemReports;
+import org.apache.accumulo.server.problems.ProblemType;
+import org.apache.accumulo.trace.instrument.Span;
+import org.apache.accumulo.trace.instrument.Trace;
+import org.apache.accumulo.tserver.Tablet.MinorCompactionReason;
+import org.apache.accumulo.tserver.compaction.MajorCompactionReason;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.log4j.Logger;
+
+public class Compactor implements Callable<CompactionStats> {
+
+ public static class CountingIterator extends WrappingIterator {
+
+ private long count;
+ private ArrayList<CountingIterator> deepCopies;
+ private AtomicLong entriesRead;
+
+ @Override
+ public CountingIterator deepCopy(IteratorEnvironment env) {
+ return new CountingIterator(this, env);
+ }
+
+ private CountingIterator(CountingIterator other, IteratorEnvironment env) {
+ setSource(other.getSource().deepCopy(env));
+ count = 0;
+ this.deepCopies = other.deepCopies;
+ this.entriesRead = other.entriesRead;
+ deepCopies.add(this);
+ }
+
+ public CountingIterator(SortedKeyValueIterator<Key,Value> source, AtomicLong entriesRead) {
+ deepCopies = new ArrayList<Compactor.CountingIterator>();
+ this.setSource(source);
+ count = 0;
+ this.entriesRead = entriesRead;
+ }
+
+ @Override
+ public void init(SortedKeyValueIterator<Key,Value> source, Map<String,String> options, IteratorEnvironment env) {
+ throw new UnsupportedOperationException();
+ }
+
+ @Override
+ public void next() throws IOException {
+ super.next();
+ count++;
+ if (count % 1024 == 0) {
+ entriesRead.addAndGet(1024);
+ }
+ }
+
+ public long getCount() {
+ long sum = 0;
+ for (CountingIterator dc : deepCopies) {
+ sum += dc.count;
+ }
+
+ return count + sum;
+ }
+ }
+
+ private static final Logger log = Logger.getLogger(Compactor.class);
+
+ static class CompactionCanceledException extends Exception {
+ private static final long serialVersionUID = 1L;
+ }
+
+ interface CompactionEnv {
+ boolean isCompactionEnabled();
+
+ IteratorScope getIteratorScope();
+ }
+
+ private Map<FileRef,DataFileValue> filesToCompact;
+ private InMemoryMap imm;
+ private FileRef outputFile;
+ private boolean propogateDeletes;
+ private AccumuloConfiguration acuTableConf;
+ private CompactionEnv env;
+ private Configuration conf;
+ private VolumeManager fs;
+ protected KeyExtent extent;
+ private List<IteratorSetting> iterators;
+
+ // things to report
+ private String currentLocalityGroup = "";
+ private long startTime;
+
+ private MajorCompactionReason reason;
+ protected MinorCompactionReason mincReason;
+
+ private AtomicLong entriesRead = new AtomicLong(0);
+ private AtomicLong entriesWritten = new AtomicLong(0);
+ private DateFormat dateFormatter = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss.SSS");
+
+ private static AtomicLong nextCompactorID = new AtomicLong(0);
+
+ // a unique id to identify a compactor
+ private long compactorID = nextCompactorID.getAndIncrement();
+
+ protected volatile Thread thread;
+
+ private synchronized void setLocalityGroup(String name) {
+ this.currentLocalityGroup = name;
+ }
+
+ private void clearStats() {
+ entriesRead.set(0);
+ entriesWritten.set(0);
+ }
+
+ protected static Set<Compactor> runningCompactions = Collections.synchronizedSet(new HashSet<Compactor>());
+
+ public static class CompactionInfo {
+
+ private Compactor compactor;
+ private String localityGroup;
+ private long entriesRead;
+ private long entriesWritten;
+
+ CompactionInfo(Compactor compactor) {
+ this.localityGroup = compactor.currentLocalityGroup;
+ this.entriesRead = compactor.entriesRead.get();
+ this.entriesWritten = compactor.entriesWritten.get();
+ this.compactor = compactor;
+ }
+
+ public long getID() {
+ return compactor.compactorID;
+ }
+
+ public KeyExtent getExtent() {
+ return compactor.getExtent();
+ }
+
+ public long getEntriesRead() {
+ return entriesRead;
+ }
+
+ public long getEntriesWritten() {
+ return entriesWritten;
+ }
+
+ public Thread getThread() {
+ return compactor.thread;
+ }
+
+ public String getOutputFile() {
+ return compactor.getOutputFile();
+ }
+
+ public ActiveCompaction toThrift() {
+
+ CompactionType type;
+
+ if (compactor.imm != null)
+ if (compactor.filesToCompact.size() > 0)
+ type = CompactionType.MERGE;
+ else
+ type = CompactionType.MINOR;
+ else if (!compactor.propogateDeletes)
+ type = CompactionType.FULL;
+ else
+ type = CompactionType.MAJOR;
+
+ CompactionReason reason;
+
+ if (compactor.imm != null)
+ switch (compactor.mincReason) {
+ case USER:
+ reason = CompactionReason.USER;
+ break;
+ case CLOSE:
+ reason = CompactionReason.CLOSE;
+ break;
+ case SYSTEM:
+ default:
+ reason = CompactionReason.SYSTEM;
+ break;
+ }
+ else
+ switch (compactor.reason) {
+ case USER:
+ reason = CompactionReason.USER;
+ break;
+ case CHOP:
+ reason = CompactionReason.CHOP;
+ break;
+ case IDLE:
+ reason = CompactionReason.IDLE;
+ break;
+ case NORMAL:
+ default:
+ reason = CompactionReason.SYSTEM;
+ break;
+ }
+
+ List<IterInfo> iiList = new ArrayList<IterInfo>();
+ Map<String,Map<String,String>> iterOptions = new HashMap<String,Map<String,String>>();
+
+ for (IteratorSetting iterSetting : compactor.iterators) {
+ iiList.add(new IterInfo(iterSetting.getPriority(), iterSetting.getIteratorClass(), iterSetting.getName()));
+ iterOptions.put(iterSetting.getName(), iterSetting.getOptions());
+ }
+ List<String> filesToCompact = new ArrayList<String>();
+ for (FileRef ref : compactor.filesToCompact.keySet())
+ filesToCompact.add(ref.toString());
+ return new ActiveCompaction(compactor.extent.toThrift(), System.currentTimeMillis() - compactor.startTime, filesToCompact,
+ compactor.outputFile.toString(), type, reason, localityGroup, entriesRead, entriesWritten, iiList, iterOptions);
+ }
+ }
+
+ public static List<CompactionInfo> getRunningCompactions() {
+ ArrayList<CompactionInfo> compactions = new ArrayList<Compactor.CompactionInfo>();
+
+ synchronized (runningCompactions) {
+ for (Compactor compactor : runningCompactions) {
+ compactions.add(new CompactionInfo(compactor));
+ }
+ }
+
+ return compactions;
+ }
+
+ Compactor(Configuration conf, VolumeManager fs, Map<FileRef,DataFileValue> files, InMemoryMap imm, FileRef outputFile, boolean propogateDeletes,
+ AccumuloConfiguration acuTableConf, KeyExtent extent, CompactionEnv env, List<IteratorSetting> iterators, MajorCompactionReason reason) {
+ this.extent = extent;
+ this.conf = conf;
+ this.fs = fs;
+ this.filesToCompact = files;
+ this.imm = imm;
+ this.outputFile = outputFile;
+ this.propogateDeletes = propogateDeletes;
+ this.acuTableConf = acuTableConf;
+ this.env = env;
+ this.iterators = iterators;
+ this.reason = reason;
+
+ startTime = System.currentTimeMillis();
+ }
+
+ Compactor(Configuration conf, VolumeManager fs, Map<FileRef,DataFileValue> files, InMemoryMap imm, FileRef outputFile, boolean propogateDeletes,
+ AccumuloConfiguration acuTableConf, KeyExtent extent, CompactionEnv env) {
+ this(conf, fs, files, imm, outputFile, propogateDeletes, acuTableConf, extent, env, new ArrayList<IteratorSetting>(), null);
+ }
+
+ public VolumeManager getFileSystem() {
+ return fs;
+ }
+
+ KeyExtent getExtent() {
+ return extent;
+ }
+
+ String getOutputFile() {
+ return outputFile.toString();
+ }
+
+ @Override
+ public CompactionStats call() throws IOException, CompactionCanceledException {
+
+ FileSKVWriter mfw = null;
+
+ CompactionStats majCStats = new CompactionStats();
+
+ boolean remove = runningCompactions.add(this);
+
+ clearStats();
+
+ String oldThreadName = Thread.currentThread().getName();
+ String newThreadName = "MajC compacting " + extent.toString() + " started " + dateFormatter.format(new Date()) + " file: " + outputFile;
+ Thread.currentThread().setName(newThreadName);
+ thread = Thread.currentThread();
+ try {
+ FileOperations fileFactory = FileOperations.getInstance();
+ FileSystem ns = this.fs.getFileSystemByPath(outputFile.path());
+ mfw = fileFactory.openWriter(outputFile.path().toString(), ns, ns.getConf(), acuTableConf);
+
+ Map<String,Set<ByteSequence>> lGroups;
+ try {
+ lGroups = LocalityGroupUtil.getLocalityGroups(acuTableConf);
+ } catch (LocalityGroupConfigurationError e) {
+ throw new IOException(e);
+ }
+
+ long t1 = System.currentTimeMillis();
+
+ HashSet<ByteSequence> allColumnFamilies = new HashSet<ByteSequence>();
+
+ if (mfw.supportsLocalityGroups()) {
+ for (Entry<String,Set<ByteSequence>> entry : lGroups.entrySet()) {
+ setLocalityGroup(entry.getKey());
+ compactLocalityGroup(entry.getKey(), entry.getValue(), true, mfw, majCStats);
+ allColumnFamilies.addAll(entry.getValue());
+ }
+ }
+
+ setLocalityGroup("");
+ compactLocalityGroup(null, allColumnFamilies, false, mfw, majCStats);
+
+ long t2 = System.currentTimeMillis();
+
+ FileSKVWriter mfwTmp = mfw;
+ mfw = null; // set this to null so we do not try to close it again in finally if the close fails
+ mfwTmp.close(); // if the close fails it will cause the compaction to fail
+
+ // Verify the file, since hadoop 0.20.2 sometimes lies about the success of close()
+ try {
+ FileSKVIterator openReader = fileFactory.openReader(outputFile.path().toString(), false, ns, ns.getConf(), acuTableConf);
+ openReader.close();
+ } catch (IOException ex) {
+ log.error("Verification of successful compaction fails!!! " + extent + " " + outputFile, ex);
+ throw ex;
+ }
+
+ log.debug(String.format("Compaction %s %,d read | %,d written | %,6d entries/sec | %6.3f secs", extent, majCStats.getEntriesRead(),
+ majCStats.getEntriesWritten(), (int) (majCStats.getEntriesRead() / ((t2 - t1) / 1000.0)), (t2 - t1) / 1000.0));
+
+ majCStats.setFileSize(fileFactory.getFileSize(outputFile.path().toString(), ns, ns.getConf(), acuTableConf));
+ return majCStats;
+ } catch (IOException e) {
+ log.error(e, e);
+ throw e;
+ } catch (RuntimeException e) {
+ log.error(e, e);
+ throw e;
+ } finally {
+ Thread.currentThread().setName(oldThreadName);
+ if (remove) {
+ thread = null;
+ runningCompactions.remove(this);
+ }
+
+ try {
+ if (mfw != null) {
+ // compaction must not have finished successfully, so close its output file
+ try {
+ mfw.close();
+ } finally {
+ if (!fs.deleteRecursively(outputFile.path()))
+ if (fs.exists(outputFile.path()))
+ log.error("Unable to delete " + outputFile);
+ }
+ }
+ } catch (IOException e) {
+ log.warn(e, e);
++ } catch (RuntimeException exception) {
++ log.warn(exception, exception);
+ }
+ }
+ }
+
+ private List<SortedKeyValueIterator<Key,Value>> openMapDataFiles(String lgName, ArrayList<FileSKVIterator> readers) throws IOException {
+
+ List<SortedKeyValueIterator<Key,Value>> iters = new ArrayList<SortedKeyValueIterator<Key,Value>>(filesToCompact.size());
+
+ for (FileRef mapFile : filesToCompact.keySet()) {
+ try {
+
+ FileOperations fileFactory = FileOperations.getInstance();
+ FileSystem fs = this.fs.getFileSystemByPath(mapFile.path());
+ FileSKVIterator reader;
+
+ reader = fileFactory.openReader(mapFile.path().toString(), false, fs, conf, acuTableConf);
+
+ readers.add(reader);
+
+ SortedKeyValueIterator<Key,Value> iter = new ProblemReportingIterator(extent.getTableId().toString(), mapFile.path().toString(), false, reader);
+
+ if (filesToCompact.get(mapFile).isTimeSet()) {
+ iter = new TimeSettingIterator(iter, filesToCompact.get(mapFile).getTime());
+ }
+
+ iters.add(iter);
+
+ } catch (Throwable e) {
+
+ ProblemReports.getInstance().report(new ProblemReport(extent.getTableId().toString(), ProblemType.FILE_READ, mapFile.path().toString(), e));
+
+ log.warn("Some problem opening map file " + mapFile + " " + e.getMessage(), e);
+ // failed to open some map file... close the ones that were opened
+ for (FileSKVIterator reader : readers) {
+ try {
+ reader.close();
+ } catch (Throwable e2) {
+ log.warn("Failed to close map file", e2);
+ }
+ }
+
+ readers.clear();
+
+ if (e instanceof IOException)
+ throw (IOException) e;
+ throw new IOException("Failed to open map data files", e);
+ }
+ }
+
+ return iters;
+ }
+
+ private void compactLocalityGroup(String lgName, Set<ByteSequence> columnFamilies, boolean inclusive, FileSKVWriter mfw, CompactionStats majCStats)
+ throws IOException, CompactionCanceledException {
+ ArrayList<FileSKVIterator> readers = new ArrayList<FileSKVIterator>(filesToCompact.size());
+ Span span = Trace.start("compact");
+ try {
+ long entriesCompacted = 0;
+ List<SortedKeyValueIterator<Key,Value>> iters = openMapDataFiles(lgName, readers);
+
+ if (imm != null) {
+ iters.add(imm.compactionIterator());
+ }
+
+ CountingIterator citr = new CountingIterator(new MultiIterator(iters, extent.toDataRange()), entriesRead);
+ DeletingIterator delIter = new DeletingIterator(citr, propogateDeletes);
+ ColumnFamilySkippingIterator cfsi = new ColumnFamilySkippingIterator(delIter);
+
+ // if(env.getIteratorScope() )
+
+ TabletIteratorEnvironment iterEnv;
+ if (env.getIteratorScope() == IteratorScope.majc)
+ iterEnv = new TabletIteratorEnvironment(IteratorScope.majc, !propogateDeletes, acuTableConf);
+ else if (env.getIteratorScope() == IteratorScope.minc)
+ iterEnv = new TabletIteratorEnvironment(IteratorScope.minc, acuTableConf);
+ else
+ throw new IllegalArgumentException();
+
+ SortedKeyValueIterator<Key,Value> itr = iterEnv.getTopLevelIterator(IteratorUtil.loadIterators(env.getIteratorScope(), cfsi, extent, acuTableConf,
+ iterators, iterEnv));
+
+ itr.seek(extent.toDataRange(), columnFamilies, inclusive);
+
+ if (!inclusive) {
+ mfw.startDefaultLocalityGroup();
+ } else {
+ mfw.startNewLocalityGroup(lgName, columnFamilies);
+ }
+
+ Span write = Trace.start("write");
+ try {
+ while (itr.hasTop() && env.isCompactionEnabled()) {
+ mfw.append(itr.getTopKey(), itr.getTopValue());
+ itr.next();
+ entriesCompacted++;
+
+ if (entriesCompacted % 1024 == 0) {
+ // Periodically update stats, do not want to do this too often since its volatile
+ entriesWritten.addAndGet(1024);
+ }
+ }
+
+ if (itr.hasTop() && !env.isCompactionEnabled()) {
+ // cancel major compaction operation
+ try {
+ try {
+ mfw.close();
+ } catch (IOException e) {
+ log.error(e, e);
+ }
+ fs.deleteRecursively(outputFile.path());
+ } catch (Exception e) {
+ log.warn("Failed to delete Canceled compaction output file " + outputFile, e);
+ }
+ throw new CompactionCanceledException();
+ }
+
+ } finally {
+ CompactionStats lgMajcStats = new CompactionStats(citr.getCount(), entriesCompacted);
+ majCStats.add(lgMajcStats);
+ write.stop();
+ }
+
+ } finally {
+ // close sequence files opened
+ for (FileSKVIterator reader : readers) {
+ try {
+ reader.close();
+ } catch (Throwable e) {
+ log.warn("Failed to close map file", e);
+ }
+ }
+ span.stop();
+ }
+ }
+
+}