Exemple #1
0
  /**
   * Check whether the contents of src and dst are the same.
   *
   * <p>Return false if dstpath does not exist
   *
   * <p>If the files have different sizes, return false.
   *
   * <p>If the files have the same sizes, the file checksums will be compared.
   *
   * <p>When file checksum is not supported in any of file systems, two files are considered as the
   * same if they have the same size.
   */
  private static boolean sameFile(
      FileSystem srcfs, FileStatus srcstatus, FileSystem dstfs, Path dstpath) throws IOException {
    FileStatus dststatus;
    try {
      dststatus = dstfs.getFileStatus(dstpath);
    } catch (FileNotFoundException fnfe) {
      return false;
    }

    // same length?
    if (srcstatus.getLen() != dststatus.getLen()) {
      return false;
    }

    // compare checksums
    try {
      final FileChecksum srccs = srcfs.getFileChecksum(srcstatus.getPath());
      final FileChecksum dstcs = dstfs.getFileChecksum(dststatus.getPath());
      // return true if checksum is not supported
      // (i.e. some of the checksums is null)
      return srccs == null || dstcs == null || srccs.equals(dstcs);
    } catch (FileNotFoundException fnfe) {
      return false;
    }
  }
Exemple #2
0
 private static void addFolder(FileSystem fs, Path p, JsonArray succeeded, JsonArray failed) {
   try {
     if (fs == null) return;
     for (FileStatus file : fs.listStatus(p)) {
       Path pfs = file.getPath();
       if (file.isDir()) {
         addFolder(fs, pfs, succeeded, failed);
       } else {
         Key k = Key.make(pfs.toString());
         long size = file.getLen();
         Value val = null;
         if (pfs.getName().endsWith(Extensions.JSON)) {
           JsonParser parser = new JsonParser();
           JsonObject json = parser.parse(new InputStreamReader(fs.open(pfs))).getAsJsonObject();
           JsonElement v = json.get(Constants.VERSION);
           if (v == null) throw new RuntimeException("Missing version");
           JsonElement type = json.get(Constants.TYPE);
           if (type == null) throw new RuntimeException("Missing type");
           Class c = Class.forName(type.getAsString());
           OldModel model = (OldModel) c.newInstance();
           model.fromJson(json);
         } else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
           FSDataInputStream s = fs.open(pfs);
           int sz = (int) Math.min(1L << 20, size); // Read up to the 1st meg
           byte[] mem = MemoryManager.malloc1(sz);
           s.readFully(mem);
           // Convert to a ValueArray (hope it fits in 1Meg!)
           ValueArray ary = new ValueArray(k, 0).read(new AutoBuffer(mem));
           val = new Value(k, ary, Value.HDFS);
         } else if (size >= 2 * ValueArray.CHUNK_SZ) {
           val =
               new Value(
                   k,
                   new ValueArray(k, size),
                   Value.HDFS); // ValueArray byte wrapper over a large file
         } else {
           val = new Value(k, (int) size, Value.HDFS); // Plain Value
           val.setdsk();
         }
         DKV.put(k, val);
         Log.info("PersistHdfs: DKV.put(" + k + ")");
         JsonObject o = new JsonObject();
         o.addProperty(Constants.KEY, k.toString());
         o.addProperty(Constants.FILE, pfs.toString());
         o.addProperty(Constants.VALUE_SIZE, file.getLen());
         succeeded.add(o);
       }
     }
   } catch (Exception e) {
     Log.err(e);
     JsonObject o = new JsonObject();
     o.addProperty(Constants.FILE, p.toString());
     o.addProperty(Constants.ERROR, e.getMessage());
     failed.add(o);
   }
 }
Exemple #3
0
  private static void addFolder2(
      FileSystem fs, Path p, ArrayList<String> keys, ArrayList<String> failed) {
    try {
      if (fs == null) return;

      Futures futures = new Futures();
      for (FileStatus file : fs.listStatus(p)) {
        Path pfs = file.getPath();
        if (file.isDir()) {
          addFolder2(fs, pfs, keys, failed);
        } else {
          long size = file.getLen();
          Key res;
          if (pfs.getName().endsWith(Extensions.JSON)) {
            throw H2O.unimpl();
          } else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
            throw H2O.unimpl();
          } else {
            Key k = null;
            keys.add((k = HdfsFileVec.make(file, futures)).toString());
            Log.info("PersistHdfs: DKV.put(" + k + ")");
          }
        }
      }
    } catch (Exception e) {
      Log.err(e);
      failed.add(p.toString());
    }
  }
 /** Added for back compatibility. */
 public static Path getLocalCache(
     URI cache,
     Configuration conf,
     Path subdir,
     FileStatus fileStatus,
     boolean isArchive,
     long confFileStamp,
     Path currentWorkDir,
     boolean honorSymLinkConf,
     MRAsyncDiskService asyncDiskService,
     LocalDirAllocator lDirAllocator)
     throws IOException {
   return getLocalCache(
       cache,
       conf,
       subdir,
       fileStatus,
       isArchive,
       confFileStamp,
       fileStatus.getLen(),
       currentWorkDir,
       honorSymLinkConf,
       asyncDiskService,
       lDirAllocator);
 }
  /**
   * Generate the list of files and make them into FileSplits. This needs to be copied to insert a
   * filter on acceptable data
   */
  @Override
  public List<InputSplit> getSplits(JobContext job) throws IOException {
    long minSize = Math.max(getFormatMinSplitSize(), getMinSplitSize(job));
    long maxSize = getMaxSplitSize(job);
    long desiredMappers =
        job.getConfiguration().getLong("org.systemsbiology.jxtandem.DesiredXMLInputMappers", 0);

    // generate splits
    List<InputSplit> splits = new ArrayList<InputSplit>();
    List<FileStatus> fileStatuses = listStatus(job);
    boolean forceNumberMappers = fileStatuses.size() == 1;
    for (FileStatus file : fileStatuses) {
      Path path = file.getPath();
      if (!isPathAcceptable(path)) // filter acceptable data
      continue;
      FileSystem fs = path.getFileSystem(job.getConfiguration());
      long length = file.getLen();
      BlockLocation[] blkLocations = fs.getFileBlockLocations(file, 0, length);
      if ((length != 0) && isSplitable(job, path)) {
        long blockSize = file.getBlockSize();
        // use desired mappers to force more splits
        if (forceNumberMappers && desiredMappers > 0)
          maxSize = Math.min(maxSize, (length / desiredMappers));

        long splitSize = computeSplitSize(blockSize, minSize, maxSize);

        long bytesRemaining = length;
        while (withinSlop(splitSize, bytesRemaining)) {
          int blkIndex = getBlockIndex(blkLocations, length - bytesRemaining);
          splits.add(
              new FileSplit(
                  path, length - bytesRemaining, splitSize, blkLocations[blkIndex].getHosts()));
          bytesRemaining -= splitSize;
        }

        if (bytesRemaining != 0) {
          splits.add(
              new FileSplit(
                  path,
                  length - bytesRemaining,
                  bytesRemaining,
                  blkLocations[blkLocations.length - 1].getHosts()));
        }
      } else if (length != 0) {
        splits.add(new FileSplit(path, 0, length, blkLocations[0].getHosts()));
      } else {
        // Create empty hosts array for zero length files
        splits.add(new FileSplit(path, 0, length, new String[0]));
      }
    }
    System.out.println("Total # of splits: " + splits.size());
    //     LOG.debug("Total # of splits: " + splits.size());
    return splits;
  }
Exemple #6
0
    /**
     * Produce splits such that each is no greater than the quotient of the total size and the
     * number of splits requested.
     *
     * @param job The handle to the JobConf object
     * @param numSplits Number of splits requested
     */
    public InputSplit[] getSplits(JobConf job, int numSplits) throws IOException {
      int cnfiles = job.getInt(SRC_COUNT_LABEL, -1);
      long cbsize = job.getLong(TOTAL_SIZE_LABEL, -1);
      String srcfilelist = job.get(SRC_LIST_LABEL, "");
      if (cnfiles < 0 || cbsize < 0 || "".equals(srcfilelist)) {
        throw new RuntimeException(
            "Invalid metadata: #files("
                + cnfiles
                + ") total_size("
                + cbsize
                + ") listuri("
                + srcfilelist
                + ")");
      }
      Path src = new Path(srcfilelist);
      FileSystem fs = src.getFileSystem(job);
      FileStatus srcst = fs.getFileStatus(src);

      ArrayList<FileSplit> splits = new ArrayList<FileSplit>(numSplits);
      LongWritable key = new LongWritable();
      FilePair value = new FilePair();
      final long targetsize = cbsize / numSplits;
      long pos = 0L;
      long last = 0L;
      long acc = 0L;
      long cbrem = srcst.getLen();
      SequenceFile.Reader sl = null;
      try {
        sl = new SequenceFile.Reader(fs, src, job);
        for (; sl.next(key, value); last = sl.getPosition()) {
          // if adding this split would put this split past the target size,
          // cut the last split and put this next file in the next split.
          if (acc + key.get() > targetsize && acc != 0) {
            long splitsize = last - pos;
            splits.add(new FileSplit(src, pos, splitsize, (String[]) null));
            cbrem -= splitsize;
            pos = last;
            acc = 0L;
          }
          acc += key.get();
        }
      } finally {
        checkAndClose(sl);
      }
      if (cbrem != 0) {
        splits.add(new FileSplit(src, pos, cbrem, (String[]) null));
      }

      return splits.toArray(new FileSplit[splits.size()]);
    }
 /**
  * Get the locally cached file or archive; it could either be previously cached (and valid) or
  * copy it from the {@link FileSystem} now.
  *
  * @param cache the cache to be localized, this should be specified as new
  *     URI(hdfs://hostname:port/absolute_path_to_file#LINKNAME). If no schema or hostname:port is
  *     provided the file is assumed to be in the filesystem being used in the Configuration
  * @param conf The Confguration file which contains the filesystem
  * @param baseDir The base cache Dir where you wnat to localize the files/archives
  * @param fileStatus The file status on the dfs.
  * @param isArchive if the cache is an archive or a file. In case it is an archive with a .zip or
  *     .jar or .tar or .tgz or .tar.gz extension it will be unzipped/unjarred/untarred
  *     automatically and the directory where the archive is unzipped/unjarred/untarred is returned
  *     as the Path. In case of a file, the path to the file is returned
  * @param confFileStamp this is the hdfs file modification timestamp to verify that the file to be
  *     cached hasn't changed since the job started
  * @param currentWorkDir this is the directory where you would want to create symlinks for the
  *     locally cached files/archives
  * @return the path to directory where the archives are unjarred in case of archives, the path to
  *     the file where the file is copied locally
  * @throws IOException
  */
 public static Path getLocalCache(
     URI cache,
     Configuration conf,
     Path baseDir,
     FileStatus fileStatus,
     boolean isArchive,
     long confFileStamp,
     Path currentWorkDir,
     MRAsyncDiskService asyncDiskService)
     throws IOException {
   return getLocalCache(
       cache,
       conf,
       baseDir,
       fileStatus,
       isArchive,
       confFileStamp,
       fileStatus.getLen(),
       currentWorkDir,
       true,
       asyncDiskService,
       new LocalDirAllocator("mapred.local.dir"));
 }
Exemple #8
0
  /**
   * Initialize DFSCopyFileMapper specific job-configuration.
   *
   * @param conf : The dfs/mapred configuration.
   * @param jobConf : The handle to the jobConf object to be initialized.
   * @param args Arguments
   */
  private static void setup(Configuration conf, JobConf jobConf, final Arguments args)
      throws IOException {
    jobConf.set(DST_DIR_LABEL, args.dst.toUri().toString());

    // set boolean values
    final boolean update = args.flags.contains(Options.UPDATE);
    final boolean overwrite = !update && args.flags.contains(Options.OVERWRITE);
    jobConf.setBoolean(Options.UPDATE.propertyname, update);
    jobConf.setBoolean(Options.OVERWRITE.propertyname, overwrite);
    jobConf.setBoolean(
        Options.IGNORE_READ_FAILURES.propertyname,
        args.flags.contains(Options.IGNORE_READ_FAILURES));
    jobConf.setBoolean(
        Options.PRESERVE_STATUS.propertyname, args.flags.contains(Options.PRESERVE_STATUS));

    final String randomId = getRandomId();
    JobClient jClient = new JobClient(jobConf);
    Path jobDirectory = new Path(jClient.getSystemDir(), NAME + "_" + randomId);
    jobConf.set(JOB_DIR_LABEL, jobDirectory.toString());

    FileSystem dstfs = args.dst.getFileSystem(conf);
    boolean dstExists = dstfs.exists(args.dst);
    boolean dstIsDir = false;
    if (dstExists) {
      dstIsDir = dstfs.getFileStatus(args.dst).isDir();
    }

    // default logPath
    Path logPath = args.log;
    if (logPath == null) {
      String filename = "_distcp_logs_" + randomId;
      if (!dstExists || !dstIsDir) {
        Path parent = args.dst.getParent();
        if (!dstfs.exists(parent)) {
          dstfs.mkdirs(parent);
        }
        logPath = new Path(parent, filename);
      } else {
        logPath = new Path(args.dst, filename);
      }
    }
    FileOutputFormat.setOutputPath(jobConf, logPath);

    // create src list, dst list
    FileSystem jobfs = jobDirectory.getFileSystem(jobConf);

    Path srcfilelist = new Path(jobDirectory, "_distcp_src_files");
    jobConf.set(SRC_LIST_LABEL, srcfilelist.toString());
    SequenceFile.Writer src_writer =
        SequenceFile.createWriter(
            jobfs,
            jobConf,
            srcfilelist,
            LongWritable.class,
            FilePair.class,
            SequenceFile.CompressionType.NONE);

    Path dstfilelist = new Path(jobDirectory, "_distcp_dst_files");
    SequenceFile.Writer dst_writer =
        SequenceFile.createWriter(
            jobfs, jobConf, dstfilelist, Text.class, Text.class, SequenceFile.CompressionType.NONE);

    Path dstdirlist = new Path(jobDirectory, "_distcp_dst_dirs");
    jobConf.set(DST_DIR_LIST_LABEL, dstdirlist.toString());
    SequenceFile.Writer dir_writer =
        SequenceFile.createWriter(
            jobfs,
            jobConf,
            dstdirlist,
            Text.class,
            FilePair.class,
            SequenceFile.CompressionType.NONE);

    // handle the case where the destination directory doesn't exist
    // and we've only a single src directory OR we're updating/overwriting
    // the contents of the destination directory.
    final boolean special = (args.srcs.size() == 1 && !dstExists) || update || overwrite;
    int srcCount = 0, cnsyncf = 0, dirsyn = 0;
    long fileCount = 0L, byteCount = 0L, cbsyncs = 0L;
    try {
      for (Iterator<Path> srcItr = args.srcs.iterator(); srcItr.hasNext(); ) {
        final Path src = srcItr.next();
        FileSystem srcfs = src.getFileSystem(conf);
        FileStatus srcfilestat = srcfs.getFileStatus(src);
        Path root = special && srcfilestat.isDir() ? src : src.getParent();
        if (srcfilestat.isDir()) {
          ++srcCount;
        }

        Stack<FileStatus> pathstack = new Stack<FileStatus>();
        for (pathstack.push(srcfilestat); !pathstack.empty(); ) {
          FileStatus cur = pathstack.pop();
          FileStatus[] children = srcfs.listStatus(cur.getPath());
          for (int i = 0; i < children.length; i++) {
            boolean skipfile = false;
            final FileStatus child = children[i];
            final String dst = makeRelative(root, child.getPath());
            ++srcCount;

            if (child.isDir()) {
              pathstack.push(child);
            } else {
              // skip file if the src and the dst files are the same.
              skipfile = update && sameFile(srcfs, child, dstfs, new Path(args.dst, dst));
              // skip file if it exceed file limit or size limit
              skipfile |=
                  fileCount == args.filelimit || byteCount + child.getLen() > args.sizelimit;

              if (!skipfile) {
                ++fileCount;
                byteCount += child.getLen();

                if (LOG.isTraceEnabled()) {
                  LOG.trace("adding file " + child.getPath());
                }

                ++cnsyncf;
                cbsyncs += child.getLen();
                if (cnsyncf > SYNC_FILE_MAX || cbsyncs > BYTES_PER_MAP) {
                  src_writer.sync();
                  dst_writer.sync();
                  cnsyncf = 0;
                  cbsyncs = 0L;
                }
              }
            }

            if (!skipfile) {
              src_writer.append(
                  new LongWritable(child.isDir() ? 0 : child.getLen()), new FilePair(child, dst));
            }

            dst_writer.append(new Text(dst), new Text(child.getPath().toString()));
          }

          if (cur.isDir()) {
            String dst = makeRelative(root, cur.getPath());
            dir_writer.append(new Text(dst), new FilePair(cur, dst));
            if (++dirsyn > SYNC_FILE_MAX) {
              dirsyn = 0;
              dir_writer.sync();
            }
          }
        }
      }
    } finally {
      checkAndClose(src_writer);
      checkAndClose(dst_writer);
      checkAndClose(dir_writer);
    }

    FileStatus dststatus = null;
    try {
      dststatus = dstfs.getFileStatus(args.dst);
    } catch (FileNotFoundException fnfe) {
      LOG.info(args.dst + " does not exist.");
    }

    // create dest path dir if copying > 1 file
    if (dststatus == null) {
      if (srcCount > 1 && !dstfs.mkdirs(args.dst)) {
        throw new IOException("Failed to create" + args.dst);
      }
    }

    final Path sorted = new Path(jobDirectory, "_distcp_sorted");
    checkDuplication(jobfs, dstfilelist, sorted, conf);

    if (dststatus != null && args.flags.contains(Options.DELETE)) {
      deleteNonexisting(dstfs, dststatus, sorted, jobfs, jobDirectory, jobConf, conf);
    }

    Path tmpDir =
        new Path(
            (dstExists && !dstIsDir) || (!dstExists && srcCount == 1)
                ? args.dst.getParent()
                : args.dst,
            "_distcp_tmp_" + randomId);
    jobConf.set(TMP_DIR_LABEL, tmpDir.toUri().toString());
    LOG.info("srcCount=" + srcCount);
    jobConf.setInt(SRC_COUNT_LABEL, srcCount);
    jobConf.setLong(TOTAL_SIZE_LABEL, byteCount);
    setMapCount(byteCount, jobConf);
  }
Exemple #9
0
    /**
     * Copy a file to a destination.
     *
     * @param srcstat src path and metadata
     * @param dstpath dst path
     * @param reporter
     */
    private void copy(
        FileStatus srcstat,
        Path relativedst,
        OutputCollector<WritableComparable<?>, Text> outc,
        Reporter reporter)
        throws IOException {
      Path absdst = new Path(destPath, relativedst);
      int totfiles = job.getInt(SRC_COUNT_LABEL, -1);
      assert totfiles >= 0 : "Invalid file count " + totfiles;

      // if a directory, ensure created even if empty
      if (srcstat.isDir()) {
        if (destFileSys.exists(absdst)) {
          if (!destFileSys.getFileStatus(absdst).isDir()) {
            throw new IOException("Failed to mkdirs: " + absdst + " is a file.");
          }
        } else if (!destFileSys.mkdirs(absdst)) {
          throw new IOException("Failed to mkdirs " + absdst);
        }
        // TODO: when modification times can be set, directories should be
        // emitted to reducers so they might be preserved. Also, mkdirs does
        // not currently return an error when the directory already exists;
        // if this changes, all directory work might as well be done in reduce
        return;
      }

      if (destFileSys.exists(absdst) && !overwrite && !needsUpdate(srcstat, destFileSys, absdst)) {
        outc.collect(null, new Text("SKIP: " + srcstat.getPath()));
        ++skipcount;
        reporter.incrCounter(Counter.SKIP, 1);
        updateStatus(reporter);
        return;
      }

      Path tmpfile = new Path(job.get(TMP_DIR_LABEL), relativedst);
      long cbcopied = 0L;
      FSDataInputStream in = null;
      FSDataOutputStream out = null;
      try {
        // open src file
        try {
          in = srcstat.getPath().getFileSystem(job).open(srcstat.getPath());
        } catch (IOException e) {
          LOG.error("Failed to open src file " + srcstat.getPath() + ", ignore and return");
          in = null;
          return;
        }
        reporter.incrCounter(Counter.BYTESEXPECTED, srcstat.getLen());
        // open tmp file
        out = create(tmpfile, reporter, srcstat);
        // copy file
        for (int cbread; (cbread = in.read(buffer)) >= 0; ) {
          out.write(buffer, 0, cbread);
          cbcopied += cbread;
          reporter.setStatus(
              String.format("%.2f ", cbcopied * 100.0 / srcstat.getLen())
                  + absdst
                  + " [ "
                  + StringUtils.humanReadableInt(cbcopied)
                  + " / "
                  + StringUtils.humanReadableInt(srcstat.getLen())
                  + " ]");
        }
      } finally {
        checkAndClose(in);
        checkAndClose(out);
      }

      if (cbcopied != srcstat.getLen()) {
        if (srcstat.getLen() == 0 && cbcopied > 0) {
          LOG.info("most likely see a WAL file corruption: " + srcstat.getPath());
        } else {
          throw new IOException(
              "File size not matched: copied "
                  + bytesString(cbcopied)
                  + " to tmpfile (="
                  + tmpfile
                  + ") but expected "
                  + bytesString(srcstat.getLen())
                  + " from "
                  + srcstat.getPath());
        }
      } else {
        if (totfiles == 1) {
          // Copying a single file; use dst path provided by user as destination
          // rather than destination directory, if a file
          Path dstparent = absdst.getParent();
          if (!(destFileSys.exists(dstparent) && destFileSys.getFileStatus(dstparent).isDir())) {
            absdst = dstparent;
          }
        }
        if (destFileSys.exists(absdst) && destFileSys.getFileStatus(absdst).isDir()) {
          throw new IOException(absdst + " is a directory");
        }
        if (!destFileSys.mkdirs(absdst.getParent())) {
          throw new IOException("Failed to craete parent dir: " + absdst.getParent());
        }
        rename(tmpfile, absdst);

        FileStatus dststat = destFileSys.getFileStatus(absdst);
        if (dststat.getLen() != srcstat.getLen()) {
          destFileSys.delete(absdst, false);
          throw new IOException(
              "File size not matched: copied "
                  + bytesString(dststat.getLen())
                  + " to dst (="
                  + absdst
                  + ") but expected "
                  + bytesString(srcstat.getLen())
                  + " from "
                  + srcstat.getPath());
        }
        updatePermissions(srcstat, dststat);
      }

      // report at least once for each file
      ++copycount;
      reporter.incrCounter(Counter.BYTESCOPIED, cbcopied);
      reporter.incrCounter(Counter.COPY, 1);
      updateStatus(reporter);
    }
  /**
   * Compare the checksums of the hdfs file as well as the local copied file.
   *
   * @author [email protected]
   * @date Fri Jan 27 06:06:00 2012
   */
  boolean compareChecksums(FileSystem fs, Path p, String sFsPath) {
    try {
      // get hdfs file info
      FileStatus stat = fs.getFileStatus(p);

      // get HDFS checksum
      FileChecksum ck = fs.getFileChecksum(p);
      String sCk, sCkShort;
      if (ck == null) {
        sCk = sCkShort = "<null>";
      } else {
        sCk = ck.toString();
        sCkShort = sCk.replaceAll("^.*:", "");
      }

      // System.out.println(p.toUri().getPath() + " len=" + stat.getLen()
      // + " " + stat.getOwner() + "/" + stat.getGroup()
      // + " checksum=" + sCk);

      // find the local file
      File fLocal = new File(sFsPath);
      if (!fLocal.exists()) {
        System.out.println("CHECKSUM-ERROR: file does not exist: " + sFsPath);
        return false;
      }
      if (!fLocal.isFile()) {
        System.out.println("CHECKSUM-ERROR: path is not a file: " + sFsPath);
        return false;
      }
      if (stat.getLen() != fLocal.length()) {
        System.out.println(
            "CHECKSUM-ERROR: length mismatch: "
                + sFsPath
                + " hdfslen="
                + stat.getLen()
                + " fslen="
                + fLocal.length());
        return false;
      }

      // get local fs checksum
      FileChecksum ckLocal = getLocalFileChecksum(sFsPath);
      if (ckLocal == null) {
        System.out.println("ERROR Failed to get checksum for local file " + sFsPath);
        return false;
      }

      // compare checksums as a string, after stripping the
      // algorithm name from the beginning
      String sCkLocal = ckLocal.toString();
      String sCkLocalShort = sCkLocal.replaceAll("^.*:", "");

      if (false == sCkShort.equals(sCkLocalShort)) {
        System.out.println(
            "CHECKSUM-ERROR: checksum mismatch: "
                + sFsPath
                + "\nhdfs = "
                + sCk
                + "\nlocal= "
                + sCkLocal);
        return false;
      }

      return true;
    } catch (IOException e) {
      System.out.println("CHECKSUM-ERROR: " + sFsPath + " exception " + e.toString());
    }

    return false;
  }
Exemple #11
0
  @Override
  public final void run() {
    try {

      // before preparing the job localize
      // all the archives
      TaskAttemptID taskid = t.getTaskID();
      LocalDirAllocator lDirAlloc = new LocalDirAllocator("mapred.local.dir");
      File jobCacheDir = null;
      if (conf.getJar() != null) {
        jobCacheDir = new File(new Path(conf.getJar()).getParent().toString());
      }
      File workDir =
          new File(
              lDirAlloc
                  .getLocalPathToRead(
                      TaskTracker.getJobCacheSubdir()
                          + Path.SEPARATOR
                          + t.getJobID()
                          + Path.SEPARATOR
                          + t.getTaskID()
                          + Path.SEPARATOR
                          + MRConstants.WORKDIR,
                      conf)
                  .toString());

      URI[] archives = DistributedCache.getCacheArchives(conf);
      URI[] files = DistributedCache.getCacheFiles(conf);
      FileStatus fileStatus;
      FileSystem fileSystem;
      Path localPath;
      String baseDir;

      if ((archives != null) || (files != null)) {
        if (archives != null) {
          String[] archivesTimestamps = DistributedCache.getArchiveTimestamps(conf);
          Path[] p = new Path[archives.length];
          for (int i = 0; i < archives.length; i++) {
            fileSystem = FileSystem.get(archives[i], conf);
            fileStatus = fileSystem.getFileStatus(new Path(archives[i].getPath()));
            String cacheId = DistributedCache.makeRelative(archives[i], conf);
            String cachePath = TaskTracker.getCacheSubdir() + Path.SEPARATOR + cacheId;
            if (lDirAlloc.ifExists(cachePath, conf)) {
              localPath = lDirAlloc.getLocalPathToRead(cachePath, conf);
            } else {
              localPath = lDirAlloc.getLocalPathForWrite(cachePath, fileStatus.getLen(), conf);
            }
            baseDir = localPath.toString().replace(cacheId, "");
            p[i] =
                DistributedCache.getLocalCache(
                    archives[i],
                    conf,
                    new Path(baseDir),
                    fileStatus,
                    true,
                    Long.parseLong(archivesTimestamps[i]),
                    new Path(workDir.getAbsolutePath()),
                    false);
          }
          DistributedCache.setLocalArchives(conf, stringifyPathArray(p));
        }
        if ((files != null)) {
          String[] fileTimestamps = DistributedCache.getFileTimestamps(conf);
          Path[] p = new Path[files.length];
          for (int i = 0; i < files.length; i++) {
            fileSystem = FileSystem.get(files[i], conf);
            fileStatus = fileSystem.getFileStatus(new Path(files[i].getPath()));
            String cacheId = DistributedCache.makeRelative(files[i], conf);
            String cachePath = TaskTracker.getCacheSubdir() + Path.SEPARATOR + cacheId;
            if (lDirAlloc.ifExists(cachePath, conf)) {
              localPath = lDirAlloc.getLocalPathToRead(cachePath, conf);
            } else {
              localPath = lDirAlloc.getLocalPathForWrite(cachePath, fileStatus.getLen(), conf);
            }
            baseDir = localPath.toString().replace(cacheId, "");
            p[i] =
                DistributedCache.getLocalCache(
                    files[i],
                    conf,
                    new Path(baseDir),
                    fileStatus,
                    false,
                    Long.parseLong(fileTimestamps[i]),
                    new Path(workDir.getAbsolutePath()),
                    false);
          }
          DistributedCache.setLocalFiles(conf, stringifyPathArray(p));
        }
        Path localTaskFile = new Path(t.getJobFile());
        FileSystem localFs = FileSystem.getLocal(conf);
        localFs.delete(localTaskFile, true);
        OutputStream out = localFs.create(localTaskFile);
        try {
          conf.writeXml(out);
        } finally {
          out.close();
        }
      }

      if (!prepare()) {
        return;
      }

      String sep = System.getProperty("path.separator");
      StringBuffer classPath = new StringBuffer();
      // start with same classpath as parent process
      classPath.append(System.getProperty("java.class.path"));
      classPath.append(sep);
      if (!workDir.mkdirs()) {
        if (!workDir.isDirectory()) {
          LOG.fatal("Mkdirs failed to create " + workDir.toString());
        }
      }

      String jar = conf.getJar();
      if (jar != null) {
        // if jar exists, it into workDir
        File[] libs = new File(jobCacheDir, "lib").listFiles();
        if (libs != null) {
          for (int i = 0; i < libs.length; i++) {
            classPath.append(sep); // add libs from jar to classpath
            classPath.append(libs[i]);
          }
        }
        classPath.append(sep);
        classPath.append(new File(jobCacheDir, "classes"));
        classPath.append(sep);
        classPath.append(jobCacheDir);
      }

      // include the user specified classpath

      // archive paths
      Path[] archiveClasspaths = DistributedCache.getArchiveClassPaths(conf);
      if (archiveClasspaths != null && archives != null) {
        Path[] localArchives = DistributedCache.getLocalCacheArchives(conf);
        if (localArchives != null) {
          for (int i = 0; i < archives.length; i++) {
            for (int j = 0; j < archiveClasspaths.length; j++) {
              if (archives[i].getPath().equals(archiveClasspaths[j].toString())) {
                classPath.append(sep);
                classPath.append(localArchives[i].toString());
              }
            }
          }
        }
      }
      // file paths
      Path[] fileClasspaths = DistributedCache.getFileClassPaths(conf);
      if (fileClasspaths != null && files != null) {
        Path[] localFiles = DistributedCache.getLocalCacheFiles(conf);
        if (localFiles != null) {
          for (int i = 0; i < files.length; i++) {
            for (int j = 0; j < fileClasspaths.length; j++) {
              if (files[i].getPath().equals(fileClasspaths[j].toString())) {
                classPath.append(sep);
                classPath.append(localFiles[i].toString());
              }
            }
          }
        }
      }

      classPath.append(sep);
      classPath.append(workDir);
      //  Build exec child jmv args.
      Vector<String> vargs = new Vector<String>(8);
      File jvm = // use same jvm as parent
          new File(new File(System.getProperty("java.home"), "bin"), "java");

      vargs.add(jvm.toString());

      // Add child (task) java-vm options.
      //
      // The following symbols if present in mapred.child.java.opts value are
      // replaced:
      // + @taskid@ is interpolated with value of TaskID.
      // Other occurrences of @ will not be altered.
      //
      // Example with multiple arguments and substitutions, showing
      // jvm GC logging, and start of a passwordless JVM JMX agent so can
      // connect with jconsole and the likes to watch child memory, threads
      // and get thread dumps.
      //
      //  <property>
      //    <name>mapred.child.java.opts</name>
      //    <value>-verbose:gc -Xloggc:/tmp/@[email protected] \
      //           -Dcom.sun.management.jmxremote.authenticate=false \
      //           -Dcom.sun.management.jmxremote.ssl=false \
      //    </value>
      //  </property>
      //
      String javaOpts = conf.get("mapred.child.java.opts", "-Xmx200m");
      javaOpts = javaOpts.replace("@taskid@", taskid.toString());
      String[] javaOptsSplit = javaOpts.split(" ");

      // Add java.library.path; necessary for loading native libraries.
      //
      // 1. To support native-hadoop library i.e. libhadoop.so, we add the
      //    parent processes' java.library.path to the child.
      // 2. We also add the 'cwd' of the task to it's java.library.path to help
      //    users distribute native libraries via the DistributedCache.
      // 3. The user can also specify extra paths to be added to the
      //    java.library.path via mapred.child.java.opts.
      //
      String libraryPath = System.getProperty("java.library.path");
      if (libraryPath == null) {
        libraryPath = workDir.getAbsolutePath();
      } else {
        libraryPath += sep + workDir;
      }
      boolean hasUserLDPath = false;
      for (int i = 0; i < javaOptsSplit.length; i++) {
        if (javaOptsSplit[i].startsWith("-Djava.library.path=")) {
          javaOptsSplit[i] += sep + libraryPath;
          hasUserLDPath = true;
          break;
        }
      }
      if (!hasUserLDPath) {
        vargs.add("-Djava.library.path=" + libraryPath);
      }
      for (int i = 0; i < javaOptsSplit.length; i++) {
        vargs.add(javaOptsSplit[i]);
      }

      // add java.io.tmpdir given by mapred.child.tmp
      String tmp = conf.get("mapred.child.tmp", "./tmp");
      Path tmpDir = new Path(tmp);

      // if temp directory path is not absolute
      // prepend it with workDir.
      if (!tmpDir.isAbsolute()) {
        tmpDir = new Path(workDir.toString(), tmp);
      }
      FileSystem localFs = FileSystem.getLocal(conf);
      if (!localFs.mkdirs(tmpDir) && !localFs.getFileStatus(tmpDir).isDir()) {
        throw new IOException("Mkdirs failed to create " + tmpDir.toString());
      }
      vargs.add("-Djava.io.tmpdir=" + tmpDir.toString());

      // Add classpath.
      vargs.add("-classpath");
      vargs.add(classPath.toString());

      // Setup the log4j prop
      long logSize = TaskLog.getTaskLogLength(conf);
      vargs.add(
          "-Dhadoop.log.dir=" + new File(System.getProperty("hadoop.log.dir")).getAbsolutePath());
      vargs.add("-Dhadoop.root.logger=INFO,TLA");
      vargs.add("-Dhadoop.tasklog.taskid=" + taskid);
      vargs.add("-Dhadoop.tasklog.totalLogFileSize=" + logSize);

      if (conf.getProfileEnabled()) {
        if (conf.getProfileTaskRange(t.isMapTask()).isIncluded(t.getPartition())) {
          File prof = TaskLog.getTaskLogFile(taskid, TaskLog.LogName.PROFILE);
          vargs.add(String.format(conf.getProfileParams(), prof.toString()));
        }
      }

      // Add main class and its arguments
      vargs.add(Child.class.getName()); // main of Child
      // pass umbilical address
      InetSocketAddress address = tracker.getTaskTrackerReportAddress();
      vargs.add(address.getAddress().getHostAddress());
      vargs.add(Integer.toString(address.getPort()));
      vargs.add(taskid.toString()); // pass task identifier

      String pidFile = null;
      if (tracker.isTaskMemoryManagerEnabled()) {
        pidFile =
            lDirAlloc
                .getLocalPathForWrite(
                    (TaskTracker.getPidFilesSubdir() + Path.SEPARATOR + taskid), this.conf)
                .toString();
      }

      // set memory limit using ulimit if feasible and necessary ...
      String[] ulimitCmd = Shell.getUlimitMemoryCommand(conf);
      List<String> setup = null;
      if (ulimitCmd != null) {
        setup = new ArrayList<String>();
        for (String arg : ulimitCmd) {
          setup.add(arg);
        }
      }

      // Set up the redirection of the task's stdout and stderr streams
      File stdout = TaskLog.getTaskLogFile(taskid, TaskLog.LogName.STDOUT);
      File stderr = TaskLog.getTaskLogFile(taskid, TaskLog.LogName.STDERR);
      stdout.getParentFile().mkdirs();
      tracker.getTaskTrackerInstrumentation().reportTaskLaunch(taskid, stdout, stderr);

      Map<String, String> env = new HashMap<String, String>();
      StringBuffer ldLibraryPath = new StringBuffer();
      ldLibraryPath.append(workDir.toString());
      String oldLdLibraryPath = null;
      oldLdLibraryPath = System.getenv("LD_LIBRARY_PATH");
      if (oldLdLibraryPath != null) {
        ldLibraryPath.append(sep);
        ldLibraryPath.append(oldLdLibraryPath);
      }
      env.put("LD_LIBRARY_PATH", ldLibraryPath.toString());
      jvmManager.launchJvm(
          this,
          jvmManager.constructJvmEnv(
              setup, vargs, stdout, stderr, logSize, workDir, env, pidFile, conf));
      synchronized (lock) {
        while (!done) {
          lock.wait();
        }
      }
      tracker.getTaskTrackerInstrumentation().reportTaskEnd(t.getTaskID());
      if (exitCodeSet) {
        if (!killed && exitCode != 0) {
          if (exitCode == 65) {
            tracker.getTaskTrackerInstrumentation().taskFailedPing(t.getTaskID());
          }
          throw new IOException("Task process exit with nonzero status of " + exitCode + ".");
        }
      }
    } catch (FSError e) {
      LOG.fatal("FSError", e);
      try {
        tracker.fsError(t.getTaskID(), e.getMessage());
      } catch (IOException ie) {
        LOG.fatal(t.getTaskID() + " reporting FSError", ie);
      }
    } catch (Throwable throwable) {
      LOG.warn(t.getTaskID() + " Child Error", throwable);
      ByteArrayOutputStream baos = new ByteArrayOutputStream();
      throwable.printStackTrace(new PrintStream(baos));
      try {
        tracker.reportDiagnosticInfo(t.getTaskID(), baos.toString());
      } catch (IOException e) {
        LOG.warn(t.getTaskID() + " Reporting Diagnostics", e);
      }
    } finally {
      try {
        URI[] archives = DistributedCache.getCacheArchives(conf);
        URI[] files = DistributedCache.getCacheFiles(conf);
        if (archives != null) {
          for (int i = 0; i < archives.length; i++) {
            DistributedCache.releaseCache(archives[i], conf);
          }
        }
        if (files != null) {
          for (int i = 0; i < files.length; i++) {
            DistributedCache.releaseCache(files[i], conf);
          }
        }
      } catch (IOException ie) {
        LOG.warn("Error releasing caches : Cache files might not have been cleaned up");
      }
      tracker.reportTaskFinished(t.getTaskID(), false);
      if (t.isMapTask()) {
        tracker.addFreeMapSlot();
      } else {
        tracker.addFreeReduceSlot();
      }
    }
  }