Why does BuffredReader get slow after reading a couple of Gigabytes?

gistfile1.java

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;

/**
 * 
 * @author Amirhossein Kiani (amir@binatechnologies.com) Created on Mar 29, 2012
 */
public class TestWriter {

  public static void main(String[] args) throws IOException {
    BufferedReader reader = new BufferedReader(new FileReader(args[0]));
    BufferedWriter writer = new BufferedWriter(new FileWriter(args[1]));

    long packetNumber = 1;
    long start;
    long packetSize = 24;
    long readerTime = 0;
    long writerTime = 0;
    long flushTime;
    Runtime runtime = Runtime.getRuntime();
    long aggregateFlushTimer = 0;
    int mb = 1024 * 1024;

    while (reader.ready() && !Thread.interrupted()) {
      packetNumber++;
      start = System.nanoTime();
      String line;
      int lineNumber = 1;
      long startWriteLine;
      long startReadLine;

      while (lineNumber <= packetSize && reader.ready() && !Thread.interrupted()) {
        startReadLine = System.nanoTime();
        line = reader.readLine();
        readerTime += (System.nanoTime() - startReadLine);


        lineNumber++;
        startWriteLine = System.nanoTime();
        writer.write(line);
        writer.newLine();
        writerTime += (System.nanoTime() - startWriteLine);

        line = null;
      }

      start = System.nanoTime();
      writer.flush();
      flushTime = (System.nanoTime() - start);
      aggregateFlushTimer += flushTime;

      if (packetNumber % 10000 == 0) {
        System.out.println("Average buffer flushing time per packet:"
            + (aggregateFlushTimer / (packetNumber * packetSize)) + " ns");
        System.out.println("Average reading from input file time per packet:"
            + (readerTime / (packetNumber * packetSize)) + " ns");
        System.out.println("Average writing to socket time per packet:"
            + (writerTime / (packetNumber * packetSize)) + " ns");
        System.out.println("Used Memory:" + (runtime.totalMemory() - runtime.freeMemory()) / mb);
      }

    }
  }
}