Runnable Jar Files slow compared to Eclipse

Question

I have found only a small number of Threats about this Problem, but nothing seems to solve it.

My code runs in Eclipse under 10 seconds. If I extract this Project into a runnable jar file it takes over 5-10 minutes.

What I do: I read two .txt files, combine them, sort them, separate them and save them. This is my code:

package de.***.timcooparser;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;

import javax.swing.JOptionPane;

import org.joda.time.DateTime;
import org.joda.time.DateTimeZone;

import com.google.code.externalsorting.ExternalSort;


public class TimCooParser {

  private static List<String> listCoordinates = new ArrayList<String>();
  private static List<String> listTimestamps = new ArrayList<String>();
  private static List<String> listTimeCoord = new ArrayList<String>();


  public static void main(String[ ] args) throws IOException {

    //Start Time
    long d1 = System.currentTimeMillis();

    //Create Path
      String path = new File("").getAbsolutePath();

    //Readfiles
    File fileTimeCoord = new File (path+"\\TimestampsCoordinates.txt");
    File fileTimeCoord2 = new File (path+"\\TimestampsCoordinates2.txt");
    File fileCoordinates = new File (path+"\\Coordinates.txt");
    File fileTimestamps = new File (path+"\\Timestamps.txt");

    try{


      if (fileTimeCoord.exists()){
        fileTimeCoord.delete();
      }
      fileCoordinates.createNewFile();

      //Read Coordinates an Timestamps and merge them
      InputStream is1 = new FileInputStream(fileTimestamps);
      InputStreamReader instrm1 = new InputStreamReader(is1);
      BufferedReader br1 = new BufferedReader(instrm1);

      InputStream is2 = new FileInputStream(fileCoordinates);
      InputStreamReader instrm2 = new InputStreamReader(is2);
      BufferedReader br2 = new BufferedReader(instrm2);

      String line = "", line2 = "";
      Integer i = 0;
      while ((line = br1.readLine()) != null){
        line2 = br2.readLine();
        String[] arrayTemp = line2.split(" ");
        listTimeCoord.add(line+","+arrayTemp[0] + "," + arrayTemp[1]);
        i++;

        if (i>=500){
          i=0;
          saveFiles(fileTimeCoord);
        }
      }
      br1.close();
      br2.close();

      //Sort File and delete old file
      ExternalSort.sort(fileTimeCoord, fileTimeCoord2);
      fileTimeCoord.delete();

      //Delete old files
      if (fileCoordinates.exists()){
        fileCoordinates.delete();
      }
      fileCoordinates.createNewFile();

      if (fileTimestamps.exists()){
        fileTimestamps.delete();
      }
      fileTimestamps.createNewFile();


      //Read TimeCoord and override Timestamps and Coordinates
      InputStream is3 = new FileInputStream(fileTimeCoord2);
      InputStreamReader instrm3 = new InputStreamReader(is3);
      BufferedReader br3 = new BufferedReader(instrm3);

      line = "";
      listCoordinates.clear();
      listTimestamps.clear();
      Integer ct = 0;
      while ((line = br3.readLine()) != null){
        String[] arrayTemp = line.split(",");
        listTimestamps.add(arrayTemp[0]);
        listCoordinates.add(arrayTemp[1] + " " + arrayTemp[2]);
        ct++;

        if (ct >= 500){
          saveFiles(fileTimestamps, fileCoordinates);
        }
      }
      br3.close();

      // Delete old Files
      fileTimeCoord2.delete();

      //get end Time
      long d2 = System.currentTimeMillis();

      //Get diff time
      long diff = d2 - d1;
      String diffTime = "Finished in " + ((diff / (60 * 60 * 1000)) % 24) + " hours " + ((diff / (60 * 1000)) % 60) + " minutes and "
          + ((diff / 1000) % 60) + " seconds";

      JOptionPane.showMessageDialog(null,  "Parser finished in: \n" + diffTime,"TimesCoord Parser", JOptionPane.INFORMATION_MESSAGE);
    }
    catch (FileNotFoundException e) {
      e.printStackTrace();
      JOptionPane.showMessageDialog(null,"Parser Error:\n" + e,"TimesCoord Parser", JOptionPane.CANCEL_OPTION);
    } 
    catch (IOException e) {
      e.printStackTrace();
      JOptionPane.showMessageDialog(null,"Parser Error:\n" + e,"TimesCoord Parser", JOptionPane.CANCEL_OPTION);
    }
  }

  private static void saveFiles(File fileTimestamps, File fileCoordinates) throws IOException {

    List<String> listCoordinates2 = new ArrayList<String>();
    List<String> listTimestamps2 = new ArrayList<String>();

    listCoordinates2.addAll(listCoordinates);
    listCoordinates.clear();

    listTimestamps2.addAll(listTimestamps);
    listTimestamps.clear();

    //Write to File
    BufferedWriter bw1 = new BufferedWriter(    new FileWriter(fileTimestamps, true));

    for (String string : listTimestamps2) {
      bw1.append(string + "\n");
    }
    bw1.close();

    //Write to File
    BufferedWriter bw2 = new BufferedWriter(    new FileWriter(fileCoordinates, true));

    for (String string : listCoordinates2) {
      bw2.append(string + "\n");
    }
    bw2.close();


  }

  private static void saveFiles(File fileTimeCoord) throws IOException {

    List<String> listTimeCoord2 = new ArrayList<String>();

    listTimeCoord2.addAll(listTimeCoord);
    listTimeCoord.clear();

    //Write to File
    BufferedWriter bw1 = new BufferedWriter(    new FileWriter(fileTimeCoord, true));

    for (String string : listTimeCoord2) {
      bw1.append(string + "\n");
    }
    bw1.close();        
  }



  public static String TimestampToDate(long stringDate)
  {
    DateTimeZone zone = DateTimeZone.forID("Europe/Berlin");
    DateTimeZone.setDefault(zone);
    DateTime actual = new DateTime(stringDate);
    String dateString = actual.toString("yyyy-MM-dd'T'HH:mm:ssZZ");
    return dateString;

  }
}

The eclipse and my PC do use the same JVM:

java version "1.8.0_20"     
Java(TM) SE Runtime Environment (build 1.8.0_20-b26)     
Java HotSpot(TM) Client VM (build 25.20-b23, mixed mode, sharing)

And here is my eclipse.ini:

-startup
plugins/org.eclipse.equinox.launcher_1.3.0.v20140415-2008.jar
--launcher.library
plugins/org.eclipse.equinox.launcher.win32.win32.x86_1.1.200.v20140603-1326
-product
org.eclipse.epp.package.java.product
--launcher.defaultAction
openFile
--launcher.XXMaxPermSize
256M
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
--launcher.appendVmargs
-vmargs
-Dosgi.requiredJavaVersion=1.6
-Xms512m
-Xmx1024m

What can I do to solve this Problem?

PS: It is independent of the "externalsortinginjava.." library.

Answer 1

Try making sure that you use the same memory options that Eclipse does when launching the app.

Looks like the command line arguments should be -Xms512m -Xmx1024m

Answer 2

I have found the line which does need a lot of time.

if (ct >= 500){
   saveFiles(fileTimestamps, fileCoordinates);
}

I changed this to

   if (ct >= 1000000000){
      saveFiles(fileTimestamps, fileCoordinates);
      ct=0;
   }
}
br3.close();
saveFiles(fileTimestamps, fileCoordinates);

And the same above the changes (the code with i>500).

Now it takes in Eclipse under 1 Second and as jar File 3 Seconds.

But why the code is faster in Eclipse as as jar file, is not solved!