Ejemplo n.º 1
0
  /*
   * This method is called to wind down the simulation.
   */
  public void finish() {
    super.finish();

    System.out.println("Terminating the simulation");

    /*
     * write CSV and XML output from simulation
     */
    File csvDataFile =
        new File(resultFilePath + "/" + description + "/" + runFilePath + "/simOutputData.csv");
    System.out.println("Output written to " + csvDataFile);

    // File xmlDataFile = new File(resultFilePath + "/" + description + "/Results/" + runFilePath +
    // "/simOutputData.xml");

    PrintWriter dataOutput;

    try {
      dataOutput = new PrintWriter(csvDataFile);
      dataOutput.print(dataStore.compileTableToString());
      dataOutput.close();

      //	dataStore.compileXMLOutput(xmlDataFile);
    } catch (Exception e) {
      e.printStackTrace();
    }

    System.out.println("Run took " + (System.currentTimeMillis() - startTime) + " milliseconds");
  }
Ejemplo n.º 2
0
  /*
   * Constructor.
   * Takes a specified seed - derived from the MASON Mersenne Twister.
   *
   * Specifying the seed is important:
   * although java will seed experiments based on the internal clock,
   * when running batch experiments on a cluster it is possible that
   * two machines will start with the same seed. When gathering data
   * to form distributions representing experiments, it is critical
   * that we do not run simulations with the same seed, they skew the
   * distributions.
   */
  public CBSimulation(long seed, String[] args) {
    super(new MersenneTwisterFast(seed), new Schedule());
    cbsim = this;
    startTime = System.currentTimeMillis();

    // System.out.println("Invoking constructor for simulation object: " + cbsim);

    // open parameter files specified for reading
    try {
      cbsim.xmlFileLocation = args[0];
      cbsim.runFilePath = args[1];
    } catch (Exception e) {
      System.out.println(
          "Parameter file not specified - default values will be used for this input...");
      cbsim.xmlFileLocation = defaultXmlFileLocation;
      cbsim.runFilePath = defaultRunFilePath;
    }

    // set up the ArrayLists that will store information about the cistromes used in the simulation
    names = new ArrayList<String>();
    sources = new ArrayList<String>();
    branchingRates = new ArrayList<Integer>();
    numsInitialReds = new ArrayList<Integer>();

    int position = xmlFileLocation.lastIndexOf("/");
    paramCopyName = xmlFileLocation.substring(position + 1);
  }
Ejemplo n.º 3
0
  public static void main(String[] args) {

    // System.out.println("In main() on CBSimulation class");

    // we're not using the GUI if we enter via this method...
    useGUI = false;

    /*
     * this starts the run off
     *
     * the parameters for the simulation will ultimately be read from the parameter file
     */
    try {
      String[] tokens = args[1].split("/");
      batchSize = Long.parseLong(tokens[0]);
      batchNumber = Long.parseLong(tokens[1]);
      jobNumber = Long.parseLong(tokens[2]);
    } catch (Exception e) {
      batchSize = defaultBatchSize;
      batchNumber = defaultBatchNumber;
      jobNumber = defaultJobNumber;
    }

    // System.out.println("Batch size is " + batchSize);
    // System.out.println("Maximum batch size is " + maxBatchSize);
    // System.out.println("Batch number is " + batchNumber);
    // System.out.println("Maximum batch number is " + maxBatchNumber);
    // System.out.println("Job number is " + jobNumber);

    seed = (batchSize * maxBatchSize * 10000000);
    seed += (batchNumber * maxBatchNumber * 10000);
    seed += jobNumber;

    // System.out.println("Random number seed used " + seed);
    CBSimulation cbsim = new CBSimulation(seed, args);

    cbsim.start();

    long steps;
    double time;

    do {

      if (!cbsim.schedule.step(cbsim)) // performs the step, and if return is false, stops looping.
      break;

      steps = cbsim.schedule.getSteps(); // How many steps have been performed?
      time = cbsim.schedule.getTime(); // retrieve the current time in the simulation.

      // System.out.println(cbsim + " currently at step: " + steps);

      final long timeNow = System.currentTimeMillis();

      if (timeNow - startTime >= (timeOut * 3600000)) break;

    } while (steps <= (simulationSteps + 4)); // stopping condition.

    cbsim.finish();
  }
Ejemplo n.º 4
0
public class CBSimulation extends SimState {

  public static CBSimulation
      cbsim; // static so that other objects can get hold of key items such as the schedule.

  public static DataStore dataStore;

  // private boolean instantiateCell = false;

  // where to look for the parameters if we don't specify a location
  // e.g. if we run via the Eclipse GUI...
  public String defaultXmlFileLocation = "cbsim_parameters_default.xml";
  public String xmlFileLocation;
  public String paramCopyName;

  public String defaultRunFilePath = "1";
  public String runFilePath;

  public String resultFilePath;
  public String description;

  public static long batchSize;
  public static long defaultBatchSize = 1;
  public static long batchNumber;
  public static long defaultBatchNumber = 1;
  public static long jobNumber;
  public static long defaultJobNumber = 1;

  public static long maxBatchSize = 1000;
  public static long maxBatchNumber = 20;

  /* if a simulation run takes longer than timeout seconds to complete,
   * then we halt the simulation and throw and exception.
   */
  private static int timeOut = Integer.MAX_VALUE; // by default there is no timeout. 								
  private static long startTime = System.currentTimeMillis();
  private static int simulationSteps = 0;
  private static long seed = 0;
  private static int initialReds = 0;
  private static int branchingRate;
  private static String name;
  private static String source;

  // ArrayList<String> moleculeNames = new ArrayList<String>();

  /*
   * the CBSimulation class will actually oversee the running of the simulation
   *
   * it needs to:
   * set up the initial conditions
   * read the simulation parameter file
   * instantiate a Cell which 'contains' the system
   *
   */

  // create a Cell object to house the system
  // this field is static since we assume that we must have only one cell in the simulation...
  // it is private because we don't want anything else to interfere with it...
  // the Cell is considered to be pluripotent - we implicitly assume that pluripotency
  // is a property of individual cells rather than a population level property
  private static Cell cell;

  // are we using the GUI or not?
  // assume yes, change to no if we need to
  private static boolean useGUI = false;

  // ArrayLists to store details of the cistromes in use that are
  // read from the simulation parameter file rather than the cistrome file...
  ArrayList<String> names;
  ArrayList<String> sources;
  ArrayList<Integer> branchingRates;
  ArrayList<Integer> numsInitialReds;

  /*
   * Constructor.
   * Takes a specified seed - derived from the MASON Mersenne Twister.
   *
   * Specifying the seed is important:
   * although java will seed experiments based on the internal clock,
   * when running batch experiments on a cluster it is possible that
   * two machines will start with the same seed. When gathering data
   * to form distributions representing experiments, it is critical
   * that we do not run simulations with the same seed, they skew the
   * distributions.
   */
  public CBSimulation(long seed, String[] args) {
    super(new MersenneTwisterFast(seed), new Schedule());
    cbsim = this;
    startTime = System.currentTimeMillis();

    // System.out.println("Invoking constructor for simulation object: " + cbsim);

    // open parameter files specified for reading
    try {
      cbsim.xmlFileLocation = args[0];
      cbsim.runFilePath = args[1];
    } catch (Exception e) {
      System.out.println(
          "Parameter file not specified - default values will be used for this input...");
      cbsim.xmlFileLocation = defaultXmlFileLocation;
      cbsim.runFilePath = defaultRunFilePath;
    }

    // set up the ArrayLists that will store information about the cistromes used in the simulation
    names = new ArrayList<String>();
    sources = new ArrayList<String>();
    branchingRates = new ArrayList<Integer>();
    numsInitialReds = new ArrayList<Integer>();

    int position = xmlFileLocation.lastIndexOf("/");
    paramCopyName = xmlFileLocation.substring(position + 1);
  }

  public static void main(String[] args) {

    // System.out.println("In main() on CBSimulation class");

    // we're not using the GUI if we enter via this method...
    useGUI = false;

    /*
     * this starts the run off
     *
     * the parameters for the simulation will ultimately be read from the parameter file
     */
    try {
      String[] tokens = args[1].split("/");
      batchSize = Long.parseLong(tokens[0]);
      batchNumber = Long.parseLong(tokens[1]);
      jobNumber = Long.parseLong(tokens[2]);
    } catch (Exception e) {
      batchSize = defaultBatchSize;
      batchNumber = defaultBatchNumber;
      jobNumber = defaultJobNumber;
    }

    // System.out.println("Batch size is " + batchSize);
    // System.out.println("Maximum batch size is " + maxBatchSize);
    // System.out.println("Batch number is " + batchNumber);
    // System.out.println("Maximum batch number is " + maxBatchNumber);
    // System.out.println("Job number is " + jobNumber);

    seed = (batchSize * maxBatchSize * 10000000);
    seed += (batchNumber * maxBatchNumber * 10000);
    seed += jobNumber;

    // System.out.println("Random number seed used " + seed);
    CBSimulation cbsim = new CBSimulation(seed, args);

    cbsim.start();

    long steps;
    double time;

    do {

      if (!cbsim.schedule.step(cbsim)) // performs the step, and if return is false, stops looping.
      break;

      steps = cbsim.schedule.getSteps(); // How many steps have been performed?
      time = cbsim.schedule.getTime(); // retrieve the current time in the simulation.

      // System.out.println(cbsim + " currently at step: " + steps);

      final long timeNow = System.currentTimeMillis();

      if (timeNow - startTime >= (timeOut * 3600000)) break;

    } while (steps <= (simulationSteps + 4)); // stopping condition.

    cbsim.finish();
  }

  /**
   * This method is called to start the simulation. the run parameters are copied to the results
   * output directory. The run output file is created ready for writing.
   */
  public void start() {
    super.start(); // call supertype's start method.

    // System.out.println("In main on CBSimulation class");

    // need to read the parameter file
    readParameters(true);

    // And I want to write the random number seed used for this run - for record keeping

    PrintWriter dataOutput;

    new File(resultFilePath + "/" + description + "/" + runFilePath).mkdirs();
    File runSeedFile =
        new File(resultFilePath + "/" + description + "/" + runFilePath + "/simRunSeed");
    System.out.println("Creating output file " + runSeedFile.getName());

    String paramCopyFile =
        resultFilePath + "/" + description + "/" + runFilePath + "/" + paramCopyName;
    copyFile(xmlFileLocation, paramCopyFile);

    try {
      dataOutput = new PrintWriter(runSeedFile);
      dataOutput.print(seed);
      dataOutput.close();
    } catch (Exception e) {
      e.printStackTrace();
    }

    // I'll need to instantiate the data store here
    // I'll schedule it from the constructor...
    dataStore = new DataStore(this);
    // System.out.println("Created DataStore object " + dataStore);

  }

  /*
   * This method is called to wind down the simulation.
   */
  public void finish() {
    super.finish();

    System.out.println("Terminating the simulation");

    /*
     * write CSV and XML output from simulation
     */
    File csvDataFile =
        new File(resultFilePath + "/" + description + "/" + runFilePath + "/simOutputData.csv");
    System.out.println("Output written to " + csvDataFile);

    // File xmlDataFile = new File(resultFilePath + "/" + description + "/Results/" + runFilePath +
    // "/simOutputData.xml");

    PrintWriter dataOutput;

    try {
      dataOutput = new PrintWriter(csvDataFile);
      dataOutput.print(dataStore.compileTableToString());
      dataOutput.close();

      //	dataStore.compileXMLOutput(xmlDataFile);
    } catch (Exception e) {
      e.printStackTrace();
    }

    System.out.println("Run took " + (System.currentTimeMillis() - startTime) + " milliseconds");
  }

  public long getStartTime() {
    return startTime;
  }

  /*
   * these methods provide us with a convenient way of stopping
   * an agent and removing it from the simulation schedule all in
   * one step  - this way we have no danger of 'zombie' agents carrying
   * on interacting after they have died...
   */
  public Stoppable stopper = null;

  public void setStopper(Stoppable stopper) {
    this.stopper = stopper;
  }

  public void stop() {
    stopper.stop();
  }

  public void addToSimulationScheduleRepeating(
      double time, int order, Steppable generator, double interval) {
    this.setStopper(cbsim.schedule.scheduleRepeating(time, order, generator, interval));
  }

  public void readParameters(boolean ic) {

    try {
      // open the xmlFileLocation to read input
      DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
      DocumentBuilder docBuilder = docBuilderFactory.newDocumentBuilder();
      Document doc = docBuilder.parse(new File(xmlFileLocation));

      Element setupComponent = (Element) doc.getElementsByTagName("simulation_setup").item(0);
      processSetupParams(setupComponent);

      // locate the <cistromes> tag
      Element cistromesComponent = (Element) doc.getElementsByTagName("cistromes").item(0);

      // process this into details of individual cistromes
      processCistromesComponent(cistromesComponent);

      // we'll pass the Cistrome components on to the Cell Object to make sense of...
      // if(instantiateCell)
      // {
      // We'll set up a Cell object to hold our Cistrome(s)
      // System.out.println("Cistrome data sources are " + sources);
      cell = new Cell(sources, this);
      // System.out.println("Created cell object " + cell);
      // }

      // System.out.println("Fetching cistrome data from " + cell);
      ArrayList<Cistrome> cistromeList = cell.getCistromeList();

      for (int c = 0; c < cistromeList.size(); c++) {
        Cistrome thisCistrome = ((Cistrome) cistromeList.get(c));

        // System.out.println("Cistrome " + c);
        thisCistrome.setName(names.get(c));
        // System.out.println("Name: " + names.get(c));
        thisCistrome.setBranchingRate(branchingRates.get(c));
        // System.out.println("Branching rate: " + branchingRates.get(c));
        thisCistrome.setInitialReds(numsInitialReds.get(c));
        // System.out.println("Initial reds: " + numsInitialReds.get(c));
      }

    } catch (Exception e) {
      e.printStackTrace();
    }
  }

  public void processSetupParams(Element setupComponents) {
    simulationSteps =
        Integer.parseInt(
            setupComponents.getElementsByTagName("simulationSteps").item(0).getTextContent());

    System.out.println("Number of simulation steps to take " + simulationSteps);

    resultFilePath =
        setupComponents.getElementsByTagName("resultFilePath").item(0).getTextContent();
    description = setupComponents.getElementsByTagName("description").item(0).getTextContent();
    timeOut =
        Integer.parseInt(setupComponents.getElementsByTagName("timeOut").item(0).getTextContent());
  }

  public void processCistromesComponent(Element cistromesComponent) {

    NodeList allCistromes = cistromesComponent.getElementsByTagName("cistrome");

    for (int i = 0; i < allCistromes.getLength(); i++) {

      Element cistromeComponent = (Element) allCistromes.item(i);
      processCistromeParameters(cistromeComponent);
    }
  }

  public void processCistromeParameters(Element cistromeComponent) {

    name = cistromeComponent.getElementsByTagName("name").item(0).getTextContent();
    System.out.println("Cistrome name found " + name);
    names.add(name);
    System.out.println(names);
    source = cistromeComponent.getElementsByTagName("source").item(0).getTextContent();
    System.out.println("Cistrome data source found " + source);
    sources.add(source);
    branchingRate =
        Integer.parseInt(
            cistromeComponent.getElementsByTagName("branchingRate").item(0).getTextContent());
    System.out.println("Cistrome branching rate found " + branchingRate);
    branchingRates.add(branchingRate);
    initialReds =
        Integer.parseInt(
            cistromeComponent.getElementsByTagName("initialReds").item(0).getTextContent());
    System.out.println("Cistrome initial reds found " + initialReds);
    numsInitialReds.add(initialReds);
  }

  public void copyFile(String source, String dest) {

    try {
      File sf = new File(source);
      File df = new File(dest);
      InputStream in = new FileInputStream(sf);
      OutputStream out = new FileOutputStream(df);

      byte[] buf = new byte[1024];
      int len;

      while ((len = in.read(buf)) > 0) {
        out.write(buf, 0, len);
      }

      in.close();
      out.close();
      System.out.println("File " + source + " copied to " + dest);

    } catch (FileNotFoundException ex) {
      System.out.println(ex.getMessage() + "in the specified directory");
    } catch (IOException e) {
      System.out.println(e.getMessage());
    }
  }

  public Cell getCell() {
    return cell;
  }

  public DataStore getDataStore() {
    return dataStore;
  }

  public int getSimulationSteps() {
    return simulationSteps;
  }

  public boolean getUsingGUI() {
    return this.useGUI;
  }

  public void setUsingGUI(boolean gui) {
    useGUI = gui;
  }
}