/*
* 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");
}
/*
* 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();
}
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;
}
}
