/*
* 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();
}
