Use the Parameters Variation
experiment.
You can access any run number on Main startup with the code int a=getEngine().getRunCount();
. You can prepare the inputs beforehand in an Excel and pass the parameters based on the count number.

You can write the outputs separately for each run. Use the following code as an inspiration where I write myVariable
at the end of each run to csv files called output0.csv, ouput1.csv, etc. (This happens in Main -> On Destroy.
int a=getEngine().getRunCount();
String filename="output"+a+".csv";
try
{
FileOutputStream fos = new FileOutputStream(filename);
PrintStream p = new PrintStream(fos);
for (int i=0; i<100;i++){
for(int j=0;j<10;j++){
p.println(myVariable.output[i][j]);}} // outputs tab delimited values
}
catch (Exception e)
{
traceln("Could not write to file.");
}