Program: 42180
Project: 42180
Buggy source:
private static void runEquivalent(ArrayList<SAFA<CharPred,Character>> safaLHS,ArrayList<SAFA<CharPred,Character>> safaRHS,ArrayList<SFA<CharPred,Character>> sfaLHS,ArrayList<SFA<CharPred,Character>> sfaRHS,long timeOut){
  try {
    long start=System.currentTimeMillis();
    SAFA<CharPred,Character> tempLeft=IntersectedSAFA(safaLHS,timeOut);
    long fullTimeSAFALeft=System.currentTimeMillis() - start;
    long solverTimeSAFALeft=0;
    long subTimeSAFALeft=0;
    start=System.currentTimeMillis();
    SAFA<CharPred,Character> tempRight=IntersectedSAFA(safaRHS,timeOut - fullTimeSAFALeft);
    long fullTimeSAFARight=System.currentTimeMillis() - start;
    long solverTimeSAFARight=0;
    long subTimeSAFARight=0;
    if (fullTimeSAFALeft + fullTimeSAFARight >= timeOut) {
      fullTimeSAFA=timeOut;
      solverTimeSAFA=timeOut;
      subTimeSAFA=timeOut;
    }
 else {
      Timers.setTimeout(Long.MAX_VALUE);
      SAFA.isEquivalent(tempLeft,tempRight,solver,SAFA.getBooleanExpressionFactory(),timeOut - fullTimeSAFALeft - fullTimeSAFARight);
      fullTimeSAFA=Timers.getFull() + fullTimeSAFALeft + fullTimeSAFARight;
      solverTimeSAFA=Timers.getSolver() + solverTimeSAFALeft + solverTimeSAFARight;
      subTimeSAFA=Timers.getSubsumption() + subTimeSAFALeft + subTimeSAFARight;
    }
  }
 catch (  Exception e) {
    fullTimeSAFA=timeOut;
    solverTimeSAFA=timeOut;
    subTimeSAFA=timeOut;
  }
  try {
    long startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempLeftSFA=IntersectedSFA(sfaLHS,timeOut);
    long endDate=System.currentTimeMillis();
    long totalTimeLeft=endDate - startDate;
    startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempRightSFA=IntersectedSFA(sfaRHS,timeOut - totalTimeLeft);
    endDate=System.currentTimeMillis();
    long totalTimeRight=endDate - startDate;
    long startDateEquiv=System.currentTimeMillis();
    tempLeftSFA.isHopcroftKarpEquivalentTo(tempRightSFA,solver,timeOut);
    long endDateEquiv=System.currentTimeMillis();
    totalTimeSFA=endDateEquiv - startDateEquiv + totalTimeLeft + totalTimeRight;
  }
 catch (  Exception e) {
    totalTimeSFA=timeOut;
  }
}

Fixed version (ground truth):
private static void runEquivalent(ArrayList<SAFA<CharPred,Character>> safaLHS,ArrayList<SAFA<CharPred,Character>> safaRHS,ArrayList<SFA<CharPred,Character>> sfaLHS,ArrayList<SFA<CharPred,Character>> sfaRHS,long timeOut){
  try {
    long start=System.currentTimeMillis();
    SAFA<CharPred,Character> tempLeft=IntersectedSAFA(safaLHS,timeOut);
    long fullTimeSAFALeft=System.currentTimeMillis() - start;
    long solverTimeSAFALeft=0;
    long subTimeSAFALeft=0;
    start=System.currentTimeMillis();
    SAFA<CharPred,Character> tempRight=IntersectedSAFA(safaRHS,timeOut - fullTimeSAFALeft);
    long fullTimeSAFARight=System.currentTimeMillis() - start;
    long solverTimeSAFARight=0;
    long subTimeSAFARight=0;
    if (fullTimeSAFALeft + fullTimeSAFARight >= timeOut) {
      fullTimeSAFA=timeOut;
      solverTimeSAFA=timeOut;
      subTimeSAFA=timeOut;
    }
 else {
      Timers.setTimeout(Long.MAX_VALUE);
      SAFA.isEquivalent(tempLeft,tempRight,solver,SAFA.getBooleanExpressionFactory(),timeOut - fullTimeSAFALeft - fullTimeSAFARight);
      fullTimeSAFA=Timers.getFull() + fullTimeSAFALeft + fullTimeSAFARight;
      solverTimeSAFA=Timers.getSolver() + solverTimeSAFALeft + solverTimeSAFARight;
      subTimeSAFA=Timers.getSubsumption() + subTimeSAFALeft + subTimeSAFARight;
    }
  }
 catch (  Exception e) {
    fullTimeSAFA=timeOut;
    solverTimeSAFA=timeOut;
    subTimeSAFA=timeOut;
  }
  try {
    long totalTimeLeft=timeOut;
    long startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempLeftSFA=IntersectedSFA(sfaLHS,totalTimeLeft);
    long endDate=System.currentTimeMillis();
    totalTimeLeft-=endDate - startDate;
    startDate=System.currentTimeMillis();
    SFA<CharPred,Character> tempRightSFA=IntersectedSFA(sfaRHS,totalTimeLeft);
    endDate=System.currentTimeMillis();
    totalTimeLeft-=endDate - startDate;
    startDate=System.currentTimeMillis();
    tempLeftSFA.isHopcroftKarpEquivalentTo(tempRightSFA,solver,totalTimeLeft);
    endDate=System.currentTimeMillis();
    totalTimeLeft-=endDate - startDate;
    totalTimeSFA=timeOut - totalTimeLeft;
  }
 catch (  Exception e) {
    totalTimeSFA=timeOut;
  }
}