Parallel programs, generated by the supercompiler, VFCS (Vienna Fortran Compilation System), are an application area for the tool, PEPSY (PErformance Prediction SYstem), which we have developed recently. PEPSY derives a performance model from an internal representation of the parallel program in the compiler, automatically, and makes performance analysis by discrete-event simulation. Several monitoring modes of PEPSY enable to analyze a parallel program behavior at the detailed and global level, evaluating static and dynamic performance indices. Performance prediction is carried out before the final target parallel code is generated, or before a real run is executed on the parallel computer, in order to optimize the parallelization strategy for VPCS. This paper is focused on the prediction of a new subset of performance indices for the parallel programs, evaluated by PEPSY, and illustrating its new monitoring facilities suitable for comparison of different versions of the program.