How can I measure the performance of an application?

The flop/s is a rate of execution of 64 bits floating point operations (either addition or multiplication) per second.
Its multiples are Mflop/s (millions), Gflop/s (billions), Tflop/s (trillions) and so on...

The theoretical peak performance is the upper bound peak rate of execution of floating point operations for a given processor.
It can be determined by counting the number of floating-point additions and multiplications (in full precision) that can be completed during the clock time of the processor.

Flop/s can give a measure of application performance: given a processor's theoretical peak performance, one can work out how efficiently the cpu's floating point units are used.
An application which runs at 10% of the peak performance has room for optimization, while one that runs over 50% is probably not going to improve much unless the underlying algorithm is rewritten.