openMotor creator here. I think you might be talking about OpenRocket, because it is a Java program and requires a JDK (Java Developer Kit). openMotor is provided as a native executable and doesn't require anything else to run.
OpenRocket is for simulating rocket flight, while openMotor simulates when happens inside of a motor. The output from openMotor can be fed into OpenRocket to go all the way from propellant properties to altitude!
To answer your original question, yes, both openMotor and OpenRocket are safe and I use both all the time.