This error occurs when you are running a simulation with a Python script set to Manual and Ashes has not received any information from the Python script for a time longer than the Maximum waiting time set in the Preferences. This can be because

the Maximum waiting time is too short and you script takes longer than that time to compute a time step. In that case, you can increase the Maximum waiting time.
your Python script has crashed, or has entered an infinite loop.
you are debugging your Python script, and you have stopped it for more than the Maximum waiting time.
you have closed your Python script while the simulation was running.