1. A computer-readable recording medium that stores therein a computer program that causes a computer to execute an ensemble weather predicting method comprising: substituting a plurality of different initial values into a weather prediction model at a predetermined time point to start computing predicted values for each time point between a first time point prior to the predetermined time point and an N-th time point subsequent to the predetermined time point with respect to each initial value, wherein N is a positive integer; comparing, at an arbitrary time point during the computation, each predicted value for a past time point prior to the arbitrary time point that has been computed with respect to the plurality of different initial values with an actual value actually observed at the past time point and determining whether a difference between each predicted value and the actual value is within a first tolerance; substituting remaining initial values of the plurality of different initial values other than the initial value corresponding to any predicted value for which the difference has been determined to be not within the first tolerance into the weather prediction model for any remaining computation of predicted values performed after the arbitrary time point.