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We present a system based on high-throughput computing (HTC) in grid environment suitable for full-wave time-domain analysis of 3D electromagnetic structures. The network-based distributed system enables to solve complex electromagnetic problems using heterogeneous computer platforms and heterogeneous networks. To validate the system, the resonance frequencies of a circular cavity resonator are calculated and compared with the expected analytical frequencies. The power of the system is shown by analyzing the computational time of the cavity resonator. To illustrate the potential application of the system, an example of a calculation of waves scattered by a complex object is given.