An operational atmospheric dispersion prediction system is implemented on a cluster supercomputer for Online Emergency Response at the Kalpakkam nuclear site. This numerical system constitutes a parallel version of a nested grid meso-scale meteorological model MM5 coupled to a random walk particle dispersion model FLEXPART. The system provides 48-hour forecast of the local weather and radioactive plume dispersion due to hypothetical airborne releases in a range of 100 km around the site. The parallel code was implemented on different cluster configurations like distributed and shared memory systems. A 16-node dual Xeon distributed memory gigabit ethernet cluster has been found sufficient for operational applications. The runtime of a triple nested domain MM5 is about 4 h for a 24 h forecast. The system had been operated continuously for a few months and results were ported on the IMSc home page.Initial and periodic boundary condition data for MM5 are provided by NCMRWF, New Delhi. An alternative source is found to be NCEP, USA. These two sources provide the input data to the operational models at different spatial and temporal resolutions using different assimilation methods. A comparative study on the results of forecast is presented using these two data sources for present operational use. Improvement is noticed in rainfall forecasts that used NCEP data, probably because of its high spatial and temporal resolution.