In this paper, we propose the design and implementation of an ensemble data assimilation (DA) framework for weather prediction at a high resolution and with a large ensemble size. We consider the deployment of this framework on the data throughput of file input/output (I/O) and multi-node communication. As an instance of the application of the proposed framework, a Local Ensemble Transform Kalman Filter (LETKF) was used with a Non-hydrostatic Icosahedral Atmospheric Model (NICAM) for the DA system. Benchmark tests were performed using the K computer, a massive parallel supercomputer with distributed file systems. The results showed an improvement in total time required for the workflow as well as satisfactory scalability of up to 10 K nodes (80 K cores). With regard to high-performance computing systems, where data throughput performance increases at a slower rate than computational performance, our new framework for ensemble DA systems promises drastic reduction of total execution time.