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Full waveform modelling and inversion are essential tools commonly used in seismic imaging. Due to the restrictions from instruments and computing resources, the seismic data are usually frequency-band limited. Thus, the resulting imaging result is a smooth version of the true Earth with the lack of scales smaller than the minimum propagating wavelength. The non-periodic homogenization technique allows for building a long-wave equivalent medium to account for wave interactions with small geological structures and producing similar waveforms as for the original medium at a controlled accuracy. The current non-periodic homogenization implementation is memory and time consuming even with parallel computing techniques. To boost its applicability on large-scale 3D problems, we propose a fully scalable non-periodic homogenization implementation. As the core of the homogenization process, the solution of elastostatic equations and the low-pass filtering operations are formulated as the linear system solution with a matrix-free conjugate-gradient algorithm to exploit highly optimized matrix-vector-product routines developed in our elastic wave modelling and inversion parallel code SEM46. For the algorithm consistency, an approximated Gaussian low-pass filtering is introduced by a cascade of PDE-defined Bessel filters without sacrificing the effectiveness. All these improvements enhance the efficiency, scalability and robustness of the non-periodic homogenization process.