Numerical simulation of seismic waves' propagation and imaging in a three-dimensional multiscale geological media is one of the main trends in the development of modern geophysics. We present the work flow for construction of the 3D digital twin of some real geological object. This object is cavernous fractured carbonate reservoir near the Riphean roof. One of the main features of this object is the presence of the family of faults filled with tectonic breccia. To simulate them, in particular, their interiors and surrounding damaged areas, we simulate paleotectonic processes with the use of 3D discrete elements technique. This simulation we do by GPU parallelization. Next, when the fine digital geological model is done, we perform 3D finite-difference simulation of the seismic waves' propagation and get the full 3D synthetic data set. To do this simulation we use an original technique based on local grid refinement in time and space. To be able to deal with huge amount of input/output data we use High-Performance Computing (HPC) systems with parallel architecture and hybrid parallelization strategy by simultaneous use of MPI and OpenMP. The final step is validation of our original multiscale algorithm for seismic imaging, which suppresses specular reflection, but accumulates weak scattered/diffracted waves. This approach opens the way to the reconstruction of subseismic geological objects, like fractures, fracture corridors and clusters of caves. To construct these images we use HPC with parallel architecture and MPI+OpenMP programming. Published under licence by IOP Publishing Ltd.