To take advantage of modern generation computing hardware, a scalable numerical method, based on higher-order compact scheme, is described to solve rotating stratified flows in cylindrical annular domains. An original approach combining 2d-pencil decomposition and reduced Parallel Diagonal Dominant is proposed to improve the parallelization performance during the computation of Poisson/Helmholtz solvers and time explicit terms. The developed technique is validated with respect to analytical solutions, using the method of manufactured solutions, and available data for two specific configurations. The purpose is to demonstrate its ability to correctly capture the flow characteristics in strato-rotational instability and in baroclinic instability with associated small-scale features. Moreover, this code is found to drastically reduce the huge execution times often preventing detailed numerical investigations of these complex phenomena. Strong scaling test is carried out to assess the performance for up to 1024 cores using grid up to 128 × 568 × 568 in radial, axial and azimuthal directions.