We show that the confinement-deconfinement phase transition of supersymmetric Yang-Mills theories with 16 supercharges in various dimensions can be realized through the Hawking-Page phase transition between the near horizon geometries of black Dp-branes and BPS Dp-branes by removing a small radius region in the geometry in order to realize a confinement phase, which generalizes the Herzogs discussion for the holographic hard-wall AdS/QCD model. Removing a small radius region in the gravitational dual corresponds to introducing an IR cutoff in the dual field theory. We also discuss the Hawking-Page phase transition between thermal $AdS_5$, $AdS_4$, $AdS_7$ spaces and R-charged AdS black holes coming from the spherical reduction of the decoupling limit of rotating D3-, M2-, and M5- branes in type IIB supergravity and 11 dimensional supergravity in grand canonical ensembles, where the IR cutoff also plays a crucial role in the existence of the phase transition.
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