Most machine learning algorithms operate on vectorized data with Euclidean structures because of the significant mathematical advantages offered by Hilbert space, but improved representational efficiency may offset more involved learning on non-Euclidean structures. Recently, a method that integrates the marginalized graph kernel into the Gaussian process regression framework was used to learn directly on molecular graphs. Here, we describe an implementation of this method for crystalline materials based on effective crystal graph representations: the molecular graphs of 128-atom supercells of body-centered cubic (BCC) iron with periodic boundary conditions. Regressors trained on hundreds of time steps of a density functional theory molecular dynamics (DFT-MD) simulation achieved root mean square errors of less than 5 meV/atom. The mechanical stability of BCC iron was investigated at high pressure and elevated temperature using regressors trained on short DFT-MD runs, including at conditions found in the inner core of the earth. Phonon dispersions obtained from the short runs show that BCC iron is mechanically stable at 360 GPa when the temperature is above 2500 K. Atoms in the super cell were displaced in the direction of the first, second, and third nearest-neighbors from selected configurations that included thermal atomic displacements, and forces exerted on the displaced atoms were computed by numerical differentiation of the regressors.