We report the largest scale deep learning with High Performance Computing (HPC) to physics analysis with the CMS simulation data in proton-proton collisions at 13 TeV. We build a Convolutional Neural Network (CNN) model that takes low-level information as images considering the geometry of the CMS detector and use this model to discriminate \textit{R}-parity violating super symmetry (RPV SUSY) events from the background events with inelastic quantum process from the Standard Model (QCD multi-jet). We compare the classification performance of the CNN method with that of the widely used cut-based method. The signal efficiency (and expected significance) of the CNN method is 1.85 (1.2) times higher than that of the cut-based method. To speed-up the training, the model training is conducted using the Nurion HPC system at the Korea Institute of Science and Technology Information, which is equipped with thousands of parallel \texttt{Xeon Phi} CPUs. Notably, our CNN model shows scalability up to 1024 nodes.