Methods, systems, and non-transitory computer readable medium for scheduling a substrate processing sequence in an integrated substrate processing system are disclosed herein. A processing device generates a processing model for a batch of semiconductor substrates. The processing model defines a corresponding start time for each semiconductor substrate in each processing chamber in the integrated substrate processing system. One or more graphics processing units (GPUs) generates parallel inputs based on the processing model and concurrently processes, by a plurality of cores of the one or more GPUs, the parallel inputs to generate parallel outputs for the batch of semiconductor substrates. Each of the parallel inputs is processed on a distinct core of the plurality of cores of the one or more GPUs to generate a corresponding parallel output. The processing device causes the batch of semiconductor substrates to be processed in the integrated substrate processing system based on the parallel outputs.