We propose to learn the time-varying stochastic computational resource usage of software as a graph structured Schr\"odinger bridge problem. In general, learning the computational resource usage from data is challenging because resources such as the number of CPU instructions and the number of last level cache requests are both time-varying and statistically correlated. Our proposed method enables learning the joint time-varying stochasticity in computational resource usage from the measured profile snapshots in a nonparametric manner. The method can be used to predict the most-likely time-varying distribution of computational resource availability at a desired time. We provide detailed algorithms for stochastic learning in both single and multi-core cases, discuss the convergence guarantees, computational complexities, and demonstrate their practical use in two case studies: a single-core nonlinear model predictive controller, and a synthetic multi-core software.