We study the computational scalability of a Gaussian process (GP) framework for solving general nonlinear partial differential equations (PDEs). This framework transforms solving PDEs to solving quadratic optimization problem with nonlinear constraints. Its complexity bottleneck lies in computing with dense kernel matrices obtained from pointwise evaluations of the covariance kernel of the GP and its partial derivatives at collocation points. We present a sparse Cholesky factorization algorithm for such kernel matrices based on the near-sparsity of the Cholesky factor under a new ordering of Diracs and derivative measurements. We rigorously identify the sparsity pattern and quantify the exponentially convergent accuracy of the corresponding Vecchia approximation of the GP, which is optimal in the Kullback-Leibler divergence. This enables us to compute $\epsilon$-approximate inverse Cholesky factors of the kernel matrices with complexity $O(N\log^d(N/\epsilon))$ in space and $O(N\log^{2d}(N/\epsilon))$ in time. With the sparse factors, gradient-based optimization methods become scalable. Furthermore, we can use the oftentimes more efficient Gauss-Newton method, for which we apply the conjugate gradient algorithm with the sparse factor of a reduced kernel matrix as a preconditioner to solve the linear system. We numerically illustrate our algorithm's near-linear space/time complexity for a broad class of nonlinear PDEs such as the nonlinear elliptic, Burgers, and Monge-Amp\`ere equations. In summary, we provide a fast, scalable, and accurate method for solving general PDEs with GPs.

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