  We calculate the D-brane superpotentials for two Calabi-Yau manifolds with
three deformations by the generalized hypergeometric GKZ systems, which give
rise to the flux superpotentials $\mathcal{W}_{GVW}$ of the dual F-theory
compactification on the relevant Calabi-Yau fourfolds in the weak decoupling
limit. We also compute the Ooguri-Vafa invariants from A-model expansion with
mirror symmetry, which are related to the open Gromov-Witten invariants.
