  We consider certain quantum spectral problems appearing in the study of local
Calabi-Yau geometries. The quantum spectrum can be computed by the
Bohr-Sommerfeld quantization condition for a period integral. For the case of
small Planck constant, the periods are computed perturbatively by deformation
of the Omega background parameters in the Nekrasov-Shatashvili limit. We
compare the calculations with the results from the standard perturbation theory
for the quantum Hamiltonian. There have been proposals in the literature for
the non-perturbative contributions based on singularity cancellation with the
perturbative contributions. We compute the quantum spectrum numerically with
some high precisions for many cases of Planck constant. We find that there are
also some higher order non-singular non-perturbative contributions, which are
not captured by the singularity cancellation mechanism. We fix the first few
orders formulas of such corrections for some well known local Calabi-Yau
models.
