From simulations on 2+1 flavor domain wall fermion ensembles at three lattice spacings with two of them at physical quark masses, we compute the spectrum of the Dirac operator up to the eigenvalue λ ∼100 MeV using the overlap fermion. The spectrum is close to a constant below λ ≤ 20 MeV as predicted by the 2-flavor chiral perturbative theory (χPT) up to the finite volume correction, and then increases linearly due to the nonvainishing strange quark mass. Furthermore, one can extract the light and strange quark masses with ∼20% uncertainties from the spectrum data with sub-percentage statistical uncertainty, using the next to leading order χPT. Using the non-perturbative RI/MOM renormalization, we obtain the chiral condensates at MS 2GeV as Σ = (260.3(0.7)(1.3)(0.7)(0.8) MeV) 3 in the N f = 2 (keeping the strange quark mass at the physical point) chiral limit and Σ0 = (232.6(0.9)(1.2)(0.7)(0.8) MeV) 3 in the N f = 3 chiral limit, where the four uncertainties come from the statistical fluctuation, renormalization constant, continuum extrapolation and lattice spacing determination. Note that Σ/Σ0 = 1.40(2)(2) is much larger than 1 due to the strange quark mass effect.