The instanton partition function of N=2, D=4 SU(2) gauge theory is obtained by taking the field theory limit of the topological open string partition function, given by a Chern-Simons theory, of a CY3-fold. The CY3-fold on the open string side is obtained by geometric transition from local F_0 which is used in the geometric engineering of the SU(2) theory. The partition function obtained from the Chern-Simons theory agrees with the closed topological string partition function of local F_0 proposed recently by Nekrasov. We also obtain the partition functions for local F_1 and F_2 CY3-folds and show that the topological string amplitudes of all local Hirzebruch surfaces give rise to the same field theory limit. It is shown that a generalization of the topological closed string partition function whose field theory limit is the generalization of the instanton partition function, proposed by Nekrasov, can be determined easily from the Chern-Simons theory.

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