In this paper, we perform the first application of the hybrid method (exact low modes plus stochastically estimated high modes) for all-to-all propagators to the HAL QCD method. We calculate the HAL QCD potentials in the $I=2$ $pipi$ scattering in order to see how statistical fluctuations of the potential behave under the hybrid method. All of the calculations are performed with the 2+1 flavor gauge configurations on $16^3 times 32$ lattice at the lattice spacing $a approx 0.12$ fm and $m_{pi} approx 870$ MeV. It is revealed that statistical errors for the potential are enhanced by stochastic noises introduced by the hybrid method, which, however, are shown to be reduced by increasing the level of dilutions, in particular, that of space dilutions. From systematic studies, we obtain a guiding principle for a choice of dilution types/levels and a number of eigenvectors to reduce noise contaminations to the potential while keeping numerical costs reasonable. We also confirm that we can obtain the scattering phase shifts for the $I=2$ $pipi$ system by the hybrid method within a reasonable numerical cost, which are consistent with the result obtained with the conventional method. The knowledge we obtain in this study will become useful to investigate hadron resonances which require quark annihilation diagrams such as the $rho$ meson by the HAL QCD potential with the hybrid method.
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