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Abstract The rapid development of the Graphics Processing Units (GPU) enables affordable Large Eddy Simulations (LES) for gas turbine combustion. This work evaluates the accuracy and the computational efficiency of a newly-developed native GPU solver on single and multiple GPUs, develops the optimal GPU numerical formulations for LES, and analyzes the solver’s capability to resolve large meshes and complex physics for a gas turbine combustor, which substantially reduces the computational costs whilst ensuring sufficient solution convergence and accuracy. The combustor investigated is the swirl-stabilized, partially-premixed methane/air PRECCINSTA burner, using LES with the WALE sub-grid scale model for turbulence, and the species transport-based Finite Rate model for combustion, combining with the Stiff Chemistry solver. Rich experimental data are available for this combustor, ideal for GPU validation purposes. To optimize the GPU calculations, the Rapid Octree meshing technique has also been utilized in this work, generating high-quality octree cells for the combustor mesh. A detailed mesh sensitivity analysis has been performed to identify the optimal mesh for the present combustor with the GPU solver. This study then compares two different LES numerical settings on their solution accuracy for the same GPU solver, finding that the GPU-dedicated, Optimized LES Numerics offer slightly more accurate results. The GPU solutions have also been validated against the available experimental data. Finally, the speed-up and the scalability performance of the GPU solver have been discussed. In summary, the best practice settings and workflows developed in this work may be helpful to the deployment of this new GPU solver to more complicated industrial gas turbine combustor simulations.