A batched Cholesky decomposition method, system, and non-transitory computer readable medium for a Graphics Processing Unit (GPU), include mirroring a second problem matrix of a second problem to a first problem matrix of a first problem as paired matrices and shifting the second problem matrix by N+1 and combining the first problem matrix and the mirrored second problem matrix into one matrix of (N+1)×N, where the first problem shared memory comprises regular intervals, where the second problem shared memory is continuous, and where the GPU performs batched dense Cholesky decomposition with the one matrix from the combining to accelerate the Cholesky decomposition.