The central engine of Gamma Ray Bursts is hidden from direct probing with photons mainly due to the high densities involved. Inferences on their properties are thus made from their cosmological setting, energetics, low-energy counterparts and variability. If GRBs are powered by hypercritical accretion onto compact objects, on small spatial scales the flow will exhibit fluctuations, which could in principle be reflected in the power output of the central engine and ultimately in the high energy prompt emission. Here we address this issue by characterizing the variability in neutrino cooled accretion flows through local shearing box simulations with magnetic fields, and then convolving them on a global scale with large scale dynamical simulations of accretion disks. The resulting signature is characteristic, and sensitive to the details of the cooling mechanism, providing in principle a discriminant for GRB central engine properties.

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