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GPUs are increasingly being used in security applications, especially for accelerating encryption/decryption. While GPUs are an attractive platform in terms of performance, the security of these devices raises a number of concerns. One vulnerability is the data-dependent timing information, which can be exploited by adversary to recover the encryption key. Memory system features are frequently exploited since they create detectable timing variations. In this paper, our attack model is a coalescing attack, which leverages a critical GPU microarchitectural feature -- the coalescing unit. As multiple concurrent GPU memory requests can refer to the same cache block, the coalescing unit collapses them into a single memory transaction. The access time of an encryption kernel is dependent on the number of transactions. Correlation between a guessed key value and the associated timing samples can be exploited to recover the secret key. In this paper, a series of hardware/software countermeasures are proposed to obfuscate the memory timing side channel, making the GPU more resilient without impacting performance. Our hardware-based approach attempts to randomize the width of the coalescing unit to lower the signal-to-noise ratio. We present a hierarchical Miss Status Holding Register (MSHR) design that can merge transactions across different warps. This feature boosts performance, while, at the same time, secures the execution. We also present a software-based approach to permute the organization of critical data structures, significantly changing the coalescing behavior and introducing a high degree of randomness. Equipped with our new protections, the effort to launch a successful attack is increased up to 1433X . 178X, while also improving encryption/decryption performance up to 7%.