Workshops Archive

Evaluating Trusted Execution Environment Performance for Genome Sequence Alignment: An AMD SEV Case Study

Workshop: 4th International Workshop on Cyber Security in High Performance Computing (S-HPC)

Authors: Robert Keßler and Lech Nieroda (University of Cologne); Simon Volpert (University of Ulm); Moritz Gräf (University Hospital Cologne); and Viktor Achter, Laslo Hunhold, and Stefan Wesner (University of Cologne)

Abstract: High-Performance Computing (HPC) systems are used for a variety of applications. An important requirement for some of them is security and protection of data, especially when dealing with highly sensitive data such as the human genome. In order to facilitate the processing of actual patient data on HPC systems, it is imperative to implement robust protective measures. In this paper we analyze the performance of two micro benchmarks and the BWA-MEM2 algorithm as genome sequencing workflow. Our evaluation matrix includes a SMP node, a VM with SEV and SME enabled and VM with only SME enabled, assessed against varying thread counts file systems configurations. Our analysis showed memory bandwidth seems to be the limiting factor as the bandwidth drops can drop to approximately 50%. Overall we observed that the overhead caused by the encryption for the genome alignment workload is adequate with 10.4% for SME and over 20.9% for SEV+SME.

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