Experiences in Managing the Performance and Reliability of a Large-Scale Genomics Cloud Platform


Michael Hao Tong, Robert L. Grossman, and Haryadi S. Gunawi, University of Chicago


We share our technical experiences in improving the performance of long-running jobs on the Genomic Data Commons (GDC), a large-scale cancer genomics cloud platform. We show how common bioinformatics workloads can cause VMs to age after several days, causing a large number of Extended Page Table (EPT) violations that significantly impact performance. We present host- and VM-level EPT monitoring and evaluate several possible mitigation scenarios. We highlight the long investigative process required for this research, with experiments requiring many days to complete.

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@inproceedings {273829,
author = {Michael Hao Tong and Robert L. Grossman and Haryadi S. Gunawi},
title = {Experiences in Managing the Performance and Reliability of a {Large-Scale} Genomics Cloud Platform},
booktitle = {2021 USENIX Annual Technical Conference (USENIX ATC 21)},
year = {2021},
isbn = {978-1-939133-23-6},
pages = {973--988},
url = {https://www.usenix.org/conference/atc21/presentation/tong},
publisher = {USENIX Association},
month = jul,

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