Phylodynamic analysis and epidemiologic data identified 3 patterns of spread of primary human immunodeficiency virus type 1 infection (PHI) among men who have sex with men (2001-2009): 420 unique PHIs, 102 small clusters (2-4 PHIs per cluster, n = 280), and 46 large clusters (5-31 PHIs per cluster, n = 450). Large clusters disproportionately increased from 25.2% of PHIs in 2005 to 39.1% in 2009 (χ(2) = 33.9, P < .001). Scalar expansion of large clusters over 11 months (interquartile range, 3.5-25.5 months) correlated with cluster membership size (r(2) = 0.174, F = 4.424, P = .047). PHI cohort data revealed variations in social networks and risk behaviors among the 3 groups, suggesting the need for tailored prevention measures.

Several benchmarks for measuring the memory performance of HPC systems along dimensions of spatial and temporal memory locality have recently been proposed. However, little is understood about the relationships of these benchmarks to real applications and to each other. We propose a methodology for producing architecture-neutral characterizations of the spatial and temporal locality exhibited by the memory access patterns of applications. We demonstrate that the results track intuitive notions of locality on several synthetic and application benchmarks. We employ the methodology to analyze the memory performance components of the HPC Challenge Benchmarks, the Apex-MAP benchmark, and their relationships to each other and other benchmarks and applications. We show that this analysis can be used to both increase understanding of the benchmarks and enhance their usefulness by mapping them, along with applications, to a 2-D space along axes of spatial and temporal locality.

Abstract.Using a large HPC platform, we investigate the effectiveness of "symbiotic space-sharing", a technique that improves system throughput by executing parallel applications in combinations and configurations that alleviate pressure on shared resources. We demonstrate that relevant benchmarks commonly suffer a 10-60% penalty in runtime efficiency due to memory resource bottlenecks and up to several orders of magnitude for I/O. We show that this penalty can be often mitigated, and sometimes virtually eliminated, by symbiotic space-sharing techniques and deploy a prototype scheduler that leverages these findings to improve system throughput by 20%.

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