Citizen science biodiversity data present great opportunities for ecology and conservation across vast spatial and temporal scales. However, the opportunistic nature of these data lacks the sampling structure required by modeling methodologies that address a pervasive challenge in ecological data collection: imperfect detection, i.e., the likelihood of under-observing species on field surveys. Occupancy modeling is an example of an approach that accounts for imperfect detection by explicitly modeling the observation process separately from the biological process of habitat selection. This produces species distribution models that speak to the pattern of the species on a landscape after accounting for imperfect detection in the data, rather than the pattern of species observations corrupted by errors. To achieve this benefit, occupancy models require multiple surveys of a site across which the site's status (i.e., occupied or not) is assumed constant. Since citizen science data are not collected under the required repeated-visit protocol, observations may be grouped into sites post hoc. Existing approaches for constructing sites discard some observations and/or consider only geographic distance and not environmental similarity. In this study, we compare ten approaches for site construction in terms of their impact on downstream species distribution models for 31 bird species in Oregon, using observations recorded in the eBird database. We find that occupancy models built on sites constructed by spatial clustering algorithms perform better than existing alternatives.

NUMA systems are characterized by Non-Uniform Memory Access times, where accessing data in a remote node takes longer than a local access. NUMA hardware has been built since the late 80's, and the operating systems designed for it were optimized for access locality. They co-located memory pages with the threads that accessed them, so as to avoid the cost of remote accesses. Contrary to older systems, modern NUMA hardware has much smaller remote wire delays, and so remote access costs per se are not the main concern for performance, as we discovered in this work. Instead, congestion on memory controllers and interconnects, caused by memory traffic from data-intensive applications, hurts performance a lot more. Because of that, memory placement algorithms must be redesigned to target traffic congestion. This requires an arsenal of techniques that go beyond optimizing locality. In this paper we describe Carrefour, an algorithm that addresses this goal. We implemented Carrefour in Linux and obtained performance improvements of up to 3.6 relative to the default kernel, as well as significant improvements compared to NUMA-aware patchsets available for Linux. Carrefour never hurts performance by more than 4% when memory placement cannot be improved. We present the design of Carrefour, the challenges of implementing it on modern hardware, and draw insights about hardware support that would help optimize system software on future NUMA systems.

When multiple threads or processes run on a multi-core CPU they compete for shared resources, such as caches and memory controllers, and can suffer performance degradation as high as 200%. We design and evaluate a new machine learning model that estimates this degradation online, on previously unseen workloads, and without perturbing the execution. Our motivation is to help data center and HPC cluster operators effectively use workload consolidation. Data center consolidation is about placing many applications on the same server to maximize hardware utilization. In HPC clusters, processes of the same distributed applications run on the same machine. Consolidation improves hardware utilization, but may sacrifice performance as processes compete for resources. Our model helps determine when consolidation is overly harmful to performance. Our work is the first to apply machine learning to this problem domain, and we report on our experience reaping the advantages of machine learning while navigating around its limitations. We demonstrate how the model can be used to improve performance fidelity and save energy for HPC workloads.

Shared state access conflicts are one of the greatest sources of error for fine grained parallelism in any domain. Notoriously hard to debug, these conflicts reduce reliability and increase development time. The standard task graph model dictates that tasks with potential conflicting accesses to shared state must be linked by a dependency, even if there is no explicit logical ordering on their execution. In cases where it is difficult to understand if such implicit dependencies exist, the programmer often creates more dependencies than needed, which results in constrained graphs with large monolithic tasks and limited parallelism.