Operator, number please : mediating access to shared resources for efficiency and isolation

The performance density of modern hardware has forced the sharing of hardware resources across applications for better utilization and efficiency. Shared infrastructure, however, weakens isolation and risks interference, which can result in degraded performance and security breaches. This thesis explores the tension between isolation and sharing with three prototype systems: Xoar, Plastic, and Decibel. All three of these systems demonstrate the value of software mediation in providing isolation on shared hardware without sacrificing either hardware resource utilization or the performance of the underlying devices. Xoar, Plastic, and Decibel provide isolation for different hardware resources: Xoar strengthens isolation between virtual machines, thereby allowing underutilized processors to be shared; Plastic transparently mitigates poor cache utilization and the performance artifacts caused by insufficient cache line isolation across cores; and Decibel provides isolation in shared non-volatile storage and guarantees throughput, even in the face of competing workloads.Science, Faculty ofComputer Science, Department ofGraduat

Breaking up is hard to do : security and functionality in a commodity hypervisor

Virtualization platforms have grown with an increasing demand for new technologies, with the modern enterprise-ready virtualization platform being a complex, feature-rich piece of software. Despite the small size of hypervisors, the trusted computing base (TCB) of most enterprise platforms is larger than that of most monolithic commodity operating systems. Several key components of the Xen platform reside in a special, highly-privileged virtual machine or the “Control VM”. We present Xoar, a modified version of the Xen platform that retrofits the modularity and isolation principles championed by microkernels onto a mature virtualization platform. Xoar divides the large, shared control VM of Xen’s TCB into a set of independent, isolated, single purpose components called shards. Shards improve security in several ways: components are restricted to the least privilege necessary for functioning and any sharing between guest VMs is explicitly configurable and auditable in tune with the desired risk exposure policies. Microrebooting components at configurable frequencies reduces the temporal attack surface. Our approach does not require any existing functionality to be sacrificed and allows components to be reused rather than rewritten from scratch. The low performance overhead leads us to believe that Xoar is viable alternative for deployment in enterprise environments.Science, Faculty ofComputer Science, Department ofGraduat

Massive haplotypes underlie ecotypic differentiation in sunflowers.

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation

Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments 1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations 2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation. Local adaptation is common in species that experience different environments across their range, often resulting in the formation of ecotypes-ecological races with distinct morphological and/or physiological characteristics that provide an environment-specific fitness advantage. Despite the prevalence of ecotypic differentiation, much remains to be understood about the genetic basis and evolutionary mechanisms that underlie its establishment and maintenance. In particular , a longstanding evolutionary question-dating to criticisms of Darwin's theories by his contemporaries 4-concerns how such ecological divergence can occur when challenged by hybridization with non-adapted populations 2. Local adaptation typically requires alleles at multiple loci that contribute to increased fitness in the same environment ; however, different ecotypes are often geographically close and interfertile, and hybridization between them should break up adaptive allelic combinations 3. To better understand the genetic basis of local adaptation and ecotypic differentiation, we conducted an in-depth study of genetic, phenotypic and environmental variation in three annual sunflower species, each of which includes multiple reproductively compatible ecotypes. Two species (H. annuus and H. petiolaris) have broad, overlapping distributions across North America. Helianthus annuus, the common sunflower, is generally found on mesic soils, but can grow in a variety of disturbed or extreme habitats, including semi-desert or frequently flooded areas. An especially well-characterized ecotype (formally known as H. annuus subsp. texanus) is adapted to the higher temperatures and herbivore pressures in Texas (USA) 5. Helianthus petiolaris, the prairie sunflower, prefers sandier soils; ecotypes of this species are adapted to sand sheets and dunes 6. The third species-H. argophyllus, the silverleaf sunflower-is endemic to southern Texas and includes both an early-flowering, coastal-island ecotype and a late-flowering inland ecotype 7. Population structure of wild sunflowers In a common garden experiment, we grew 10 plants from each of 151 populations of the 3 species, selected from across their native range (Fig. 1a); for each of these populations, we collected corresponding soil samples. We generated extensive records of developmental and morphological traits, and resequenced the genomes of 1,401 individual plants. We resequenced an additional 105 H. annuus plants to fill gaps in geographical coverage, as well as 12 outgroup taxa (Supplementary Table 1). Sunflower genomes are relatively large (H. annuus, 3.5 Gbp; https://doi