Microarchitecture Choices and Tradeoffs for Maximizing Processing Efficiency.

This thesis is concerned with hardware approaches for maximizing the number of independent instructions in the execution core and thereby maximizing the processing efficiency for a given amount of compute bandwidth. Compute bandwidth is the number of parallel execution units multiplied by the pipelining of those units in the processor. Keeping those computing elements busy is key to maximize processing efficiency and therefore power efficiency. While some applications have many independent instructions that can be issued in parallel without inefficiencies due to branch behavior, cache behavior, or instruction dependencies, most applications have limited parallelism and plenty of stalling conditions. This thesis presents two approaches to this problem, which in combination greatly increases the efficiency of the processor utilization of resources. The first approach addresses the problem of small basic blocks that arise when code has frequent branches. We introduce algorithms and mechanisms to predict multiple branches simultaneously and to fetch multiple non-continuous basic blocks every cycle along a predicted branch path. This makes what was previously an inherently serial process into a parallelized instruction fetch approach. For integer applications, the result is an increase in useful instruction fetch capacity of 40% when two basic blocks are fetched per cycle and 63% for three blocks per cycle. For floating point benchmarks, the associated improvement is 27% and 59%. The second approach addresses increasing the number of independent instructions to the execution core through simultaneous multi-threading (SMT). We compare to another multithreading approach, Switch-on-Event multithreading, and show that SMT is far superior. Intel Pentium 4 SMT microarchitecture algorithms are analyzed, and we look at the impact of SMT on power efficiency of the Pentium 4 Processor. A new metric, the SMT Energy Benefit is defined. Not only do we show that the SMT Energy Benefit for a given workload with SMT can be quite significant, we also generalize the results and build a model for what other future processors’ SMT Energy Benefit would be. We conclude that while SMT will continue to be an energy-efficient feature, as processors get more energy-efficient in general the relative SMT Energy Benefit may be reduced.Ph.D.Computer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/61740/1/dtmarr_1.pd

Testing and characterization of the TESS CCDs

The Transiting Exoplanet Survey Satellite (TESS) is an Explorer-class mission dedicated to finding planets around bright, nearby stars so that more detailed follow-up studies can be done. TESS is due to launch in 2017 and careful characterization of the detectors will need to be completed on ground before then to ensure that the cameras will be within their photometric requirement of 60ppm/hr. TESS will fly MITLincoln Laboratories CCID-80s as the main scientific detector for its four cameras. They are 100μm deep depletion devices which have low dark current noise levels and can operate at low light levels at room temperature. They also each have a frame store region, which reduces smearing during readout and allows for near continuous integration. This paper describes the hardware and methodology that were developed for testing and characterizing individual CCID-80s. A dark system with no stimuli was used to measure the dark current. Fe 55 and Cd 109 X-ray sources were used to establish gain at low signal levels and its temperature dependence. An LED system that generates a programmable series of pulses was used in conjunction with an integrating sphere to measure pixel response non-uniformity (PRNU) and gain at higher signal levels. The same LED system was used with a pinhole system to evaluate the linearity and charge conservation capability of the CCID-80s.United States. National Aeronautics and Space Administration (contract number NNG14FC03C

Sporangiospore Size Dimorphism Is Linked to Virulence of Mucor circinelloides

Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (−) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (−) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have occurred during speciation of the M. circinelloides complex

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications

Increasing the Instruction Fetch Rate via Multiple Branch Prediction and a Branch Address Cache

High performance computer implementation today is increasingly directed toward parallelism in the hardware. Superscalar machines, where the hardware can issue more than one instruction each cycle, are being adopted by more implementations. As the trend toward wider issue rates continues, so too must the ability to fetch more instructions each cycle. Although compilers can improve the situation by increasing the size of basic blocks, hardware mechanisms to fetch multiple possibly non-consecutive basic blocks are also needed. Viable mechanisms for fetching multiple non-consecutive basic blocks have not been previously investigated. We present a mechanism for predicting multiple branches and fetching multiple non-consecutive basic blocks each cycle which is both viable and effective. We measured the effectiveness of the mechanism in terms of the IPC f, the number of instructions fetched per clock for a machine front-end. For one, two, and three basic blocks, the IPC f of integer benchmark..