Fast Byte Copying: A Re-Evaluation of the Opportunities for Optimization

High-performance byte copying is important for many operating systems because it is the principle method used for transferring data between kernel and user protection domains. For example, byte copying is commonly used for transferring data from kernel buffers to user buffers during file system read and IPC recv calls and to kernel buffers from user buffers during \u27Write and-send calls. Because of its impact on overall system performance, commercial operating systems tend to employ many specialized byte copy routines, each one optimized for a different circumstance. This paper revisits the opportunities for optimizing byte copy performance by discussing a series of experiments run under HP-UX 9.03 on a range of Hewlett-Packard PA-RISC processors. First, we compare the performance improvements that result from several existing byte copy optimizations. Then we show that byte copy performance is dominated by cache effects that arise when source and target addresses overlap. Finally, we discuss the opportunities and difficulties associated with choosing appropriate source and target addresses to optimize byte copy performance

Fast Byte Copying: A Re-Evaluation of the Opportunities for Optimization

High-performance byte copying is important for many operating systems because it is the principle method used for transferring data between kernel and user protection domains. For example, byte copying is commonly used for transferring data from kernel buffers to user buffers during file system read and IPC recv calls and to kernel buffers from user buffers during \u27Write and-send calls. Because of its impact on overall system performance, commercial operating systems tend to employ many specialized byte copy routines, each one optimized for a different circumstance. This paper revisits the opportunities for optimizing byte copy performance by discussing a series of experiments run under HP-UX 9.03 on a range of Hewlett-Packard PA-RISC processors. First, we compare the performance improvements that result from several existing byte copy optimizations. Then we show that byte copy performance is dominated by cache effects that arise when source and target addresses overlap. Finally, we discuss the opportunities and difficulties associated with choosing appropriate source and target addresses to optimize byte copy performance

A Technique for Visualizing Software Architectures

Software architecture appeared in the early 1990s as a distinct discipline within software engineering. Models based on software architecture attempt to reduce the complexity of software by providing relatively coarse-grained structures for representing different aspects of software development. A software architecture typically consists of various components and connections arranged in a specific topology. Elements of the topology can serve as abstractions on (for example) modules, objects, protocols or interfaces. The meaning of the topology depends on viewpoint. Software architectures\u27 can be described using an architecture description language (ADL). The key goals of ADLs are to communicate alternate designs to the different individuals involved in software development (such individuals are referred to as stakeholders ), to detect reusable structures, and to record design decisions. A major problem in software architecture has been the difficulty of creating different representations of an architecture to accommodate differing viewpoints of stakeholders. Ideally, different viewpoints would be conveyed in a way that is both comprehensive enough for specialists but consistent enough for generalists. The representation problem has been one of reconciling and integrating different viewpoints. This dissertation provided a solution to the representation problem by creating a tool for three-dimensional visualization of software architectures using the Virtual Reality Modeling Language (VRML). Different architectural viewpoints were first defined in an ADL called the Visually Translatable Architecture Description Language (VT ADL). When VT ADL was translated into VRML, software architectures were embodied within three-dimensional worlds through which stakeholders may navigate. Each viewpoint was a separate VRML world. A viewpoint could be related to other viewpoints, representing different facets of software architectures, to reflect different stakeholder requirements. Traceability from design to requirements was possible through VRML hyperlinks from the visualized architecture. The goal of the dissertation was to develop a prototype for demonstrating the visualization technique. Based on the successful results of two visualization case studies, we concluded that the goal was achieved. Refinement of the prototype into a polished visualization tool was recommended. In future research, the refined version should be used for realistic evaluation of the technique in an actual software development environment

Porting Chorus to the PA-RISC: Building, Debugging, Testing and Validation

This document is part of a series of reports describing the design decisions made in porting the Chorus Operating System to the Hewlett-Packard 9000 Series 800 workstation. This document describes the environment for building the Chorus kernel, the various kernel tests, and the debugging environment used for porting the Chorus operating system to the HP PA-RISC. The information contained in this paper will be of interest to people who wish to: • Use the PA-Chorus kernel for development and/or modification, • Know about the build environment for Chorus kernel on PA-RISC, • Know about the PA-Chorus approach to debugging, • Know about the Chorus kernel tests, their buHd environment, and the modifications made to the kernel tests to port them to PA-ruse. The aim of the document is to give a detailed overview of the various items mentioned above. The document does not delve into the specific tails of configuration like the values for various global macros and so on. For an in-depth understanding, one would have to study the sources. For the purposes of this document the word kernel and nucleus mean the same and will be used interchangeably

Porting the Chorus Supervisor and Related Low-Level Functions to the PA-RISC

This document is part of a series of reports describing the design decisions made in porting the Chorus Operating System to the Hewlett-Packard 9000 Series 800 workstation. The Supervisor is the name given by Chorus to a collection of low-level functions that are machine dependent and have to be implemented when Chorus is ported from one machine to another. The Supervisor is responsible for interrupt, trap and exception handling, managing low-level thread initialization, context switch, kernel initialization, managing simple devices (timer and console) and offering a low-level debugger. This document describes the port of the Supervisor and related low-level functions. The informacion contained in this paper will be of interest, to people who wish to understand: • The main characteristics of Chorus and PA-RISC architecture that are useful in understanding the port of the Chorus Supervisor. • The requirements and implementation of the Chorus Supervisor. • The requirements and implementation of Chorus page fault interface • The requirements and implementation Chorus System call interface • The requirements and implementation of \u27mutex\u27 interface which is a part of the Chorus system call interface for efficient thread synchronization. • Reasons for the modifications to the portable layers of Chorus kernel to implement the above requirements. A summary of the modifications is also presented. It is useful to read the port overview before reading this document. It is also a good idea to have the Precision Architecture and Instruction Set Reference Manual and Chorus v3.3 implementation guide on hand although it is not absolutely necessary

Customizable Operating Systems

A customizable operating system is one that can adapt to improve its functionality or performance. The need for customizable and application-specific operating systems has been recognized for many years, but they have yet to appear in the commercial market. This paper explores the notion of operating system customizability and examines the limits of existing approaches. The paper begins by surveying system structuring approaches for the safe and efficient execution of customizable operating systems. Then it discusses the burden that existing approaches impose on application software, and explores techniques for reducing this burden. Finally, support for customizability in the Synthetix project is described and illustrated through two examples: a dynamically specialized file system read call, and an adaptive Internet-based MPEG video player

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Background Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and Lactobacillus abundance and between Lactobacillus abundance and BP. Methods and Results We studied a population sample of 6953 Finns aged 25 to 74 years (mean age, 49.212.9 years; 54.9% women). The participants underwent a health examination, which included BP measurement, stool collection, and 24-hour urine sampling (N=829). Gut microbiota was analyzed using shallow shotgun metagenome sequencing. In age- and sex-adjusted models, the alpha (within-sample) and beta (between-sample) diversities of taxonomic composition were strongly related to BP indexes (P diversity was only associated with diastolic BP (P=0.032). However, we observed significant, mainly positive, associations between BP indexes and 45 microbial genera (P Conclusions Although the associations between overall gut taxonomic composition and BP are weak, individuals with hypertension demonstrate changes in several genera. We demonstrate strong negative associations of certain Lactobacillus species with sodium intake and BP, highlighting the need for experimental studies.Peer reviewe

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting

The gut microbiome has shown promise as a predictive biomarker for various diseases. However, the potential of gut microbiota for prospective risk prediction of liver disease has not been assessed. Here, we utilized shallow shotgun metagenomic sequencing of a large population-based cohort (N > 7,000) with -15 years of follow-up in combination with machine learning to investigate the predictive capacity of gut microbial predictors individually and in conjunction with conventional risk factors for incident liver disease. Separately, conventional and microbial factors showed comparable predictive capacity. However, microbiome augmentation of conventional risk factors using machine learning significantly improved the performance. Similarly, disease free survival analysis showed significantly improved stratification using microbiome-augmented models. Investigation of predictive microbial signatures revealed previously unknown taxa for liver disease, as well as those previously associated with hepatic function and disease. This study supports the potential clinical validity of gut metagenomic sequencing to complement conventional risk factors for prediction of liver diseases.Peer reviewe

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

Background:Several small-scale animal studies have suggested that gut microbiota and blood pressure (BP) are linked. However, results from human studies remain scarce and conflicting. We wanted to elucidate the multivariable-adjusted association between gut metagenome and BP in a large, representative, well-phenotyped population sample. We performed a focused analysis to examine the previously reported inverse associations between sodium intake and Lactobacillus abundance and between Lactobacillus abundance and BP.Methods and Results:We studied a population sample of 6953 Finns aged 25 to 74 years (mean age, 49.212.9 years; 54.9% women). The participants underwent a health examination, which included BP measurement, stool collection, and 24-hour urine sampling (N=829). Gut microbiota was analyzed using shallow shotgun metagenome sequencing. In age- and sex-adjusted models, the alpha (within-sample) and beta (between-sample) diversities of taxonomic composition were strongly related to BP indexes (PConclusions:Although the associations between overall gut taxonomic composition and BP are weak, individuals with hypertension demonstrate changes in several genera. We demonstrate strong negative associations of certain Lactobacillus species with sodium intake and BP, highlighting the need for experimental studies.</div