Unix-like Operating Systems Research Articles

The LINUX Operating System: An Introduction

Linux is a Unix-like operating system for Intel 386/486/ Pentium based IBM-PCs and compatibles. The kernel of this operating system was written from scratch by Linus Torvalds and, although copyright by the author, may be freely distributed. A world-wide group of enthusiastic volunteers has collaborated in developing many aspects of Linux on the Internet. Linux can run the powerful set of compilers and programming tools (the 'GNU' corpus) of the Free Software Foundation, and XFree86, a port of the X Window System from MIT. Most capabilities associated with high performance workstations, such as networking, shared file systems, electronic mail, TEX, I*TE.X, etc. are freely available for Linux. It can thus transform cheap IBM-PC compatible machines into Unix workstations with considerable capabilities. The author explains how Linux may be obtained, installed and networked. He also describes some interesting applications for Linux that are freely available. One useful feature of Linux is its ability to coexist with other operating systems. Thus a user who has made an investment in DOS/ MS Windows software, may continue running these applications on his machine and install Linux on a separate partition on his existing hard disk. If needed, files from DOS/ MS Windows partitions can be accessed by Linux. The enormous consumer market for IBM-PC compatible machines continually drives down prices of CPU chips, memory, hard disks, CDROMs etc. Linux can convert such machines into powerful workstations that can be used for teaching, research and software development. For professionals who use Unix based workstations at work, Linux permits virtually identical working environments on their personal home machines. For cost conscious educational institutions (especially in developing nations), Linux can create world-class computing environments from cheap, easily maintained, PC clones. Finally, for university students, especially in science and engineering, Linux provides an essentially cost-free path away from DOS into the world of Unix and X Windows

NGSpop: A desktop software that supports population studies by identifying sequence variations from next-generation sequencing data.

Next-generation sequencing (NGS) is widely used in all areas of genetic research, such as genetic disease diagnosis and breeding, and it can produce massive amounts of data. The identification of sequence variants is an important step when processing large NGS datasets; however, currently, the process is complicated, repetitive, and requires concentration, which can be taxing on the researcher. Therefore, to support researchers who are not familiar enough with bioinformatics to identify sequence variations regularly from large datasets, we have developed a fully automated desktop software, NGSpop. NGSpop includes functionalities for all the variant calling and visualization procedures used when processing NGS data, such as quality control, mapping, filtering details, and variant calling. In the variant calling step, the user can select the GATK or DeepVariant algorithm for variant calling. These algorithms can be executed using pre-set pipelines and options or customized with the user-specified options. NGSpop is implemented using JavaFX (version 1.8) and can thus be run on Unix-like operating systems such as Ubuntu Linux (version 16.04, 18.0.4). Although several pipelines and visualization tools are available for NGS data analysis, most integrated environments do not support batch processes; thus, variant detection cannot be automated for population-level studies. The NGSpop software developed in this study has an easy-to-use interface and helps in rapid analysis of multiple NGS data from population studies. According to a benchmark test, it effectively reduced the carbon footprint in bioinformatics analysis by expending the least central processing unit heat and power. Additionally, this software makes it possible to use the GATK and DeepVariant algorithms more flexibly and efficiently than other programs by allowing users to choose between the algorithms. As a limitation, NGSpop currently supports only the sequencing reads in fastq format produced by the Illumina platform. NGSpop is freely available at https://sourceforge.net/projects/ngspop/.

Configurable Test System for RTOS of BAGET Family

The article describes a test system designed for verification of the real-time operating system BAGET Family for embedded systems, developed and used at the Scientific Research Institute for System Analysis of the Russian Academy of Sciences (SRISA RAS). This Unix-like operating system is based on the POSIX and ARINC-653 pro­gramming standards. Of course, there is specialized software for automating testing of Unix-like operating systems, for example, Avocado, LAVA, Linux Test Project, Linux Distribution Checker, Open POSIX Test Suite, UnixBench, etc. But the use of such ready-made software systems is not always convenient since they either contain only highly specialized test suites, support only specific hardware, or do not contain a flexible configuration system. Therefore, In SRISA RAS, its own original test system was developed. The task was to create a convenient testing tool for both software testers and programmers. Many years of experience in utilizing the test system has shown the effectiveness of its use to improve the quality of software products, reduction of time spent on testing and analysis of results, maximum automation of software testing process, speed up the process of developing new software versions, as well as simplify the process of debugging, finding and fixing errors by software developers.

Rate Control Optimization Algorithm of Ubiquitous Power Sensor Network Tester Based on Multimedia

With more and more video application scenarios and increasing complexity, the popularization of multimedia information and the urgent need to update wireless sensor networks have led to the emergence and development of wireless multimedia sensor networks. This paper focuses on the rate control optimization algorithm of multimedia-based ubiquitous power sensor network, which is mainly studied from three aspects: constructing algorithm verification platform based on multimedia technology, performance analysis, and optimization of rate control optimization algorithm based on multimedia technology. An algorithm verification platform is established based on multimedia technology. This article uses a scalable video coding method to design a client-driven scalable video transmission system. The simulation results show that the algorithm can effectively improve the video quality. The algorithm of rate control based on multimedia technology is proposed. A reliable multipath routing algorithm based on AODV is proposed. Based on the energy balance algorithm, the node-independent routing mechanism and link quality estimation model are introduced. An independent and reliable active/standby communication link to the node of the destination node is established. Linux, the full name of GNU/Linux, is a free-to-use and freely disseminated Unix-like operating system. It is a POSIX-based multiuser, multitasking, multithreaded, and multi-CPU operating system. With the development of the Internet, Linux has gained support from software enthusiasts, organizations, and companies all over the world. In addition to maintaining a strong momentum of development in servers, it has made considerable progress in personal computers and embedded systems. Under the Linux platform, a large number of tests are performed and the performance of the control code rate is analyzed. The so-called sensor network is a distributed intelligent network system that is composed of a large number of small sensor nodes with wireless communication and computing capabilities deployed in the active area through a self-organizing method that can autonomously complete designated tasks according to the environment. The distance between the nodes of the sensor network is very short, and the multihop wireless communication method is generally used for communication. The sensor network can run in an independent environment, or it can be connected to the Internet through a gateway so that users can access it remotely. It is concluded that ABR is the most suitable rate control algorithm for video transmission. According to the CQP experiment results, the QP value set in the improved ABR algorithm is at most 40; the security from the construction of the ubiquitous power sensor network to the final monitoring data collection and upload process is verified by simulating the hypothesis attacks and faults. It is proved that the construction of ubiquitous power sensor network can reduce the energy consumption and delay of monitoring data collection and verify the superiority of constructing ubiquitous power sensor network.

Defense and Attack Techniques Against File-Based TOCTOU Vulnerabilities: A Systematic Review

File-based <i>Time-of-Check to Time-of-Use</i> (TOCTOU) race conditions are a well-known type of security vulnerability. A wide variety of techniques have been proposed to detect, mitigate, avoid, and exploit these vulnerabilities over the past 35 years. However, despite these research efforts, TOCTOU vulnerabilities remain unsolved due to their non-deterministic nature and the particularities of the different filesystems involved in running vulnerable programs, especially in Unix-like operating system environments. In this paper, we present a systematic literature review on defense and attack techniques related to the file-based TOCTOU vulnerability. We apply a reproducible methodology to search, filter, and analyze the most relevant research proposals to define a global and understandable vision of existing solutions. The results of this analysis are finally used to discuss future research directions that can be explored to move towards a universal solution to this type of vulnerability.

Toward Long-Term and Archivable Reproducibility

Analysis pipelines commonly use high-level technologies that are popular when created, but are unlikely to be readable, executable, or sustainable in the long term. A set of criteria is introduced to address this problem: completeness (no execution requirement beyond a minimal Unix-like operating system, no administrator privileges, no network connection, and storage primarily in plain text); modular design; minimal complexity; scalability; verifiable inputs and outputs; version control; linking analysis with narrative; and free and open-source software. As a proof of concept, we introduce “Maneage” (managing data lineage), enabling cheap archiving, provenance extraction, and peer verification that has been tested in several research publications. We show that longevity is a realistic requirement that does not sacrifice immediate or short-term reproducibility. The caveats (with proposed solutions) are then discussed and we conclude with the benefits for the various stakeholders. This article is itself a Maneage'd project (project commit 313db0b). Appendices-Two comprehensive appendices that review the longevity of existing solutions are available as supplementary “Web extras,” which are available in the IEEE Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/MCSE.2021.3072860. Reproducibility-All products available in zenodo.4913277, the Git history of this paper's source is at git.maneage.org/paper-concept.git, which is also archived in Software Heritage Heritage: swh:1:dir:33fea87068c1612daf011f161b97787b9a0df39f. Clicking on the SWHIDs in the digital format will provide more “context” for same content.

HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS.

Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking. Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface. HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https://github.com/Angelovici-Lab/HAPPI.GWAS.git). Supplementary data are available at Bioinformatics online.

ЗАСТОСУВАННЯ ТЕХНОЛОГІЙ ВІРТУАЛІЗАЦІЇ UNIX-ПОДІБНИХ ОПЕРАЦІЙНИХ СИСТЕМ У ПІДГОТОВЦІ БАКАЛАВРІВ ІНФОРМАТИКИ

Despite the widespread use of virtualization technologies in education the problem of individual selection of virtualization tools for teaching certain courses, including teaching operating systems to Bachelors of Computer Science, remains scarcely studied. Research of operating systems teaching process to Bachelors of Computer Science found a range of issues in using virtualization technologies. These are as listed: hardware and software failures; low performance of virtualized operating systems; lack of adapted instructions; dependence on specific computer laboratories; unequal conditions of independent work with virtualized operating systems. Comparison of Bachelors of Computer Science scores in Operating Systems course which included studying Linux and Windows operating systems and also Fundamentals of Operating Systems Theory, resulted in general lower level of learning outcomes in Linux compared to the ones of the entire academic subject. A survey of Ukrainian teachers of Operating Systems course shows a number of differences in teaching process. It includes differences in teachers’ experience of using virtualization technologies, variety of virtualization technologies applied during the course, factors estimation for selecting virtualization tools. The article proposes the methodology of using unix-like operating systems virtualization technologies in professional training of Bachelors of Computer Science based on the variable approach to using mentioned technologies. The approach involves combining several virtualization tools in the frames of one course of Operating Systems to meet specific features of teaching the course as well as individual students’ needs and ensures hardware and software fault tolerance. Didactic model underlying the proposed methodology is described in the article. Experimental results on methodology effectiveness are provided.

SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles.

SummaryTo unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP, a Semantic Annotation Platform with Provenance. SAPP is designed as an infrastructure supporting FAIR de novo computational genomics but can also be used to process and analyze existing genome annotations. SAPP automatically predicts, tracks and stores structural and functional annotations and associated dataset- and element-wise provenance in a Linked Data format, thereby enabling information mining and retrieval with Semantic Web technologies. This greatly reduces the administrative burden of handling multiple analysis tools and versions thereof and facilitates multi-level large scale comparative analysis.Availability and implementationSAPP is written in JAVA and freely available at https://gitlab.com/sapp and runs on Unix-like operating systems. The documentation, examples and a tutorial are available at https://sapp.gitlab.io.

AM : Towards A Hardware Unix Accelerator for Many-Cores

This article advocates the use of new architectural features commonly found in many-cores to replace the machine model underlying Unix-like operating systems. We present a general Abstract Many-core Machine Model (AM $^3$ ), a proof-of-concept implementation and first evaluation results in the context of an emerging many-core, hardware multi-threaded architecture without support for interrupts. Our proposed approach makes it possible to reuse off-the-shelf multithreaded/multiprocess software on massively parallel architectures, without need to change code to use custom programming models like CUDA or OpenCL. Benefits include higher hardware utilization, higher performance and higher energy efficiency for workloads common to general-purpose platforms, such as in datacenters and clouds. The benefits also include simpler software control over the hardware platform, an enabling factor for the further evolution of parallel programming languages.

Unix Philosophy and the Real World: Control Software for Humanoid Robots

Robot software combines the challenges of general purpose and real-time software, requiring complex logic and bounded resource use. Physical safety, particularly for dynamic systems such as humanoid robots, depends on correct software. General purpose computation has converged on unix-like operating systems -- standardized as POSIX, the Portable Operating System Interface -- for devices from cellular phones to supercomputers. The modular, multi-process design typical of POSIX applications is effective for building complex and reliable software. Absent from POSIX, however, is an interproccess communication mechanism that prioritizes newer data as typically desired for control of physical systems. We address this need in the Ach communication library which provides suitable semantics and performance for real-time robot control. Although initially designed for humanoid robots, Ach has broader applicability to complex mechatronic devices -- humanoid and otherwise -- that require real-time coupling of sensors, control, planning, and actuation. The initial user space implementation of Ach was limited in the ability to receive data from multiple sources. We remove this limitation by implementing Ach as a Linux kernel module, enabling Ach's high-performance and latest-message-favored semantics within conventional POSIX communication pipelines. We discuss how these POSIX interfaces and design principles apply to robot software, and we present a case study using the Ach kernel module for communication on the Baxter robot.

PRay — A graphical user interface for interactive visualization and modification of rayinvr models

PRay is a graphical user interface for interactive displaying and editing of velocity models for seismic refraction. It is optimized for editing rayinvr models but can also be used as a dynamic viewer for ray tracing results from other software. The main features are the graphical editing of nodes and fast adjusting of the display (stations and phases). It can be extended by user-defined shell scripts and links to phase picking software. PRay is open source software written in the scripting language Perl, runs on Unix-like operating systems including Mac OS X and provides a version controlled source code repository for community development (https://sourceforge.net/projects/pray-plot-rayinvr/).

КРИТЕРІЇ ДОБОРУ ПРОГРАМНИХ ЗАСОБІВ ВІРТУАЛІЗАЦІЇ У НАВЧАННІUNIX-ПОДІБНИХ ОПЕРАЦІЙНИХ СИСТЕМ

Unix-like operating systems tend to be one of the top platforms as far as they illustrate most of modern operating systems basic principles and usually belong to free and open source software. For the above-mentioned reasons unix-like operating systems are widely used in education, particularly in teaching operating systems in undergraduate informatics education. The purpose of this study is to formulate the criteria for selecting virtualization software for applying of this software in teaching unix-like operating systems in undergraduate informatics education. Using the formulated criteria, the contrastive analysis of virtualization technologies,including type I, type II and hybrid hypervisors based on dynamic translation, paravirtualization and both of these virtualization methods, and virtual containers. Along with virtualization technologies, alternative virtualization-free ways of teaching unix-like operating systems(installing virtualized operating system as the only system on the computer and multi-booting) are also considered. According to the obtained results the contrastive analysis of virtualizationsoftware basing on preselected virtualization technologies is done. The attention is paid on both virtualized operating systems which are placed locally and systems which are accessed over local area network or the Internet.

Different approaches for the detection of SSH anomalous connections

The Secure Shell Protocol (SSH) is a well-known standard protocol, mainly used for remotely accessing shell accounts on Unix-like operating systems to perform administrative tasks. As a result, the SSH service has been an appealing target for attackers, aiming to guess root passwords performing dictionary attacks or to directly exploit the service itself. To identify such situations, this article addresses the detection of SSH anomalous connections from an intrusion detection perspective. The main idea is to compare several strategies and approaches for a better detection of SSH-based attacks. To test the classification performance of different classifiers and combinations of them, SSH data coming from a real-world honeynet are gathered and analysed. For comparison purposes and to draw conclusions about data collection, both packet-based and flow data are analysed. A wide range of classifiers and ensembles are applied to these data, as well as different validation schemes for better analysis of the obtained results. The high-rate classification results lead to positive conclusions about the identification of malicious SSH connections.

A Tracing Toolset for Embedded Linux Flash File Systems

NAND flash memory integration in the traditional I/O software stack of Unix-like operating systems (OS) was achieved without modifying most of the OS layers. In fact, one can dissociate two categories of flash memory devices: (1) those which intricacies are abstracted to the OS (e.g. SSDs, USB sticks), and (2) raw flash memory chips driven by a specific Flash File System (FFS) such as JFFS2 and UBIFS. In the latter case, the operating system I/O software stack low level layers (i.e. file system and driver) were upgraded while the higher levels (virtual file system and related buffers) were not. In order to optimize the system behavior in such a case, one must understand the interactions between the different I/O software management layers, and the performance impact of each layer for a given I/O workload. For this sake, we developed a tracing toolset allowing to understand the impact of each layer on the I/O request flow, for instance: caching, overheads, and fragmentation. The developed framework proved to be precious to apprehend the interactions between OS flash specific layers and traditional layers for a better system performance understanding.

C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison

We present C-Sibelia, a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies. C-Sibelia takes as input two FASTA files and produces: (1) a VCF file containing all identified single nucleotide variations and indels; (2) an XMFA file containing alignment information. The software also produces Circos diagrams visualizing high level genomic architecture for rearrangement analyses. C-Sibelia is a part of the Sibelia comparative genomics suite, which is freely available under the GNU GPL v.2 license at http://sourceforge.net/projects/sibelia-bio. C-Sibelia is compatible with Unix-like operating systems. A web-based version of the software is available at http://etool.me/software/csibelia.

C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.

We present C-Sibelia, a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies. C-Sibelia takes as input two FASTA files and produces: (1) a VCF file containing all identified single nucleotide variations and indels; (2) an XMFA file containing alignment information. The software also produces Circos diagrams visualizing high level genomic architecture for rearrangement analyses. C-Sibelia is a part of the Sibelia comparative genomics suite, which is freely available under the GNU GPL v.2 license at http://sourceforge.net/projects/sibelia-bio. C-Sibelia is compatible with Unix-like operating systems. A web-based version of the software is available at http://etool.me/software/csibelia.

Design of Mini Multi-Process Micro-Kernel Embedded OS on ARM

This paper describes the design and implementation of a mini multi-process micro-kernel embedded Unix-like operating system on ARM platform in technical details, including MMU and memory space mapping, init process, inter-process communication, process management, TTY and tiny shell, multi-level priority-queue schedule, and signaling. The mini OS is developed on Linux platform with GNU tool chain by the author of this paper. The architecture of the mini OS is analogous to that of Minix. Based on it, other operating system components such as file system, network management, and copy-on-write can be appended to form a full-featured embedded operating system. The mini OS can be used for both embedded system application development and related curriculum teaching.

A Multithreaded Modular Software Toolkit for Control of Complex Experiments

A multithreaded modular software toolkit has been developed for centralized monitoring and control of complex scientific experiments and instruments. The Modular Control Toolkit (MCT) supports Unix-like operating systems and provides a reusable framework for user-developed modules to share data, setup software interlocks, and utilize a dedicated thread for hardware communication.

SAWdoubler: A program for counting self-avoiding walks

This article presents SAWdoubler, a package for counting the total number ZN of self-avoiding walks (SAWs) on a regular lattice by the length-doubling method, of which the basic concept has been published previously by us. We discuss an algorithm for the creation of all SAWs of length N, efficient storage of these SAWs in a tree data structure, and an algorithm for the computation of correction terms to the count Z2N for SAWs of double length, removing all combinations of two intersecting single-length SAWs.We present an efficient numbering of the lattice sites that enables exploitation of symmetry and leads to a smaller tree data structure; this numbering is by increasing Euclidean distance from the origin of the lattice. Furthermore, we show how the computation can be parallelised by distributing the iterations of the main loop of the algorithm over the cores of a multicore architecture. Experimental results on the 3D cubic lattice demonstrate that Z28 can be computed on a dual-core PC in only 1 h and 40 min, with a speedup of 1.56 compared to the single-core computation and with a gain by using symmetry of a factor of 26. We present results for memory use and show how the computation is made to fit in 4 GB RAM. It is easy to extend the SAWdoubler software to other lattices; it is publicly available under the GNU LGPL license. Program summaryProgram title: SAWdoublerCatalogue identifier: AEOB_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOB_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU Lesser General Public LicenceNo. of lines in distributed program, including test data, etc.: 2101No. of bytes in distributed program, including test data, etc.: 19816Distribution format: tar.gzProgramming language: C.Computer: Any computer with a UNIX-like operating system and a C compiler. For large problems, use is made of specific 128-bit integer arithmetic provided by the gcc compiler.Operating system: Any UNIX-like system; developed under Linux and Mac OS 10.Has the code been vectorised or parallelised?: Yes. A parallel version of the code is available in the “Extras” directory of the distribution file.RAM: Problem dependent (2 GB for counting SAWs of length 28 on the 3D cubic lattice)Classification: 16.11.Nature of problem: Computing the number of self-avoiding walks of a given length on a given lattice.Solution method: Length-doubling.Restrictions: The length of the walk must be even. Lattice is 3D simple cubic.Additional comments: The lattice can be replaced by other lattices, such as BCC, FCC, or a 2D square lattice.Running time: Problem dependent (2.5 h using one processor core for length 28 on the 3D cubic lattice).