Linux Operating System Research Articles

Data Acquisition Software for CBM-TOF Super Module Quality Control

The time-of-flight (TOF) system in the Compressed Baryonic Matter (CBM) experiment is composed of super modules based on multi-gap Resistive Plate Chambers (MRPC) for high-denseness, high-resolution time measurement. In order to evaluate the quality of detectors during the mass production, a distributed data readout system is developed to meet with the high data rate of 6.4Gbps, and a related data acquisition (DAQ) software is implemented under Linux operating system to test and verify the feasibility of the distributed data readout method. In this paper, the DAQ software is focused on data collection, event building, status monitoring and system controlling. Laboratory tests confirmed the function of the DAQ software and show that the overall data transfer rate of a single data transmission path can reach up to about 550Mbps which already meet the demand.

Librarians’ perceptions about adoption and uses of the Koha integrated library software in Punjab, Pakistan

Purpose This study aims to find out the reasons of adopting Koha integrated library software, discovers the problems faced by librarians during its implementation, and gets the perceptions of librarians about the performances of Koha in Punjab, a province of Pakistan. Design/methodology/approach Survey method was used to collect the data through questionnaire from the purposefully selected sample (N = 66) of university librarians of Punjab, a province of Pakistan. Findings The librarians adopted Koha due to the availability of Web online public access catalog (OPAC), provision of MARC21 standards for cataloging and its free availability. During implementation, the librarians were faced with the problems of lack of technical skills, lack of knowledge about the Linux operating system, shortage of skilled manpower, slow internet speeds and approval from their organization. They highly rated the performance of the cataloguing, circulation, patron and OPAC modules of Koha. Originality/value This research provides a brief picture of librarians’ perceptions about Koha adoption and satisfaction levels. The findings highlighted the issues and problems faced during the implementation of Koha. This study will be helpful for librarians in the selection, implementation and usage of the Koha software in their libraries.

About Detection of Code Reuse Attacks

When exploiting software vulnerabilities such as buffer overflows, code reuse techniques are often used today. Such attacks allow you to bypass the protection against the execution of code in the stack, which is implemented at the software and hardware level in modern information systems. At the heart of these attacks lies the detection, in the vulnerable program of suitable areas, of executable code — gadgets — and chaining these gadgets into chains. The article proposes a way to protect applications from attacks that use code reuse. For this purpose, features that distinguish the chains of gadgets from typical chains of legal basic blocks of the program are highlighted. The appearance of an atypical chain of the base block during program execution may indicate the execution of a malicious code. An algorithm for identifying atypical chains has been developed. A feature of the algorithm is that it is focused on identifying all currently known techniques of re-execution of the code. The developed algorithm is based on a modified QEMU virtualization system. One of the hallmarks of the chain of gadgets is the execution at the end of the chain of instructions of the processor used to call the function of the operating system. For the Linux operating system based on the x86/64 architecture, experiments have been conducted showing the importance of this feature in detecting the execution of the malicious code.

Clock Skew Based Computer Identification on Different Types of Area Networks

The increase of client devices along with the growth of internet access currently affects to security threats at the user's identity. Identifiers that commonly used today, such as SSID, IP address, MAC address, cookies, and session IDs have a weakness, which is easy to duplicate. Computer identification based on clock skew is an identification method that is not easily duplicated because it is based on the hardware characteristics of the device. Clock skew is the deviation of the clock to the true time which causes each clock to run at a slightly different speed. This study aims to determine the effect of network types to the clock skew stability as a reliable device identification method. This research was conducted on five client computers which running windows and linux operating systems. The measurement was conducted based on three different types of area networks, i.e., LAN, MAN, and WAN. The skew estimation was done using two linear methods i.e., linear programming and linear regression. The measurement results show that the most stable clock skew is found on the LAN measurement because it meets the threshold tolerance limit i.e., ±1 ppm. Skew estimation using linear programming method has better accuracy than linear regression method.

Validator – a Web-Based Interactive Tool for Validation of Ocean Models at Oceanographic Stations

Numerical ocean models, like other geoscientific models, are a strongly simplified representation of real oceans. They are used as tools to answer research questions about the real-world systems. Therefore, their thorough validation is essential to ensure that the conclusions drawn from the model experiment are valid in reality. We demonstrate a software which allows an interactive model validation through a web interface based on the R Shiny framework. At pre-defined stations, different kinds of plots can be rendered within a few seconds, according to the user’s choice, allowing a live validation of different model parameters even in model simulations which are still running. This makes it different from validation approaches which generate a pre-defined set of plots after the calculations have finished and make it particularly useful for model tuning purposes. Observation data can be read in from text files or can be extracted from a database. Once set up, the validation tool requires no technical skills to use. It can be used for single- or multi-model validation and allows saving the generated plots as high-resolution images suitable for use in scientific publications. A Linux operating system is required for the Validator app, but via a virtual machine, the software can run on Windows or MacOS hosts as well. A Dockerfile is supplied which allows to test the software with example data without installation. Funding statement: This software was developed at the Leibniz Institute for Baltic Sea Research Warnemunde (IOW) on institutional funding.

Towards comprehensive dependability-driven resource use and message log-analysis for HPC systems diagnosis

Failure analysis plays an important role in the reliability of data centers and high-performance computing (HPC) systems. Recent work have shown that both resource use data and failure logs can, separately and together, be used to detect system failure-inducing errors and diagnose system failures; the result of error propagation and (unsuccessful) execution of error recovery mechanisms. For more accurate and detailed failure diagnosis, knowledge of error propagation patterns and unsuccessful error recovery is important. To improve system reliability, knowledge of recovery protocols deployment is important. This paper describes and demonstrates application of a new diagnostics framework (CORRMEXT). CORRMEXT analyzes and reports error propagation patterns and degrees of success and failure of error recovery protocols. The steps in the framework are correlations of resource use metrics and error messages, and identification of the earliest times of change of system behaviour. The framework is illustrated with analyses of resource use data and message logs for three HPC systems operated by the Texas Advanced Computing Center (TACC). The illustrations are focused on groups of resource use counters and groups of errors; they reveal many interesting insights into patterns of: (i) network data and software errors, (ii) Lustre file-system and Linux operating system process errors, and (iii) memory and storage errors. We also confirm that: (i) correlations of resource use and errors can only be identified by applying different correlation algorithms, and (ii) the earliest times of change in system behaviour can only be identified by analyzing both the correlated resource use counters and correlated errors. We believe CORRMEXT is the first tool that have diagnosed error propagation paths and error recovery attempts on three different HPC systems. CORRMEXT will be put on the public domain to support systems administrators in diagnosing HPC system failures, on August 2018.

Improving Real Time Performance of Linux System Using RT-Linux

The Linux operating system is a general-purpose operating system, and its serious lack of real-time performance limits its development in the embedded field. This paper analyses the current development status of Linux system, and uses RT-Linux patch to improve its real time activity. In order to test the real-time differences between RT-Linux and Linux, the RT-test test tool is employed. The experimental results show that the Linux kernel optimized by RT-Linux patch consumes less delay than the Linux kernel in multi-thread scheduling, which fully verify the real-time optimization of RT-Linux patches.

Implementasi Voip Server Berbasis IPV6 Dengan Raspberry PI

Voice over Internet Protocol (VoIP) is a telecommunications technology that is able to pass the communication service in Internet Protocol networks so as to allow communicating between users in an IP network. However VoIP technology still has weakness in the Quality of Service (QoS). VOPI weaknesses is affected by the selection of the physical servers used. In this research, VoIP is configured on Linux operating system with Asterisk as VoIP application server and integrated on a Raspberry Pi by using wired and wireless network as the transmission medium. Because of depletion of IPv4 capacity that can be used on the network, it needs to be applied to VoIP system using the IPv6 network protocol with supports devices. The test results by using a wired transmission medium that has obtained are the average delay is 117.851 ms, jitter is 5.796 ms, packet loss is 0.38%, throughput is 962.861 kbps, 8.33% of CPU usage and 59.33% of memory usage. The analysis shows that the wired transmission media is better than the wireless transmission media and wireless-wired.

ED-255EK Embeded Education Platform Sebagai Modul Praktikum Embeded System Dengan Robot Arm Module Dan Voice Module

Abstract— Literally embedded systems are defined as equipment that computes a particular job. Embedded Linux System was also developed as a means of education, one of which is ED-255EK Embedded Education Platform, designed to be very practical and consume very low power. ED-255EK is also equipped with a PXA255 processor that is compatible with ARM version 5TE ISA, so it can be used to carry out various kinds of lab work or experiments on embedded systems. The working principle of this tool begins with the configuration of data communication between Fedora Linux and ED-255EK. When the communication goes well, it is downloaded by the ED-255EK system to a laptop or computer that has been installed with the Fedora 9.0 Linux operating system. To take advantage of the ED-255FPGA module, driver module installation is required first, after which the application program is installed. Laptops or computers that have installed the Fedora 9.0 Linux operating system will act as input and output programs making it easier to monitor each module that is being run. The module used is the ARM 1923 Robot Module and Voice Module ED4321.

KVEFS: Encrypted File System Based on Distributed Key-Value Stores and FUSE

File System is an important component of a secure operating system. The need to build data protection systems is extremely important in open source operating systems, high mobility hardware systems, and miniaturization of storage devices that make systems available. It is clear that the value of the data is much larger than the value of the storage device. Computers access protection mechanism does not work if the thief retrieves the hard drive from the computer and reads data from it on another computer. Encrypted File System (EFS) is a secure level of operating system kernel. EFS uses cryptography to encrypt or decrypt files and folders when they are being saved or retrieved from a hard disk. EFS is often integrated transparently in operating system There are many encrypted filesystems commonly used in Linux operating systems. However, they have some limitations, which are the inability to hide the structure of the file system. This is a shortcoming targeted by the attacker, who will try to decrypt a file to find the key and then decrypt the entire file system. In this paper, we propose a new architecture of EFS called KVEFS which is based on cryptographic algorithms, FUSE library and key-value store. Our method makes EFS portable and flexible; Kernel size will not increase in Operating System.

Raspberry Pi-Based Low-Cost Connected Device for Assessing Road Surface Friction

Measuring friction between the tyres of a vehicle and the road, often and on as many locations on the road network as possible, can be a valuable tool for ensuring traffic safety. Rather than by using specialised equipment for sequential measurements, this can be achieved by using several low-cost measuring devices on vehicles that travel on the road network as part of their daily assignments. The presented work proves the hypothesis that a low cost measuring device can be built and can provide measurement results comparable to those obtained from expensive specialised measuring devices. As a proof of concept, two copies of a prototype device, based on the Raspberry Pi single-board computer, have been developed, built and tested. They use accelerometers to measure vehicle braking deceleration and include a global positioning receiver for obtaining the geolocation of each test. They run custom-developed data acquisition software on the Linux operating system and provide automatic measurement data transfer to a server. The operation is controlled by an intuitive user interface consisting of two illuminated physical pushbuttons. The results show that for braking tests and friction coefficient measurements the developed prototypes compare favourably to a widely used professional vehicle performance computer.

Design of Virtual Instrument Interface Based on Embedded Linux+QT

This paper mainly summarizes the technical scheme of replacing traditional pointer automotive instrument with full liquid crystal by choosing hardware platform and software platform. Emphasis is laid on the application of QT graphical development environment in embedded Linux operating system. The full liquid crystal can solve the display and instruction of various monitoring information on automotive instrument. Qt Quick tool is used in the dynamic pointer design of full liquid crystal instrument, and how to use QML (descriptive scripting language) and C++ language mixed programming technology. A practical and mature instrument system can be designed for users, and a set of reasonable construction ideas and methods can be provided.

RTHybrid: A Standardized and Open-Source Real-Time Software Model Library for Experimental Neuroscience.

Closed-loop technologies provide novel ways of online observation, control and bidirectional interaction with the nervous system, which help to study complex non-linear and partially observable neural dynamics. These protocols are often difficult to implement due to the temporal precision required when interacting with biological components, which in many cases can only be achieved using real-time technology. In this paper we introduce RTHybrid (www.github.com/GNB-UAM/RTHybrid), a free and open-source software that includes a neuron and synapse model library to build hybrid circuits with living neurons in a wide variety of experimental contexts. In an effort to encourage the standardization of real-time software technology in neuroscience research, we compared different open-source real-time operating system patches, RTAI, Xenomai 3 and Preempt-RT, according to their performance and usability. RTHybrid has been developed to run over Linux operating systems supporting both Xenomai 3 and Preempt-RT real-time patches, and thus allowing an easy implementation in any laboratory. We report a set of validation tests and latency benchmarks for the construction of hybrid circuits using this library. With this work we want to promote the dissemination of standardized, user-friendly and open-source software tools developed for open- and closed-loop experimental neuroscience.

ANALISIS DAN IMPLEMENTASI JARINGAN THIN CLIENT MENGGUNAKAN LINUX TERMINAL SERVER PROJECT PADA JARINGAN LAN

The development of computer technology both in software and hardware is very fast. These two aspects are interrelated with each other and cannot be separated. LTSP, Linux Terminal Server Project is a project started by James A McQuillan as a diskless networking project based on the GNU/Linux operating system. Called a diskless network, because the client is not equipped with a hard disk. All application software and operating systems needed by the client computer are served and managed by the server computer. In this design, a laptop with an Intel processor is used as a server and a PC as a client. LTSP will be integrated into the Linux operating system ubuntu 16.04, and as a provider of diskless thin client service platforms is LTSP (Linux Terminal Server Project). With LTSP, the construction of a diskless network is expected to be more efficient. Diskless network technology is one solution that can be applied in dealing with the problem of investing in computer technology hardware with predetermined specifications.

Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

BackgroundRecent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes.ResultsWe present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. Gen2Epi is a command-line tool integrating third-party software and tailored specifically for N. gonorrhoeae. For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. The assemblies were generated using raw as well as trimmed short reads. The median genome coverage of full-length scaffolds and “N” statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Molecular antimicrobial resistant (AMR) determinants identified by Gen2Epi reproduced information for the 1484 samples as previously reported, including NG-MLST, NG-MAST, and NG-STAR molecular sequence types.ConclusionsGen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. Gen2Epi is publicly available under “CC BY-NC 2.0 CA” Creative Commons licensing as a VirtualBox image containing the constituent software components running on the LINUX operating system (CentOS 7). The image and associated documentation are available via anonymous FTP at ftp://www.cs.usask.ca/pub/combi or ftp://ftp.cs.usask.ca/pub/combi

EasyCodeML: A visual tool for analysis of selection using CodeML.

The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user‐friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication‐quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch‐site, and clade models of selection. The program allows comparison of major codon‐based models for analyses of selection. EasyCodeML is a stand‐alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML.

Secure execution environment for critical applications in embedded systems based on Elbrus family computing facilities

The problems of security computing are becoming increasingly relevant in connection with the integration of systems into a unified global Internet. Elbrus secure computing technology allows protecting the system from the internal program errors as well as external threats. The article describes the hardware and software components of a secure execution environment for critical applications in embedded systems based on computing means of the Elbrus family. The authors describe the basis of the Elbrus secure computing concept - the idea of a descriptor and external tags. They consider the revision of the main parts of the C language library and the kernel of the Linux operating system necessary for the implementation of this environment. The study investigates the issue of passing parameters to system calls from applications running in a secure environment. For such applications, the authors consider the process of dynamic binding of the modules loaded into memory. The method for detecting cases of the use of hung links due to the use of descriptors and external tags is presented in relation to the mechanism of orders and the release of dynamic memory. The authors suggest the container virtualization technology to detect memory leaks in a safe execution environment.

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

BackgroundWith the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software for detecting footprints of WGDs has been restricted to a well-assembled genome. However, the massive poor quality genomes and the more accessible transcriptomes have been largely ignored, and in theoretically they are also likely to contribute to detect WGD using dS based method. Here, to resolve these problems, we have designed a universal and simple technical tool WGDdetector for detecting WGDs using either genome or transcriptome annotations in different organisms based on the widely used dS based method.ResultsWe have constructed WGDdetector pipeline that integrates all analyses including gene family constructing, dS estimating and phasing, and outputting the dS values of each paralogs pairs processed with only one command. We further chose four species (Arabidopsis thaliana, Juglans regia, Populus trichocarpa and Xenopus laevis) representing herb, wood and animal, to test its practicability. Our final results showed a high degree of accuracy with the previous studies using both genome and transcriptome data.ConclusionWGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system.

Package Network Model: A Way to Capture Holistic Structural Features of Open-Source Operating Systems

Open-source software has become a powerful engine for the development of the software industry. Its production mode, which is based on large-scale group collaboration, allows for the rapid and continuous evolution of open-source software on demand. As an important branch of open-source software, open-source operating systems are commonly used in modern service industries such as finance, logistics, education, medical care, e-commerce and tourism, etc. The reliability of these systems is increasingly valued. However, a self-organizing and loosely coupled development approach complicates the structural analysis of open-source operating system software. Traditional methods focus on analysis at the local level. There is a lack of research on the relationship between internal attributes and external overall characteristics. Consequently, conventional methods are difficult to adapt to complex software systems, especially the structural analysis of open-source operating system software. It is therefore of great significance to capture the holistic structure and behavior of the software system. Complex network theory, which is adequate for this task, can make up for the deficiency of traditional software structure evaluation methods that focus only on local structure. In this paper, we propose a package network model, which is a directed graph structure, to describe the dependency of open-source operating system software packages. Based on the Ubuntu Kylin Linux Operating system, we construct a software package dependency network of each distributed version and analyze the structural evolution through the dimensions of scale, density, connectivity, cohesion, and heterogeneity of each network.

Prototyping Flow-Net Logging for Accountability Management in Linux Operating Systems

Accountability in conjunction with preventative countermeasures is necessary to satisfy the needs of real-world computer security. A common method to achieve accountability is via logging and auditing. To achieve better accountability, a logging system should be capable of capturing activities as well as the relationships among the activities in a computer system or network. Existing logging techniques record activity events in isolation and rely on attributes and time stamps of the logged events to establish their relationships, and this approach leads to probable loss of event relationships among large and complex logs and a confusion during auditing. Prior works have indicated that flow-net is effective in addressing this problem by organizing events in a direct acyclic graph and preserving event relationships during logging. In this work, we provide a prototypical design and implementation of a flow-net accountable logging framework in the Linux operating system. Particularly, it can be applied to Internet of Things (IoTs) with Android Operating Systems. We measure the performance overhead introduced by the flow-net logging prototype via experiments in Linux. The results indicate that the flow-net prototype only introduces a small overhead when compared with existing logging methods. In addition, we show by examples enforcement of accountability policies in the flow-net logging framework and its performance overhead. This work thus constitutes a further step to advance flow-net in addressing accountability in computer systems and networks.