Linux Operating System Research Articles

MBBench: WCET Kıyaslama Kümesi

One of the important features of any real-time software is the worst-case execution time (WCET). To get an understanding of the timing behavior of real-time systems and to prove that the real-time software meets its deadlines, WCET analysis is performed. Today, researchers actively develop new WCET analysis methods and tools. Therefore, they need benchmark programs to evaluate and compare their work. To meet this need, in this study we present a new benchmark suite, called MBBench. MBBench includes a collection of C programs for Linux operating system and RTEMS real-time operating system. Its main aim is to help the evaluation and comparison of measurement-based WCET analysis methods/tools. MBBench has been published as open source. It can be obtained freely over the Internet.

MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification.

SummaryMass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected.Availability and implementationWe implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3.

Support for working with the ALSA sound subsystem in a binary compiler of application level x86→«Elbrus»

The success of a hardware platform is mainly determined by the software available for it. That is why the problem of enlarging the number of applications launched on the «Elbrus» platform is very acute. One of its possible solutions is the usage of binary compilation technology. The work of many modern applications is somehow related to sound processing. One of the most popular modern libraries for working with sound devices in Linux operating systems is the ALSA library. Its functionality is based on the set of ioctl system call commands. They were not supported in the x86→«Elbrus» binary compiler until recently. Therefore, occurred the issue of implementing support for ALSA-ioctl commands in binary compiler. In order to solve this problem, it was necessary to study the Linux kernel implementation of this technology. The gained knowledge was used to develop proprietary tools for the binary compiler making it possible to use the ALSA in applications translated under the «Elbrus» architecture.

A Sustainable Solution to Support Data Security in High Bandwidth Healthcare Remote Locations by Using TCP CUBIC Mechanism

Long distance high bandwidth networks are spanning several continents and many remote Healthcare centers are centralizing their data centers for economic reasons. For the best performance of their data centers, TCP (Transmission Control Protocol) performance and data security are the main critical issues in these network scenarios. TCP performance is directly related to its congestion control mechanism which is responsible for detecting and reacting to the overload traffic on the network. Data security is related to the security mechanism being used by sender and receiver nodes during communication. Linux users, which have rapidly increased in the last five years and most of the Healthcare data centers are being deployed on the Linux operating system, focus the researchers to work on Linux to enhance its performance and security accordingly. The Linux operating system uses TCP CUBIC as a congestion control mechanism with TCP during communication. TCP CUBIC became the default congestion control mechanism of Linux in 2006 after kernel 2.6.18. TCP CUBIC is fundamentally a loss based TCP congestion control mechanism and at each packet loss detection, it reduces its Congestion Window ( $cwnd$ c w n d ) size 20 percent instead of 50 percent as in trademark congestion control mechanism Standard TCP. The aim of this paper is to design a new security mechanism that will work with TCP CUBIC to achieve the maximum possible performance and security over the network link. In this paper, Network Simulator 2 (NS-2) is used to compare the performance of TCP CUBIC with state-of-the-art mechanisms in long and short Round Trip Time (RTT), high bandwidth network scenarios. Results show that when new security mechanism is used with TCP CUBIC, overall better performance in the form of protocol fairness, TCP friendliness, goodput, and convergence time is achieved over the network link.

Automated Surface Measurements of Drilling Fluid Properties: Field Application in the Permian Basin

Summary Accurate and frequent mud checking is essential for optimum drilling operations. Careful measurement and maintenance of drilling fluid properties (density and rheology) maintain the primary well control barrier and optimize fluid hydraulics and hole-cleaning ability. However, a full mud report while drilling is provided only once or twice a day. Moreover, the measurements are mostly performed using traditional equipment. Test interpretation is subjective and might be biased and difficult to verify independently. In this paper, we present an automated mud skid unit (MSU), which performs continual drilling fluid sampling and measurements at variable temperatures. The unit provides the non-Newtonian rheological constants characterizing a yield-power law fluid as well as the real-time friction factor and critical Reynolds number using a pipe-viscometer measurement approach. Other important fluid properties such as pressurized density, oil/water ratio, and temperature are provided using high-quality in-line sensors. The unit is controlled by a programmable logic controller coupled with a Linux operating system for data analysis. The system sends real-time data to WITSML data servers and provides detailed mud reports to engineers working either on-site or remotely. The MSU was deployed in the Permian Basin by an independent operator for automated mud monitoring during unconventional shale drilling operations. Rheology, density, and phase content measurements were compared with conventional mud reports provided by the on-site mud engineer. High accuracy (error < 5%) was observed in mud rheology tests. The pressurized mud-density measurements provided by the MSU proved to be more accurate than nonpressurized mud balance measurements, which were affected by mud aeration. Moreover, the MSU provided mud check data 25 times more frequent than those generated by the mud engineer at temperatures of 50 and 65.5°C. Drilling-fluid-related issues, such as chemical overtreatment as well as sudden changes in mud density, rheology, and oil/water ratio, were reported immediately to the drilling crew. This paper provides details about the measurement technology as well as the results from the field deployment of the MSU.

Actinide Minor Addition on Uranium Plutonium Nitride Fuel for Modular Gas Cooled Fast Reactor

This study has made a calculation of Actinide Minor Addition on Uranium Plutonium Nitride Fuel for Modular Gas Cooled Fast Reactor. The purpose of this study was to determine the characteristics of minor actinides when incorporated into plutonium nitride uranium fuel. Neutronics calculation was design by using SRAC Code version 2006 (Standard Reactor Analysis Code) with the data nuclides from JENDL-4.0 under the Linux Operating System with nuclear data library JENDL4.0. Neutronic calculations were done through some steps of parameter survey to obtain the ultimate optimization results. The initial calculation was calculation of fuel cell (PIJ calculation) by using hexagonal cell and then followed by calculation of core reactor (CITATION calculation) by using program code SRAC2006. The addition of minor actinide has been calculated in this research. The minor actinides which were added were americium (Am-241 and Am-243) and neptunium 237. They were put into the uranium plutonium nitride material to decrease the k-eff value. The addition of minor actinide into the reactor aimed to reduce the number of minor actinides in the world. Minor actinide is a nuclear waste fuel or often called spent nuclear fuel (SNF) which has high toxicity. Neptunium 237 is a minor actinide with the highest percentage of SNF.

Parallelization of torsion finite element code using compressed stiffness matrix algorithm

In the current study, the problems of elastic and elastoplastic torsion were formulated by finite element method. The finite element code was parallelized on both shared and distributed memory architectures. An assembling method with high parallelism ability and consuming minimum memory was proposed to obtain compressed global stiffness matrix directly. Parallel programming principles were expressed in two shared memory and distributed memory approaches; moreover, parallel well-known mathematical libraries were briefly expressed. In this paper, the main focus was on a lucid explanation of parallelization mechanisms in detail on two memory architectures such as some settings of Linux operating system for large-scale problems. To verify the ability of the proposed method and its parallel performance, several benchmark examples were represented with different mesh sizes and were compared with their respective analytical solutions. Considering the obtained results, the proposed sparse assembling algorithm decreased required memory significantly (about 103.5 to 105.5 times) and the obtained speedup was about 3.4 for the elastoplastic torsion problem in a simple multicore computer.

Jurnal Review: Perbandingan Sistem Operasi Linux Dengan Sistem Operasi Windows

Operating Systems are four components that must not be absent for Information Systems. For companies that have implemented a computerized system as part of the company's operational support, must pay attention to what Operating Systems are good for the company. Including the advantages and company budget for Information Technology. To get a good Operating System in accordance with office needs, a comparison of the Windows Operating System and Linux Operating System. The results of the comparison of these two Operating Systems can be input for deciding which Operating System is suitable for the company.

PRM navigation in trading drone and Gazebo simulation

Starting from a commercial drone AR Dron Parrot 2.0, an autonomous navigation process is developed with a PRM probabilistic route planner in real time, through a ROS network between the drone and the Gazebo simulation software. Using the robotics system toolbox from software Matlab that interacts with Gazebo, it is possible to study the desired trajectory planner, in addition, the creation and connection of the ROS network on the Linux operating system, where the navigation algorithm is analyzed from the practical vs., simulation points of views. The errors that are presented are minimal, taking into account the propagation delays and the control algorithm; this is in charge of receiving location information in order to correct and minimized the mean square error.

Mapping and Location Using Genetic Algorithm with Autonomous Vehicle

Teknolojik gelişmeler ve bu zamana kadar biriken bilgilerin ışığında otonom sistemlerde muazzam bir ilerleme kaydedilmiştir. Bu sayede otonom sistemler çarpışmadan kaçınma, trafik işareti tespiti, haritalama vb. sayısız akıllı işlevleri gerçekleştirebilmektedir. Gerçek zamanlı otonom araçların en zorlu problemi aracın kendi kendine haritalandırma ve lokasyon işlemlerini yapabilmesidir. Genetik Algoritma (GA) kullanarak optimize edilmiş lokasyon uygulaması ile otonom araçlar için sürüş güvenliğinin artması beklenmektedir. Bu çalışmada lazer tabanlı bir lokalizasyon ve haritalama tekniğinin üzerine odaklanılmıştır. Gerçekleştirilen sistemde sanal bir test ortamı kurulmuş ve bir otonom araç üzerinde denemeler yapılmıştır. Çalışma kapsamında sanal makineler oluşturularak üzerlerine Linux işletim sistemi kurulmuştur. Sonra bu sanal makinelere ROS ortamında TurtleBot3 kurulmuş ve iç mekân lokalizasyonu yapılarak bir harita elde edilmiştir. Bu harita genetik algoritma ile en kısa mesafelerin bulunmasını sağlamak için kullanılmaktadır. Gözlemler neticesinde simülasyon ortamındaki robot yüksek başarımla istenilen konuma gidebildiği sonucuna ulaşılmıştır.

Hardware-software implementation of HEVC decoder on Zynq

This paper presents an efficient implementation of the High Efficiency Video Coding (HEVC) decoder using Hardware/Software (HW/SW) co-design approach on the Zynq System on Chip (SoC) Platform. The reference software decoder HM 10.0 has been implemented under embedded Linux Operating System (OS). For real-time decoding, we provide hardware acceleration for the most computationally intensive parts of the HEVC decoder, which are the interpolation filters. The proposed design improves the processing throughput targeting on the resolution of 3840 × 2160 at a frame rate of 60 fps. HW/SW validation is achieved and examined in terms of resource utilization, throughput and power consumption. In order to improve the total decoding time, we propose to enable the Direct Memory Access (DMA) mode that can help speed page access and minimize the transfer time between the processor and hardware accelerators.

Neutronic analysis of comparation UN-PuN fuel and ThN fuel for 300MWth Gas Cooled Fast Reactor long life without refueling

Neutronic analysis of comparation UN-PuN fuel and ThN fuel for 300MWth Gas Cooled Fast Reactor long life without refueling has been done. Gas Cooled Fast Reactor is a Generation IV reactor with gas coolant (i.e. helium) and using fast spectrum neutron. The neutronic calculation was carried out using SRAC (Standard Reactor Analysis Code) version 2006 under the Linux Operating System with nuclear data library JENDL4.0. The first calculation is fuel pin cell calculation (PIJ-method) by using a hexagonal cell and then followed by the calculation of the core reactor (CITATION-method). The calculation of the core reactor used homogeneous and heterogeneous core configuration. The UN-PuN fuel use plutonium as a fissile material and natural uranium as a fertile material and the ThN fuel use U233 as a fissile material and natural thorium as a fertile material. The percentages of fissile material are varied in heterogeneous core configuration. It is used to decrease the peaking power in the center of the core. The heterogeneous core configuration contains of Fuel 1 (F1) 8% fissile materials, Fuel 2 (F2) 10% fissile materials, and Fuel 3 (F3) 12% fissile materials. F1 is located in the central core, F2 middle core and F3 outer core. The diameter and height active core are 240 cm and 100 cm. The reflector radial-axial width is 50 cm. All of the calculations can reach burn up time more than 20 years with excess reactivity less than 1 percent (Δk/k <1%) both UN-PuN fuel and ThN fuel. It means that the reactor stable in 20 years. The average of power density both of UN-PuN fuel and ThN fuel are around 66 Watt/cc. The maximum power density of UN-PuN fuel is 94Watt/cc and ThN fule is 129Watt/cc. The UN-PuN fuel has lower maximum power density value than ThN fuel. So, for fast neutron spectrum reactor especially Gas Cooled Fast Reactor type, it is better used UN-PuN fuel than ThN fuel.

Отладчик параллельных программ для ОС Linux

The paper presents a debugger for parallel programs in С/C++, or FORTRAN, which are executed in high-performance computers. The debugger’s program components and mechanism of their interaction are described. The graphic user’s interface capabilities are discussed and the profiling procedure using built-in profiling tools is described. The paper contains of the description of the new parallel debugger capabilities such as a communication treelike scheme of his components connection, and a non-interactive debugging mode, and the support of Nvidia’s graphic accelerators. Currently, the debugger provides launching of debug jobs in the systems of batch processing of jobs such as Open PBS / Torque, SLURM, and CSP JAM but it can be configured for other systems. The PD debugger allows to debug program processes and threads, manage breakpoints and watchpoints, logically divide program processes into subsets, manage them, change and view variables, and profile the debugged program using the free Google Performance Tools and mpiP. The PD debugger is written in the Java programming language, intended for debugging programs on Unix / Linux operating systems, and it uses free software components such as SwingX, JHDF5, Jzy3D, RSyntaxTextArea, and OpenGL.

Parallel performance evaluation for curing process of thermoset nanocomposites materials

The investigation towards rate of growth for the curing process of thermoset nanocomposites materials is of great concern to most engineering and chemistry researchers since it is closely related to our natural resources, and has valuable properties. It is important to tailor and control the waste composite materials temperature profile during curing process to reproduce and improve its efficiency. Due to this phenomenon, temperature profile during curing process between two layers of composite materials is considered in this study. The mathematical model of 1D convection–diffusion of the heat equation of thick thermoset composite during its curing process has been employed. We predicted the temperature behavior for separating two layers of nanocomposites materials. Mathematical modelling to represent the problem were discretized numerically by employing central Finite Different Method (FDM) with weight parameter θ. The Linear System Equation (LSE) resulted from the discretization are solved by three numerical methods, Alternating Group Explicit (AGE), Red Black Gauss Seidel (RBGS) and Jacobi (JB). Results acquired from RBGS and JB methods have become the benchmarks for evaluating the results from AGE methods. Then, we developed parallel algorithms on the mathematical model based on AGE, RBGS and JB methods. Finally, we evaluated and analyzed the performance indicators based on the parallel performance evaluation (PPE) in solving the PDE. Parallel algorithm is computed in Parallel Virtual Machine (PVM) programming on Linux operating system (Fedora 21) as a platform in order to accelerate the sequential execution as well as the convergence rate. Parallel AGE has significantly outperformed their counterparts compared with the benchmark classical methods (RBGS and JB) for two dimensional problems. Despite having huge computational complexity, results obtained from Parallel AGE methods have proven valuable since it enables to provide solution with higher accuracy and stability.

Docking Study on Anti-HIV-1 Activity of Secondary Metabolites from Zingiberaceae Plants.

ABSTRACTIntroduction:Human immunodeficiency virus type-1 (HIV-1) that causes acquired immunodeficiency syndrome (AIDS) has become a worldwide health problem today. There are approximately 30 anti-HIV-1 drugs that have been used in the treatment of AIDS. However, effective anti HIV-1 agents with less side affect and high inhibition potency are still in demand.Objective:The objective of this study was to identify the potential compounds from Zingiberaceae plants that might be active as anti-HIV-1 by molecular docking.Materials and Methods:Molecular docking simulation was performed by using AutoDock 4.2 on Linux operation system. Docking protocol was validated by using root mean square deviation (RMSD) value using redocking and cross-docking methods. The reported metabolites from Zingiberaceae plants were docked on HIV-1 protease, integrase, and reverse transcriptase protein enzymes.Results:The docking result showed that the genera of Zingiber, Etlingera, Alpinia, Hedychium, and Boesenbergia have potential metabolites that inhibit HIV protease, integrase, and reverse transcriptase enzymes by possessing lower docking energy than native ligand of amprenavir, raltegravir, and nevirapine. Among the metabolites, noralpindenoside B and alpindenoside A from Alpinia densespicata inhibited protease enzymes with the lowest docking energy of -18.02 and -17.90 kcal/mol, respectively. Meanwhile, panduratin E from Boesenbergia pandurata Roxb. and 5α,8α-epidioxyergosta-6,22-dien-3β-ol from Etlingera elatior showed the lowest docking energy on integrase protein with docking energy of -11.97 and -11.41 kcal/mol, respectively. Pahangensin A from Alpinia pahangensis Ridley showed the lowest docking energy on reverse transcriptase enzyme with docking energy of -13.76 kcal/mol.Conclusion:The docking molecular study has identified the possible potential compounds from Zingiberaceae plants that might be used for anti-HIV-1 treatment. So, this study suggested further isolation and purification of the predicted compounds.

SchedCust: Design &amp; Development of scheduling policy customization framework for ARM based System on Chip

Abstract Selecting a right scheduling strategy for the specific embedded application has a significant impact on system’s performance. To adapt to the requirements of a particular embedded application, the embedded operating system can be customized manually or automatically. In this paper, the standard process for customizing the CPU scheduling policy in an open source Linux operating system (OS) has been discussed. The paper also focuses on the design & development of the CPU scheduling customization framework for ARM based Raspberry Pi 3, tagged as SchedCust, that allows the CPU scheduler to be configured to execute a particular scheduling policy. The SchedCust framework helps the users to automatically develop the scheduling policy specific custom operating system (OS) for the selected processor. The experimental results have been computed for FIFO and RR scheduling policy, with respect to four distinct parameters. The data collected from user testing showed that the manual process of developing a custom OS takes more time and efforts when compared to the automated process.

Elastic Computing in the Fog on Internet of Things to Improve the Performance of Low Cost Nodes

The Internet of Things (IoT) is a network widely used with the purpose of connecting almost everything, everywhere to the Internet. To cope with this goal, low cost nodes are being used; otherwise, it would be very expensive to expand so fast. These networks are set up with small distributed devices (nodes) that have a power supply, processing unit, memory, sensors, and wireless communications. In the market, we can find different alternatives for these devices, such as small board computers (SBCs), e.g., Raspberry Pi (RPi)), with different features. Usually these devices run a coarse version of a Linux operating system. Nevertheless, there are many scenarios that require enhanced computational power that these nodes alone are unable to provide. In this context, we need to introduce a kind of collaboration among the devices to overcome their constraints. We based our solution in a combination of clustering techniques (building a mesh network using their wireless capabilities); at the same time we try to orchestrate the resources in order to improve their processing capabilities in an elastic computing fashion. This paradigm is called fog computing on IoT. We propose in this paper the use of cloud computing technologies, such as Linux containers, based on Docker, and a container orchestration platform (COP) to run on the top of a cluster of these nodes, but adapted to the fog computing paradigm. Notice that these technologies are open source and developed for Linux operating system. As an example, in our results we show an IoT application for soundscape monitoring as a proof of concept that it will allow us to compare different alternatives in its design and implementation; in particular, with regard to the COP selection, between Docker Swarm and Kubernetes. We conclude that using and combining these techniques, we can improve the overall computation capabilities of these IoT nodes within a fog computing paradigm.

RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow.

RNA-Seq analysis has revolutionized researchers' understanding of the transcriptome in biological research. Assessing the differences in transcriptomic profiles between tissue samples or patient groups enables researchers to explore the underlying biological impact of transcription. RNA-Seq analysis requires multiple processing steps and huge computational capabilities. There are many well-developed R packages for individual steps; however, there are few R/Bioconductor packages that integrate existing software tools into a comprehensive RNA-Seq analysis and provide fundamental end-to-end results in pure R environment so that researchers can quickly and easily get fundamental information in big sequencing data. To address this need, we have developed the open source R/Bioconductor package, RNASeqR. It allows users to run an automated RNA-Seq analysis with only six steps, producing essential tabular and graphical results for further biological interpretation. The features of RNASeqR include: six-step analysis, comprehensive visualization, background execution version, and the integration of both R and command-line software. RNASeqR provides fast, light-weight, and easy-to-run RNA-Seq analysis pipeline in pure R environment. It allows users to efficiently utilize popular software tools, including both R/Bioconductor and command-line tools, without predefining the resources or environments. RNASeqR is freely available for Linux and macOS operating systems from Bioconductor (https://bioconductor.org/packages/release/bioc/html/RNASeqR.html).

An Empirical Study of Fault Triggers in the Linux Operating System: An Evolutionary Perspective

This paper presents an empirical study of 5741 bug reports for the Linux kernel from an evolutionary perspective, with the aim of obtaining a deep understanding of bug characteristics in the Linux operating system. Bug classification is performed based on the fault triggering conditions, followed by an analysis of the proportions and evolution of the bug types as well as comparisons among versions, products, and repair locations. In addition, an analysis of regression bugs and the relationship between the types of bugs and the time needed to fix them are presented. Moreover, a procedure for the analysis of bug type characteristics based on complex network metrics is proposed, and four network metrics, i.e., degree, clustering coefficient, betweenness, and closeness, are utilized to further investigate the relationship between bug types and software metrics. In this paper, 22 interesting findings based on the empirical results are revealed, and guidance based on these findings is provided for developers and users.

PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

BackgroundPhylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building.ResultsHere, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree.ConclusionsTogether with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).