Efficient computation of Hash Hirschberg protein alignment utilizing hyper threading multi-core sharing technology

Due to current technology enhancement,molecular databases have exponentially grown requesting faster efficient methods that can handle these amounts of huge data.There-fore,Multi-processing CPUs technology can be used including physical and logical processors(Hyper Threading)to significantly increase the performance of computations.Accordingly,sequence comparison and pairwise alignment were both found contributing significantly in calculating the resemblance between sequences for constructing optimal alignments.This research used the Hash Table-NGram-Hirschberg(HT-NGH)algo-rithm to represent this pairwise alignment utilizing hashing capabilities.The authors propose using parallel shared memory architecture via Hyper Threading to improve the performance of molecular dataset protein pairwise alignment.The proposed parallel hyper threading method targeted the transformation of the HT-NGH on the datasets decomposition for sequence level efficient utilization within the processing units,that is,reducing idle processing unit situations.The authors combined hyper threading within the multicore architecture processing on shared memory utilization remarking perfor-mance of 24.8%average speed up to 34.4%as the highest boosting rate.The benefit of this work improvement is shown preserving acceptable accuracy,that is,reaching 2.08,2.88,and 3.87 boost-up as well as the efficiency of 1.04,0.96,and 0.97,using 2,3,and 4 cores,respectively,as attractive remarkable results.

基于RT-Thread的液压支架监控分站的设计

为提高煤矿生产的安全性和效率,降低生产成本,设计了基于嵌入式实时操作系统RT-Thread的液压支架监控分站。该分站通过CAN总线将综采工作面液压支架的工作数据上传到主站并接收主站下达的指令;此外,通过支架控制器可以实现对液压支架的远程控制。软件设计利用信号量和事件集进行线程间通信同步;同时采用多线程优先级抢占调度机制,实现任务的并发运行。实验证明,该分站具有精度高、可靠性强和实时响应等特点,达到工程实际应用需求。

Adaptive threading strategy based on rolling characteristics analysis in hot strip rolling

In order to improve the threading stability and the head thickness precision in tandem hot rolling process, an adaptive threading strategy was proposed. The proposed strategy was realized by the rolling characteristics analysis, and factors which affect the rolling force and the final thickness were determined and analyzed based on the influence coefficients calculation process. An objective function consisting of the influenced factors was founded, and the disturbance quantity was obtained by minimizing the function with the Nelder-Mead simplex method, and the proposed adaptive threading strategy was realized based on the calculation results. The adaptive threading strategy has been applied to one 7-stand hot tandem mill successfully, actual statistics data show that the predicted rolling force prediction in the range of +/- 5.0% is improved to 97.8%, the head thickness precision in the range of +/- 35 mu m is improved to 98.5%, and the threading stability and the head thickness precision are enhanced to a high level.

Evaluation of threading dislocation density of strained Ge epitaxial layer by high resolution x-ray diffraction

The analysis of threading dislocation density （TDD） in Ge-on-Si layer is critical for developing lasers, light emitting diodes （LEDs）, photodetectors （PDs）, modulators, waveguides, metal oxide semiconductor field effect transistors （MOSFETs）, and also the integration of Si-based monolithic photonics. The TDD of Ge epitaxial layer is analyzed by etching or transmission electron microscope （TEM）. However, high-resolution x-ray diffraction （HR-XRD） rocking curve provides an optional method to analyze the TDD in Ge layer. The theory model of TDD measurement from rocking curves was first used in zinc-blende semiconductors. In this paper, this method is extended to the case of strained Ge-on-Si layers. The HR-XRD 2θ/ω scan is measured and Ge （004） single crystal rocking curve is utilized to calculate the TDD in strained Ge epitaxial layer. The rocking curve full width at half maximum （FWHM） broadening by incident beam divergence of the instrument, crystal size, and curvature of the crystal specimen is subtracted. The TDDs of samples A and B are calculated to be 1.41108 cm-2 and 6.47108 cm-2, respectively. In addition, we believe the TDDs calculated by this method to be the averaged dislocation density in the Ge epitaxial layer.

Electronic and optical properties of GaN/AlN quantum dots with adjacent threading dislocations

We present a theory to simulate a coherent GaN QD with an adjacent pure edge threading dislocation by using a finite element method. The piezoelectric effects and the strain modified band edges are investigated in the framework of multi-band κ · p theory to calculate the electron and the heavy hole energy levels. The linear optical absorption coefficients corresponding to the interband ground state transition are obtained via the density matrix approach and perturbation expansion method. The results indicate that the strain distribution of the threading dislocation affects the electronic structure. Moreover, the ground state transition behaviour is also influenced by the position of the adjacent threading dislocation.

Simultaneous Multithreading Fault Tolerance Processor

Transient fault detection mechanism is added to simultaneous multithreading architecture. By exploiting both ILP (Instruction Level Parallelism) and TLP (Thread Level Parallelism), Simultaneous Multithreading (SMT) Fault Tolerance Processor can be expected to achieve better tradeoff between performance and hardware cost than traditional Fault Tolerance Processors. Detailed simulations of 3 of SPEC95 benchmarks show that executing two redundant programs on the fault-tolerant microarchitecture takes only 40%–61%longer than running a single version of the program. The new instruction fetch algorithm enhances the performance by 0.4%～1%to most of the benchmarks we choose randomly.

Multi-threaded Fast Distance Field Computation Using Spatial Partition

This article describes three algorithms for distance field generation on triangulated model: brute force algorithm, single-threaded algorithm based on spatial partition and multi-threaded algorithm based on spatial partition. Spatial partition algorithm use equidistant network divide the bounding box into equal-sized cubes, calculates the maximum and minimum distances between the sample point and each of the small cubes,taking the minimum value from the maximum distance as the minimum distance from the sample point to the model named d1, comparing d1 with the distance from sample point to every little cube's minimum distance d2, if d1 <d2, the sample point's distance to all triangles inside this cube are greater than d1, skip this cube, otherwise, calculated the distance from the point to all the triangles intersect with the cube, then alternative d1 with the minimum value, circulate all small cubes intersect with the model. Comparing the calculation results, it can be seen that the algorithm about the multi-threaded distance field relative to the other two algorithms in computational speed is greatly improved especially for complex models.

An HLA/RTI Architecture Based on Multi-thread Processing

In order to improve the real-time performance of the real-time HLA(high level architecture) in the application of massive data communication volume,multi-thread processing was adopted,thread pool structure was introduced into the system,different threads to handle corresponding message queues was utilized to respond different message requests.Furthermore,an allocation strategy of semi-complete deprivation of priority was adopted,which reduces thread switching cost and processing burden in the system,provided that the message requests with high priority can be responded in time,thus improves the system's overall performance.The design and experiment results indicate that the method proposed in this paper can improve the real-time performance of HLA in distributed system applications greatly.

Numerical investigation on threading dislocation bending with InAs/GaAs quantum dots

The threading dislocations(TDs)in GaAs/Si epitaxial layers due to the lattice mismatch seriously degrade the performance of the lasers grown on silicon.The insertion of InAs quantum dots(QDs)acting as dislocation filters is a pretty good alternative to solving this problem.In this paper,a finite element method(FEM)is proposed to calculate the critical condition for InAs/GaAs QDs bending TDs into interfacial misfit dislocations(MDs).Making a comparison of elastic strain energy between the two isolated systems,a reasonable result is obtained.The effect of the cap layer thickness and the base width of QDs on TD bending are studied,and the results show that the bending area ratio of single QD(the bending area divided by the area of the QD base)is evidently affected by the two factors.Moreover,we present a method to evaluate the bending capability of single-layer QDs and multi-layer QDs.For the QD with 24-nm base width and 5-nm cap layer thickness,taking the QD density of 10^(11) cm^(-2) into account,the bending area ratio of single-layer QDs(the area of bending TD divided by the area of QD layer)is about 38.71%.With inserting five-layer InAs QDs,the TD density decreases by 91.35%.The results offer the guidelines for designing the QD dislocation filters and provide an important step towards realizing the photonic integration circuits on silicon.

Design of cable tester based on multi-thread parallel testing technology

In order to realize the efficiency, reliability and safety tests on the complex cable network of an electronic system, an efficient cable network resistance tester is designed. Firstly, the design background and hardware structure are briefly described. Then aiming at the multi task parallelism considering real time measurement of parameters and real time control of the system in the tester testing, a real time muhi task control software is developed by using multi thread testing technology in parallel test to realize multi task complex control. Finally, the least squares method is used to improve the test accuracyof the tester. The test results show that the test error is basically within 0.3%, and the test speed can reach 345 point/min.

Dental Precautions for the Golden Thread Lift Procedure

In cosmetic surgery, golden threads have been used in thread lift procedures, wherein golden threads are placed under the skin of the neck and chin. These are mainly applied in the maxillofacial region adjacent to the sites of dental treatment to achieve cosmetic benefits. However, as dentists typically lack sufficient knowledge about the golden thread lift procedure, it may present a challenge to dental examinations and treatments. It is therefore crucial for dentists to have a comprehensive understanding of the procedure. This case report covers our experience with the dental examination of a patient with golden threads. We emphasize the dental complications and precautions that should be taken for such cases. These golden threads are made of pure gold, nonabsorbable, and can be broken. These can obstruct dental examination, as well as cause metal allergies and foreign body granulomas. Additionally, it is difficult to completely remove these threads when they break apart. In the future, since more patients are expected to undergo this procedure, it is possible to encounter these golden threads as artifacts on imaging. Therefore, it is important to educate dentists about the golden thread lift procedure and its dental implications. It is also imperative to determine whether the patient has undergone the golden thread lift procedure in the medical questionnaire prior to the magnetic resonance imaging examination. Thus, dentists should be able to conduct a detailed interview with the patient, determine the feasibility of examination or treatment, and communicate this assessment to the patient.

Dynamically Translating Binary Code for Multi-Threaded Programs Using Shared Code Cache

mc211vm is a process-level ARM-to-x86 binary translator developed in our lab in the past several years. Currently, it is able to emulate singlethreaded programs. We extend mc211vm to emulate multi-threaded programs. Our main task is to reconstruct its architecture for multi-threaded programs. Register mapping, code cache management, and address mapping in mc2llvm have all been modified. In addition, to further speed up the emulation, we collect hot paths, aggressively optimize and generate code for them at run time. Additional threads are used to alleviate the overhead. Thus, when the same hot path is walked through again, the corresponding optimized native code will be executed instead. In our experiments, our system is 8.8X faster than QEMU （quick emulator） on average when emulating the specified benchmarks with 8 guest threads.

Roller Screw and Threaded Chain Speed Reducer: An Experimental Evaluation

We are developing a speed reducer that can be considered a transformation of a worm gear reducer: the worm is replaced by an inverted roller screw, and the gear is replaced by a threaded chain drive. This configuration lessens wear, increases load capacity, and improves efficiency. The threaded chain consists of nut-shaped links. This paper presents the results of tests carried out on a prototype with a reduction ratio of 46.

基于RT-Thread的可信软件栈的设计和实现

针对基于Linux和TCG软件栈(Trusted computing group Software Stack,TSS)的复杂性问题,提出一种轻量级的可信软件栈。分析了TSS的基本结构与TSS在嵌入式系统的局限,总结出基于嵌入式系统的可信软件栈设计需求,设计出软件栈命令调用的机制和软件栈的结构。此外,分析了TSS密钥管理缓存算法,在flash中定义一块密钥槽空间,方便密钥管理中直接访问,阐述密钥生成的逻辑过程,实现面向嵌入式系统的可信软件系统。经实验验证,该软件栈可以结合RT-Thread实时系统实现基本的可信计算功能。

基于RT-Thread的卫星导航控制系统研究

随着制造业的发展,自动引导车被广泛应用于现代工业领域,由于作业环境复杂程度变高,对车辆控制系统硬件的稳定性、灵活性,软件系统的实时性、模块化程度有了更高要求。从自动引导车的需求出发,对导航控制系统的硬件及软件进行了设计,后针对路径规划与路径追踪模块,提出了一种路径规划与追踪控制方法,通过输入不同的横向误差与速度进行指定模糊规则,最终得到合适的预瞄距离,从而使车辆实现自适应预瞄距离的功能,提高车辆的自适应能力。试验结果证明了设计的可行性,为后续自动引导车的控制系统研究提供参考。

基于RT-thread的精确时间同步系统设计

分布式智能采集终端需要一致的时间基准,用于多种数据和事件的时间标记。为满足智能采集终端对高精度时间同步的需求,选择IEEE 1588精确时间同步协议实现时间同步;设计基于纯国产32 bit双核微控制器HPM6750和以太网收发器RTL8211FS(I)-VS的精确时间同步系统,选用国产开源嵌入式实时操作系统RT-thread操作系统,实现在物理层获取时间戳来运行IEEE 1588协议;构建测试平台对该时间同步系统进行主从时钟同步精度测试。测试结果表明,设计在物理层获取时间戳时达到的时间同步精度在±250 ns以内,与在数据链路层获取时间戳时达到±10μs的时间同步精度相比较,有效提高了时间同步精度,可广泛应用于对时间同步精度有较高要求的智能采集终端。

基于 RT-Thread 的玉米对行收获控制系统 研发与测试

为提高玉米机械化收获效率,减轻驾驶员劳动强度,研发玉米收获对行控制系统。该系统包括玉米边界行感知模块和对行控制模块,采用激光雷达获取玉米行点云数据,提出基于STM32处理器和RT-Thread实时操作系统的点云数据快速分析处理方法,实现玉米行边界点的提取,通过边界点计算得到横向偏差;设计系统通信拓扑架构,实现感知、处理、对行控制模块之间的高效通信。对该系统的性能开展田间试验验证,结果表明:收割机与玉米行实际边界线的平均横向偏差为0.06 m,最大横向偏差为0.126 m,满足玉米对行收获作业要求,为玉米对行收获提供一定的参考。

基于RT-Thread的温湿度数据采集监测系统设计

温湿度数据的采集和监测在各行各业中发挥着重要作用。本文基于RT-Thread设计了一个分布式温湿度采集监测系统。该系统以STM32开发板为主控模块,在芯片中嵌入RT-Thread实时操作系统,可实时采集分布式节点的温湿度数据,并通过无线网络将数据上传至OneNET云平台。该系统提高了数据采集的实时性,实现了温湿度数据的可视化显示和远程实时监测功能。

RT-Thread操作系统的电池管理系统设计

为了保证电池在充放电过程中的安全,针对目前电池管理系统存在可移植性差、不便于功能扩展等问题,提出一种智能电池管理系统。系统采用国产嵌入式实时操作系统RT-Thread,并选用STM32作为主控制器芯片,使整个系统的监控、调试更加方便。测试结果表明,该系统可以实时监控电池的充放电过程,预留的接口可以方便以后做功能扩展。