Combined hardware–software multi-parallel prefiltering on the Convey HC-1 for fast homology detection

Protein databases used in research are huge and still grow at a fast pace. Many comparisons need to be done when searching similar (homologous) sequences for a given query sequence in these databases. Comparing a query sequence against all sequences of a huge database using the well-known Smith–Waterman algorithm is very time-consuming. Hidden Markov Models pose an opportunity for reducing the number of entries of a database and also enable to find distantly homologous sequences. Fewer entries are achieved by clustering similar sequences in a Hidden Markov Model. Such an approach is used by the bioinformatics tool HHblits. To further reduce the runtime, HHblits uses two-level prefiltering to reduce the number of time-consuming Viterbi comparisons. Still, prefiltering is very time-consuming. Highly parallel architectures and huge bandwidth are required for processing and transferring the massive amounts of data. In this article, we present an approach exploiting the reconfigurable, hybrid computer architecture Convey HC-1 for migrating the most time-consuming part. The Convey HC-1 with four FPGAs and high memory bandwidth of up to 76.8 GB/s serves as the platform of choice. Other bioinformatics applications have already been successfully supported by the HC-1. Limited by FPGA size only, we present a design that calculates four first-level prefiltering scores per FPGA concurrently, i.e. 16 calculations in total. This score calculation for the query profile against database sequences is done by a modified Smith–Waterman scheme that is internally parallelized 128 times in contrast to the original Streaming ‘Single Instruction Multiple Data (SIMD)’ Extensions (SSE)-supported implementation where only 16-fold parallelism can be exploited and where memory bandwidth poses the limiting factor. Preloading the query profile, we are able to transform the memory-bound implementation to a compute- and resource-bound FPGA design. We tightly integrated the FPGA-based coprocessor into the hybrid computing system by employing task-parallelism for the two-level prefiltering. Despite much lower clock rates, the FPGAs outperform SSE-based execution for the calculation of the prefiltering scores by a factor of 7.9.     

基于振动实测的非均质地层钻头失效分析与对策

四川盆地作为国内页岩气开发的重点区域,通过近几年的不断攻关和实践,机械钻速得到了提高,但由于受地层复杂、可钻性差、非均质性强等地质因素的影响,导致井下钻柱系统不良振动剧烈,容易出现钻头损坏严重、钻速较低等问题,严重影响了钻井时效。为了解决上述难题,以该盆地涪陵工区上二叠统龙潭组—中二叠统茅口组为例,采用井下振动高频测量工具的实测手段,测量了钻头—钻柱系统的动态振动加速度参数,结合地层的岩性和矿物组分分析,研究钻头失效原因与对策,并开展了现场试验。研究结果表明:①在非均质地层中钻进的钻头—钻柱系统产生了大于40 m/s~2的高幅值瞬时冲击振动,高幅值的瞬时冲击是导致钻头先期失效的主要原因;②提出了抑制高幅值的瞬时冲击振动采用"减振+增压"工具组合和避免井下工具共振的钻井参数;③采用钻井新参数的试验井比邻井的高幅值瞬时振动降低了17%,单只钻头进尺增加24%,钻头工作环境得到了较大的改善,钻头使用数量减少。结论认为,该研究成果能够有效地改善钻头—钻柱系统的振动状态,有利于达成延长钻头使用寿命的目标。     

陆东凹陷油气藏烃类组成非均质性及其意义

陆东凹陷原油和油砂抽提物中烃类的宏观组成存在着明显的非均质性。在高孔隙度(>15%)储层单元中,饱和烃的含量高,占总组成的含量均大于40%,而极性化合物则相对较低,一般不足40%;相反,在低孔隙度(<15%)储层单元中,饱和烃的含量明显降低,而极性化合物则显著增加。此外,陆东凹陷原油和油砂抽提物中烃类成熟度亦存在着非均质性:在高孔隙度储层中,原油和油砂烃类的成熟度参数高,而在低孔隙度储层中原油和油砂烃类的成熟度参数低。根据原油和油砂抽提物中烃类的宏观组成特征和成熟度参数的变化规律,提出了陆东凹陷油气聚集模式。     

NUMERICAL ANALYSIS OF THE EFFECTS OF LOCAL HYDRODYNAMICS ON MASS TRANSFER IN HETEROGENEOUS POROUS MEDIA

Many engineering problems require the estimation of mass transfer coefficients in porous materials. In heterogeneous materials or in cases where mass transfer sites are not spatially uniform, empirical equations for mass transfer coefficients vary widely, and the origin of these differences is not well understood. In this article, we use a stochastic algorithm to model mass transfer from single particles in a two-dimensional heterogeneous packed bed. The computed mass transfer coefficients are used to generate a distribution of local Peclet numbers in the bed. Detailed hydrodynamics are then used to interpret variations in the local Peclet number. The results show clear relationships between pore structure, streamline patterns, and mass transfer rates.     

ENHANCED RECOVERY OF MEDIUM CRUDE OIL IN HETEROGENEOUS RESERVOIRS USING AIR INJECTION/IN SITU COMBUSTION—HORIZONTAL WELL TECHNOLOGY

A simple 3-D physical model has been developed to investigate the use of in-situ combustion in heterogeneous reservoirs. Gas over-ride phenomena is one of the major causes of instability of combustion process; gas override results in poor sweep efficiency with subsequent low oil recovery. However, the use of horizontal wells in direct line drive arrangement has shown a great deal of combustion stability and propagation by means of controlling gas override This paper has extended the scope of using horizontal wells in direct line drive configuration in heterogeneous reservoirs. Three cases of reservoir heterogeneity were investigated in this study. In the first case, a dual-layer permeability of sand was used (a high permeability layer on top and a low permeability layer on bottom); in the second case, placement of the aforementioned layers was swapped, and in the third case, a high permeability streak was sandwiched between two low permeability layers of fine sand. The results indicated that a stable combustion front has been achieved in the first two cases with a high oil recovery, however the performance of the combustion process markedly deteriorated when a high permeability streak layer was utilised as a result of a severe low temperature oxidation due to oxygen channelling through the streak, with subsequent poor sweep efficiency and in turn low oil recovery. The use of horizontal wells as producers and injectors in a line drive configuration is beneficial and effective for minimising the effect of reservoir heterogeneity to some extent.     

Microstress estimate of stochastically heterogeneous structures by the functional perturbation method: A one dimensional example

A new functional perturbation method (FPM) for calculating the probabilistic response of stochastically heterogeneous, linear elastic structures is developed. The method is based on treating the governing differential operator as well as the unknown displacement function as a functional of material modulus field. By executing a functional perturbation around the homogeneous case, a set of successive differential equations is obtained and solved, from which the average and variance of any local parameter (displacements, stresses, strains) can be found. For a linear problem, the equations to be solved in each approximation order differ from the one for the homogeneous case by a pseudo external loading (right hand side) part only. Thus, only the Green function for the homogeneous case is needed for an analytical solution of the corresponding heterogeneous problem. A one dimensional stochastically heterogeneous rod embedded in a uniform shear resistant elastic medium is solved as an example. The statistical variance of displacements and stresses are found analytically, including the edge regions. Morphological (grain size) and material (modulus) effects on the stochastic response are demonstrated. The above results are essential for estimating the stochastic features of local stress concentrations, which are the source for many strength-related macro properties of materials. Extensive usage of generalized functions (Dirac operator and its derivatives) is needed for the analysis.     

Motional heterogeneity of polystyrene-block-polybutadiene: a spin probe study

Polystyrene-block-polybutadiene copolymers (SB) with 0.5 mass fraction of styrene were studied by electron spin resonance (ESR) of nitroxide spin probes. The influence of the block length ( and ) and the solvation power of casting solvents on the motional dynamics of spin probe were measured over a wide temperature range. Two nitroxide radicals as spin probes were selected: 2,2,6,6-tetramethyl-4-hydroxypiperidine-1-oxyl benzoate (BzONO) and 2,2,6,6-tetramethyl-4-hydroxypiperidine-1-oxyl (Tempol). Irrespective of the spin probe used two ESR spectral components differing in their motional properties above the phase transition of polybutadiene blocks (PB) were observed. The fast component was assigned to spin probes located in polybutadiene-rich domains and the slow component to spin probes in polystyrene-rich domains. The range of two spectral components and the phase transition of the slow ESR component, T_5mT, depend on the block length. The influence of the interphase and accumulation of free volume in the interphase on the Tempol probe motion was investigated by changing copolymer morphology in the films casted from selective and nonselective solvents. The analysis of the motional heterogeneity from the ratio of the fast and slow motional component presents evidence that in the selective solvent for polystyrene (PS) blocks (2-butanone) the most irregular structure with a large interphase is formed. The difference in fast motion of spin probes indicates that the motional dynamic is related to the change of domain structure.     

DynamicCloudSim: Simulating heterogeneity in computational clouds

Simulation has become a commonly employed first step in evaluating novel approaches towards resource allocation and task scheduling on distributed architectures. However, existing simulators fall short in their modeling of the instability common to shared computational infrastructure, such as public clouds. In this work, we present DynamicCloudSim which extends the popular simulation toolkit CloudSim with several factors of instability, including inhomogeneity and dynamic changes of performance at runtime as well as failures during task execution. As a validation of the introduced functionality, we simulate the impact of instability on scientific workflow scheduling by assessing and comparing the performance of four schedulers in the course of several experiments both in simulation and on real cloud infrastructure. Results indicate that our model seems to adequately capture the most important aspects of cloud performance instability. The source code of DynamicCloudSim and the examined schedulers is available at https://code.google.com/p/dynamiccloudsim/.     

云存储环境下副本选择策略研究

云存储服务提供商为了满足各类云用户的存储需求,一般采用划分固定大小的数据块、冗余备份等技术来存储数据,关于块放置、最佳副本选择、副本粒度等存储机制的研究一直是加快大文件存取速度的重要内容。面向云存储系统中存储节点的异构性,设计了一种采用层次分析法对节点性能指标加权并依据加权指标改进粒子群算法的策略(AHPPSO)。通过引入与存储节点性能相关的加权评价矩阵,使得粒子群算法向综合性能较高的节点进化,在不增加存储空间成本的基础上,加快了存取数据的速度。在自主搭建的云存储系统中实现了该策略,实验结果显示该策略能够适应多种用户需求,并且在一定程度上实现系统负载均衡。     

Scalability of MANET routing protocols for heterogeneous and homogenous networks

In Mobile Ad hoc Network (MANET), mobility, traffic and node density are main network conditions that significantly affect performance of routing protocols. Much of the previous research in MANET routing have focused on developing strategies, which suit one specific networking scenario. Therefore, there is no existing protocol that can work well in all different networking scenarios. This paper reviews characteristics of several different classes of routing protocols. Moreover, most of current routing protocols assume homogeneous networking conditions where all nodes have the same capabilities and resources. This paper presents extensive studies simulations for DSR, AODV, LAR1, FSR and WRP in homogenous and heterogeneous networks that consist of different nodes with different resources. The results showed that while all protocols perform reasonably well in homogenous networking conditions, their performance suffer significantly over heterogonous networks.