Elimination of the diagonalization bottleneck in parallel Direct-SCF methods

Summary It is shown that the matrix diagonalization bottleneck associated with thesequential O(N _BFN ³ ) diagonalization of the fock matrix within each iteration of the Direct-SCF procedure may be eliminated, and replaced instead with a combination ofparallel O(N _BFN ^<4 ) andsequential O(N _Sub ³ ) steps. For large basis sets, the relation N_Sub N_BFN between the dimension of the expansion subspace and the number of basis functions leads to a method of wave-function optimization in which the sequential bottleneck is eliminated. As a side benefit, the second-order iterative procedure on which this method is based displays superior convergence properties, and provides greater insight into the behavior of the energy with respect to orbital variations, than the traditional first-order, fixed-point, iterative approaches. The implementation of this method may be incorporated into essentially any existing Direct-SCF program with only minimal, and localized, changes.     

Discontinuous Galerkin methods on graphics processing units for nonlinear hyperbolic conservation laws

We present a novel implementation of the modal DG method for hyperbolic conservation laws in two dimensions on graphics processing units (GPUs) using NVIDIA's Compute Unified Device Architecture. Both flexible and highly accurate, DG methods accommodate parallel architectures well as their discontinuous nature produces element‐local approximations. High‐performance scientific computing suits GPUs well, as these powerful, massively parallel, cost‐effective devices have recently included support for double‐precision floating‐point numbers. Computed examples for Euler equations over unstructured triangle meshes demonstrate the effectiveness of our implementation on an NVIDIA GTX 580 device. Profiling of our method reveals performance comparable with an existing nodal DG‐GPU implementation for linear problems. Copyright © 2014 John Wiley & Sons, Ltd.     

The Construction of DNA Logic Gates Restricted to Certain Live Cells Based on the Structure Programmability and Aptamer-Cell Affinity of G-Quadruplexes

DNA computation is considered a fascinating alternative to silicon-based computers; it has evoked substantial attention and made rapid advances. Besides realizing versatile functions, implementing spatiotemporal control of logic operations, especially at the cellular level, is also of great significance to the development of DNA computation. However, developing simple and efficient methods to restrict DNA logic gates performing in live cells is still a challenge. In this work, a series of DNA logic gates was designed by taking full advantage of the diversity and programmability of the G-quadruplex (G4) structure. More importantly, by further using the high affinity and specific endocytosis of cells to aptamer G4, an INHIBIT logic gate has been realized whose operational site is precisely restricted to specific live cells. The design strategy might have great potential in the field of molecular computation and smart bio-applications.     

Statistical assertion: A more powerful method for debugging scientific applications

Traditional debuggers are of limited value for modern scientific codes that manipulate large complex data structures. Current parallel machines make this even more complicated, because the data structure may be distributed across processors, making it difficult to view/interpret and validate its contents. Therefore, many applications’ developers resort to placing validation code directly in the source program. This paper discusses a novel debug-time assertion, called a “Statistical Assertion”, that allows using extracted statistics instead of raw data to reason about large data structures, therefore help locating coding defects. In this paper, we present the design and implementation of an ‘extendable’ statistical-framework which executes the assertion in parallel by exploiting the underlying parallel system. We illustrate the debugging technique with a molecular dynamics simulation. The performance is evaluated on a 20,000 processor Cray XE6 to show that it is useful for real-time debugging.     

Flexible composition and execution of large scale applications on distributed e-infrastructures

Computer simulation is finding a role in an increasing number of scientific disciplines, concomitant with the rise in available computing power. Marshalling this power facilitates new, more effective and different research than has been hitherto possible. Realizing this inevitably requires access to computational power beyond the desktop, making use of clusters, supercomputers, data repositories, networks and distributed aggregations of these resources. The use of diverse e-infrastructure brings with it the ability to perform distributed multiscale simulations. Accessing one such resource entails a number of usability and security problems; when multiple geographically distributed resources are involved, the difficulty is compounded. In this paper we present a solution, the Application Hosting Environment,³ which provides a Software as a Service layer on top of distributed e-infrastructure resources. We describe the performance and usability enhancements present in AHE version 3, and show how these have led to a high performance, easy to use gateway for computational scientists working in diverse application domains, from computational physics and chemistry, materials science to biology and biomedicine.     

Simple matching vs linear assignment in scheduling models with positional effects: A critical review

This paper addresses scheduling models in which a contribution of an individual job to the objective function is represented by the product of its processing time and a certain positional weight. We review most of the known results in the area and demonstrate that a linear assignment algorithm as part of previously known solution procedures can be replaced by a faster matching algorithm that minimizes a linear form over permutations. Our approach reduces the running time of the resulting algorithms by up to two orders, and carries over to a wider range of models, with more general positional effects. Besides, the same approach works for the models with no prior history of study, e.g., parallel machine scheduling with deterioration and maintenance to minimize total flow time.     

Point availability of Gaver’s duplex system supervised by a safety device unit

We analyse the point availability of Gaver’s parallel system supervised by a safety device. For safety reasons, no unit is allowed to operate without supervision. The entire system is attended by two heterogeneous repairmen. Our methodology is based on the theory of sectionally holomorphic functions combined with the notion of dual transforms. As an application we consider Coxian repair time distributions.     

基于荧光光谱技术的菜籽油氧化状态智能评价

菜籽油在加工及贮藏过程中，易受氧气、温度、光照等因素的影响，产生氧化酸败现象。为准确判断油脂氧化程度，实现不同氧化模式下菜籽油品质的快速判别，采用三维同步荧光光谱技术结合平行因子分析法及BP神经网络法建立菜籽油氧化状态的智能评价模型。以冷榨菜籽油为原料，将样品分别置于常温、Schaal烘箱、高温模式中氧化处理，期间采集菜籽油的三维同步荧光光谱数据及理化指标，当理化指标超出国标限定范围时，停止采集数据。结果表明，菜籽油中荧光物质在不同氧化模式中的演变规律呈显著差异，氧化温度对菜籽油荧光光谱有明显影响。常温氧化350 d与第1 d相比，菜籽油的特征荧光峰位置无变化，仅在激发波长Ex为620和660 nm附近荧光峰强度发生微弱变化；Schaal烘箱氧化26 d后，在激发波长Ex为620和660 nm附近荧光峰强度显著减弱，且在激发波长Ex为350～450 nm之间有新的荧光峰生成；高温氧化48 h后，Ex为620和660 nm处荧光峰消失，在Ex为400～550 nm处产生显著荧光峰，相对Schaal烘箱氧化，荧光波长发生一定程度红移，这是由于高温氧化过程中油脂氧化生成的物质稳定性较差引起的。利用平行因子分析法对三维同步荧光光谱数据进行分解获取有效的二维荧光光谱数据，当组分数为6，Δλ=60 nm时激发波长的载荷值最大，不同样品间差异最显著。选定Δλ=60 nm波段的二维荧光光谱数据用于智能评价，作为BP神经网络模型的输入值，以极性组分作为模型输出值，分别对菜籽油三种氧化模式数据建模训练。实验结果表明，三种氧化模式对应的训练集、验证集、测试集模型相关系数r均能达到0.9以上，其中常温氧化模式中验证集及测试集模型的相关系数r为1，输出值与目标值较接近，模型的预测效果较好；综合三种氧化模式数据建模，对应训练集、验证集、测试集模型的相关系数分别为0.999，0.913和0.988，均方误差均较小，说明该模型能准确判断菜籽油的不同氧化状态。因此，三维同步荧光光谱技术结合平行因子分析法、BP神经网络法建立快速检测模型能实现菜籽油不同氧化状态的判别，为菜籽油的氧化程度的评价提供新方法，同时为其他食用油的品质评价提供参考。