Computing in Science and Engineering

PrePrint: GPU Computing for Atmospheric Modeling Experience with a small kernel and implications for a full model
Much success has been achieved using GPUs to accelerate existing applications that are highly data parallel, or that are dominated by small, intense computational kernels. What are the prospects for porting existing large scientific models that do not fit this mold? We take an expensive routine from the CAM atmosphere model, and port it to a GPU using CUDA. We use the experience gained as a guide in thinking about porting the full application to an accelerator based system. We consider the best path forward for getting large scientific models running on accelerator based systems, and identify cases where porting may be feasible, and where a complete redesign may be the best option.

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PrePrint: Simulation Of Ion Permeation In Biological Membranes
Ion channels, as part of natures’ solution for regulating biological environments, are particularly interesting to device engineers seeking to understand how nanoscale molecular systems realize device-like functions, such as bio-sensing of organic analytes. What’s more, attaching molecular adaptors in desired orientations inside genetically engineered ion channels enhances the system functionality as a biosensor. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained ion channel simulator, offers a powerful and general approach to study ion channel permeation. In this paper, we have employed BioMOCA to study genetically engineered mutations of α-Hemolysin, with covalently attached β-Cyclodextrin. While the wild type α-Hemolysin is known to be slightly anion selective, the mutations introduce a slightly different charge distribution in the protein, resulting in stronger selectivity towards anions.

PrePrint: Developing an End-to-End Scientific Workflow: a Case Study of Using a Reliable, Lightweight, and Comprehensive Workflow Platform in e-Science
Service-oriented workflow provides a mechanism to automate the coordination of a sequence of tasks within a process, whereas each task is presented as a Web service and integrated into the workflow. It has become increasingly important to have an appropriate workflow platform to manage the scientific workflow lifecycle. In order to address this need, we propose to use Pipeline Pilot to manage the lifecycle of grid-based scientific workflow using SOA approach. Pipeline Pilot is a commercial software package dedicated to scientific research. It is reliable, lightweight and comprehensive. We then describe a case study of how we employ Pipeline Pilot to manage a workflow lifecycle for calculating material dielectric properties in grid environment. We also discuss lessons we learned in managing lifecycle of a service-oriented scientific workflow within e-Science.

PrePrint: The quantification of mountains in China Based on Geographic Information System
Two criteria are chosen to determine the boundaries of mountains in China. One is the domestic criterion (DC) in China; the other is an international criterion (IC). According to the DC, there are 4 000 265 km2 mountain areas; while according to the IC, there are 4 426 130 km2 mountain areas. The mountains are classified into six categories: C1.300～1 000 m;C2.1 000～1 500 m;C3.1 500～2 500 m;C4.2 500～3 500 m;C5.3 500～4 500 m;C6.≥4 500 m. The areas of mountains in the two criteria over 3 500 m are equal (C5 & C6). Except the area of C1 in DC is larger than international criterion (the value is 324 508 km2), the areas of C2, C3 and C4 in IC are larger than DC (the values are 2 273 km2, 336 186 km2 and 133 432 km2, separately).

PrePrint: Mutation Sensitivity Testing
In the process of testing their codes, computational scientists frequently encounter challenges that are not typically encountered by software engineers who develop testing techniques. In response to this oversight, we have developed a research technique, called Mutation Sensitivity Testing. Using this technique we found that a few well-designed tests were able to detect a high percentage of the code faults that were introduced into small MATLAB functions. Our experiments also showed that it is often more effective to reduce error tolerances than to conduct more tests. These results suggest that, in the field of testing, software engineers and computational scientists have much to offer each other.

PrePrint: Introducing: The libflame Library for Dense Matrix Computations
As part of the FLAME project, we have been dilligently developing new methodologies for analyzing, designing, and implementing linear algebra libraries. While we did not know it when we started, these techniques appear to solve many of the programmability problems that now face us with the advent of multicore and many-core architectures. These efforts have culminated in a new library, libflame, which strives to replace similar libraries that date back to the late 20th century. With this paper, we introduce the scientific computing community to this library.

PrePrint: The Accelerated Universe
The advent of powerful cosmological surveys demands a new generation of high-precision, large-volume, and high dynamic range simulations of structure formation in the Universe. Key aims of these simulations are understanding why the expansion of the Universe is accelerating and what dark matter is made of. The availability of Roadrunner, the world's first petaflop platform, led us to develop a new hybrid cosmology simulation code making essential use of hardware acceleration. We describe the strategies underlying the code and aspects of its implementation.

PrePrint: Globally Convergent Numerical Methods for Coefficient Inverse Problems for Imaging Inhomogeneities
How can we differentiate between an underground stone and a land mine? We discuss a class of new numerical methods for solving such problems. This class of methods concerns globally convergent algorithms for Coefficient Inverse Problems, unlike conventional locally convergent algorithms. Numerical results are presented modeling imaging of the spatially distributed dielectric permittivity function in an environment where antipersonnel land mines are embedded along with stones. While these results are concerned with the first generation of globally convergent algorithms, images obtained by the most recent second generation are also presented for a generic case of imaging of the dielectric permittivity function. The mathematical apparatus is sketched only very briefly with references to corresponding publications.

PrePrint: Scientific Computing in the Cloud
We investigate the feasibility of high-performance scientific computation using cloud computing resources, as an alternative to traditional resources. The availability of large, virtualized pools of computational resources raises the possibility of a new, advantageous compute paradigm for scientific research. To achieve this, we have developed a set of tools which make the cloud platform behave virtually like a local homogeneous computer cluster. We show that for research groups who do not need advanced network performance, cloud computing can provide convenient access to reliable, high-performance clusters, without the need to purchase and maintain or even understand sophisticated hardware and high-performance computational methods. For developers, cloud virtualization allows scientific codes to be optimized and pre-installed, facilitating control over the computational environment. Preliminary tests are presented for serial and parallelized versions of the widely used x-ray spectroscopy and electronic structure code FEFF on the Amazon elastic compute cloud, including CPU and network performance.

Computing in Science and Engineering - January/February 2010 (Vol. 12, No. 1)
Computing in Science and Engineering

PrePrint: All-Optical Binary Coded Decimal (BCD) Adder with the help of Terahertz Optical Asymmetric Demultiplexer
An all-optical binary-coded decimal (BCD) adder with the help of Terahertz Optical Asymmetric Demultiplexer (TOAD) is proposed and described. The paper describes the all optical BCD adder by using a set of all-optical full-adder, optical beam combiner, and optical switch. In electronic computing systems, BCD is an encoding scheme for decimal numbers in which each digit is represented by its own 4-bits binary sequence. Its main virtue is that it allows easy conversion to decimal digits for printing or display and faster decimal calculations. Numerical simulation result confirming described methods and conclusion are given in this paper.

PrePrint: Atomistic Modeling of Realistically extended Semiconductor Devices with NEMO / OMEN
The Nanoelectronic Modeling (NEMO) Toolset has been continually developed over the past 15 years to provide insight into nano-scale semiconductor devices that are dominated by quantum mechanical effects. The ability to represent realistically large devices in an atomistic basis has been the key element to match experimental data and to guide experiments. Now these insights flow into the creation of a new simulation engine called OMEN. Critical modeling requirements, scaling on parallel computers, and sample scientific results are discussed

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PrePrint: Report from the Second International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE 09)
Motivated by the general lack of interaction between software engineering researchers and computational scientists/engineers, a the Second International Workshop onon Software Engineering for Computational Science and Engineering (SE-CSE09) was held during the 2009 International Conference on Software Engineering in Vancouver, Canada. This report is a summary of the workshop and a description of the outcomes.

PrePrint: Rapid Assessment of the Secondary Disasters Induced by the Wenchuan Earthquake
The Wenchuan earthquake on May 12, 2008 led to large quantities of secondary mountain disasters. When the river channels were blocked by masses from the earthquake, the barrier lakes were formed. They were hazardous when the river inundated the farmlands and forests. If the damming objects collapsed, the flood could lead to massive casualties and property losses. Exploiting the real-time multi-platform remote sensing imagery data, we have discovered the barrier lakes induced by the earthquake, acquired the distribution information of the barrier lakes, and assessed the fatalness of them to prevent possible disastrous consequences. Also, after combining the multi-platform remote sensing data after the earthquake with that before the earthquake, we have assessed the farmland and forest losses. This work has been carried out within two weeks right after the earthquake, which helps the government visualize the disaster and plan emergency responses.

PrePrint: Ch MPI: Interpretive Parallel Computing in C
The Message Passing Interface (MPI) allows users to develop portable message-passing programs for parallel computing in C, C++, and Fortran. Ch is an embeddable C/C++ interpreter for executing C/C++ programs interpretively. Combining Ch with an MPI C/C++ library provides the functionality for rapid prototyping of MPI C/C++ programs without compilation and linking. In this article, the method of interfacing Ch scripts with MPI C libraries is introduced by using the MPICH2 C library as an example. Running MPI programs through the MPICH2-based Ch MPI package across heterogeneous platforms consisting of Linux and Windows machines is illustrated using different application examples. The performance of Ch MPI has been compared with the binary executable and MatlabMPI. For the calculation of $\pi$, Ch and Ch MPI are 2.35 times faster than Matlab and MatlabMPI. The study shows that Ch MPI can be used for rapid prototyping and cross-platform parallel scientific computing.

PrePrint: Automated Software Testing for MATLABĀ®
This paper describes the basic mechanics of automated unit testing for a general scientific and engineering audience. Using MATLAB xUnit, a unit test framework for MATLAB, the paper illustrates how to write and run tests, construct test cases, organize test files, and deal with the special issue of floating-point representation and arithmetic. The paper discusses the framework's design and architecture, including how various xUnit principles have been implemented and how procedural test-writing has been accommodated. The paper concludes with a brief introduction to test-driven development.

PrePrint: Evaluating the ecological suitability for Olive tree in Sichuan using GIS and comprehensive fuzzy method: Methodological development and application
We have used the Geographic Information System’s (GIS) spatial analysis functions and comprehensive fuzzy sets to evaluate and analyze the ecological suitability of the olive trees in Sichuan, China. The over-years experience of olive planting and amelioration data has also been used as an aid to this analysis taking consideration of climate, soil, and topography which are closely related to the olive growing habit. The results are representing the actual distribution of olive while providing alternative adaptive regions for olive growing, thus we are able to offer guidance for the olive cultivation in the region.

PrePrint: Report from the Second International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE 09)
Motivated by the general lack of interaction between software engineering researchers and computational scientists/engineers, a the Second International Workshop onon Software Engineering for Computational Science and Engineering (SE-CSE09) was held during the 2009 International Conference on Software Engineering in Vancouver, Canada. This report is a summary of the workshop and a description of the outcomes.

PrePrint: Managing Chaos: Bridging the cultural divide between engineers and scientists working within the life sciences
Within the rather chaotic atmosphere of scientific research the adoption of a software process, and the structured development of software, can be out of place. It is important to realize that the advancement of science is paramount, and so a balance must always be drawn between the cost and the benefit of the introduction of process into a research environment. This necessity presents a unique set of challenges to software development within the life sciences. These unique challenges are due to the cultural disconnect between life science research and software engineering. This paper outlines these challenges, and also discusses the software process used by the Institute for Systems Biology (ISB) to address them.

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