Computing in Science and Engineering

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: 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 MATLAB®
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: Engineering the Software for Understanding Climate Change
Climate scientists build large, complex simulations with little or no software engineering training, and do not readily adopt the latest software engineering tools and techniques. In this paper, we describe an ethnographic study of the culture and practices of climate scientists at the Met Office Hadley Centre. The findings show that climate scientists have developed customized techniques for verification and validation that are tightly integrated into their approach to scientific research. Their software practices share many features of both agile and open source projects, in that they rely on self-organisation of the teams, extensive use of informal communication channels, and developers who are also users and domain experts. These observations suggest that domain-independent software development process models are unlikely to be useful for this type of scientific software development.

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.

Computing in Science and Engineering - September/October 2009 (Vol. 11, No. 5)
Computing in Science and Engineering

Comments (0) - Read and Add your own Comments