Comparing parallel algorithms for van der waals energy with cell-list technique for protein structure prediction / Comparando algoritmos paralelos para energia de van der waals com técnica de lista de células para predição de estrutura de proteína

The discovery of the structure of a protein is a difficult and expensive task, because it requires minimizing different energies related to them. The van der Waals energy hás the most expensive evaluation in this context, and computational methods have been developed in this way, such as Genetic Algorithm (GA) and cell-list technique, which reduces its the complexity from O(n2) to O(n). Even with the support of GA and cell lists, the van der Waals energy evaluation still requires a long computing time, even for a small protein. Parallel Computing is capable to reduce the runtime to predict the structure of proteins. Parallel algorithms in such context are usually specific for one programming model and computer architecture, resulting in limited speedups. This paper compares the runtime of three distinct parallel algorithms for the evaluation of an ab initio and full-atom approach based on GA and cell-list technique, in order to minimize the van der Waals energy. The three parallel algorithms are in C and use one of these programming models: MPI, OpenMP or hybrid (MPI+Open MP). Our results show that van der Waals Energy are executed faster and with better speedups when using hybrid and more flexible parallel algorithms to predict the structure of larger proteins. We also show that for small proteins the communication of MPI imposes a high overhead for the parallel execution and, thus the Open MP presents a better relation cost x benefit in such cases

An Empirical Evaluation of the Cost and Effectiveness of Structural Testing Criteria for Concurrent Programs

AbstractConcurrent program testing is not a trivial task. Features like nondeterminism, communication and synchronization impose new challenges that must be considered during the testing activity. Some initiatives have proposed testing approaches for concurrent programs, in which different paradigms and programming languages are considered. However, in general, these contributions do not present a well-formed experimental study to validate their ideas. The problem is that the data used and generated during the validation is not always available, hampering the replication of studies in the context of other testing approaches. This paper presents an experimental study, taking into account the concepts of the Experimental Software En- gineering to evaluate the cost, effectiveness and strength of the structural testing criteria for message-passing programs. The evaluation was conducted considering a benchmark composed of eight MPI programs. A set of eight structural testing criteria defined for message-passing programs was evaluated with the ValiMPI testing tool, which provides the support required to apply the investigated testing criteria. The results indicate the complementary aspect of the criteria and the information about cost and effectiveness has contributed to the establishment of an incremental testing strategy to apply the criteria. All material generated during the experimental study is available for further comparisons

Science handbook

2006 handbook for the faculty of Scienc

Science handbook

2006 handbook for the faculty of Scienc

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance