Reliability and Makespan Optimization of Hardware Task Graphs in Partially Reconfigurable Platforms

This paper addresses the problem of reliability and makespan optimization of hardware task graphs in reconfigurable platforms by applying fault tolerance (FT) techniques to the running tasks based on the exploration of the Pareto set of solutions. In the presented solution, in contrast to the existing approaches in the literature, task graph scheduling, tasks parallelism, reconfiguration delay, and FT requirements are taken into account altogether. This paper first presents a model for hardware task graphs, task prefetch and scheduling, reconfigurable computer, and a fault model for reliability. Then, a mathematical model of an integer nonlinear multi-objective optimization problem is presented for improving the FT of hardware task graphs, scheduled in partially reconfigurable platforms. Experimental results show the positive impacts of choosing the FT techniques selected by the proposed solution, which is named Pareto-based. Thus, in comparison to nonfault-tolerant designs or other state-of-the-art FT approaches, without increasing makespan, about 850% mean time to failure (MTTF) improvement is achieved and, without degrading reliability, makespan is improved by 25%. In addition, experiments in fault-varying environments have demonstrated that the presented approach outperforms the existing state-of-the-art adaptive FT techniques in terms of both MTTF and makespan

Real-Time Scheduling in Heterogeneous Systems Considering Cache Reload Time Using Genetic Algorithms

Abstract. Since optimal assignment of tasks in a multiprocessor system is, in almost all practical cases, an NP-hard problem, in recent years some algorithms based on genetic algorithms have been proposed. Some of these algorithms have considered real-time applications with multiple objectives, total tardiness, completion time, etc. Here, we propose a suboptimal static scheduler of nonpreemptable tasks in hard real-time heterogeneous multiprocessor systems considering time constraints and cache reload time. The approach makes use of genetic algorithm to minimize total completion time and number of processors used, simultaneously. One important issue which makes this research different from previous ones is cache reload time. The method is implemented and the results are compared against a similar method

Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images