autoAx: An Automatic Design Space Exploration and Circuit Building Methodology utilizing Libraries of Approximate Components

Approximate computing is an emerging paradigm for developing highly energy-efficient computing systems such as various accelerators. In the literature, many libraries of elementary approximate circuits have already been proposed to simplify the design process of approximate accelerators. Because these libraries contain from tens to thousands of approximate implementations for a single arithmetic operation it is intractable to find an optimal combination of approximate circuits in the library even for an application consisting of a few operations. An open problem is "how to effectively combine circuits from these libraries to construct complex approximate accelerators". This paper proposes a novel methodology for searching, selecting and combining the most suitable approximate circuits from a set of available libraries to generate an approximate accelerator for a given application. To enable fast design space generation and exploration, the methodology utilizes machine learning techniques to create computational models estimating the overall quality of processing and hardware cost without performing full synthesis at the accelerator level. Using the methodology, we construct hundreds of approximate accelerators (for a Sobel edge detector) showing different but relevant tradeoffs between the quality of processing and hardware cost and identify a corresponding Pareto-frontier. Furthermore, when searching for approximate implementations of a generic Gaussian filter consisting of 17 arithmetic operations, the proposed approach allows us to identify approximately $10^3$ highly important implementations from $10^{23}$ possible solutions in a few hours, while the exhaustive search would take four months on a high-end processor.Comment: Accepted for publication at the Design Automation Conference 2019 (DAC'19), Las Vegas, Nevada, US

Nmag micromagnetic simulation tool - software engineering lessons learned

We review design and development decisions and their impact for the open source code Nmag from a software engineering in computational science point of view. We summarise lessons learned and recommendations for future computational science projects. Key lessons include that encapsulating the simulation functionality in a library of a general purpose language, here Python, provides great flexibility in using the software. The choice of Python for the top-level user interface was very well received by users from the science and engineering community. The from-source installation in which required external libraries and dependencies are compiled from a tarball was remarkably robust. In places, the code is a lot more ambitious than necessary, which introduces unnecessary complexity and reduces main- tainability. Tests distributed with the package are useful, although more unit tests and continuous integration would have been desirable. The detailed documentation, together with a tutorial for the usage of the system, was perceived as one of its main strengths by the community.Comment: 7 pages, 5 figures, Software Engineering for Science, ICSE201

Experimental library screening demonstrates the successful application of computational protein design to large structural ensembles

The stability, activity, and solubility of a protein sequence are determined by a delicate balance of molecular interactions in a variety of conformational states. Even so, most computational protein design methods model sequences in the context of a single native conformation. Simulations that model the native state as an ensemble have been mostly neglected due to the lack of sufficiently powerful optimization algorithms for multistate design. Here, we have applied our multistate design algorithm to study the potential utility of various forms of input structural data for design. To facilitate a more thorough analysis, we developed new methods for the design and high-throughput stability determination of combinatorial mutation libraries based on protein design calculations. The application of these methods to the core design of a small model system produced many variants with improved thermodynamic stability and showed that multistate design methods can be readily applied to large structural ensembles. We found that exhaustive screening of our designed libraries helped to clarify several sources of simulation error that would have otherwise been difficult to ascertain. Interestingly, the lack of correlation between our simulated and experimentally measured stability values shows clearly that a design procedure need not reproduce experimental data exactly to achieve success. This surprising result suggests potentially fruitful directions for the improvement of computational protein design technology

Formal Verification of Security Protocol Implementations: A Survey

Automated formal verification of security protocols has been mostly focused on analyzing high-level abstract models which, however, are significantly different from real protocol implementations written in programming languages. Recently, some researchers have started investigating techniques that bring automated formal proofs closer to real implementations. This paper surveys these attempts, focusing on approaches that target the application code that implements protocol logic, rather than the libraries that implement cryptography. According to these approaches, libraries are assumed to correctly implement some models. The aim is to derive formal proofs that, under this assumption, give assurance about the application code that implements the protocol logic. The two main approaches of model extraction and code generation are presented, along with the main techniques adopted for each approac