BioDiVinE: A Framework for Parallel Analysis of Biological Models

In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are described and their application is demonstrated by means of a case study

Tiramisu: A Polyhedral Compiler for Expressing Fast and Portable Code

This paper introduces Tiramisu, a polyhedral framework designed to generate high performance code for multiple platforms including multicores, GPUs, and distributed machines. Tiramisu introduces a scheduling language with novel extensions to explicitly manage the complexities that arise when targeting these systems. The framework is designed for the areas of image processing, stencils, linear algebra and deep learning. Tiramisu has two main features: it relies on a flexible representation based on the polyhedral model and it has a rich scheduling language allowing fine-grained control of optimizations. Tiramisu uses a four-level intermediate representation that allows full separation between the algorithms, loop transformations, data layouts, and communication. This separation simplifies targeting multiple hardware architectures with the same algorithm. We evaluate Tiramisu by writing a set of image processing, deep learning, and linear algebra benchmarks and compare them with state-of-the-art compilers and hand-tuned libraries. We show that Tiramisu matches or outperforms existing compilers and libraries on different hardware architectures, including multicore CPUs, GPUs, and distributed machines.Comment: arXiv admin note: substantial text overlap with arXiv:1803.0041

Non-uniform dependences partitioned by recurrence chains

Non-uniform distance loop dependences are a known obstacle to find parallel iterations. To find the outermost loop parallelism in these �irregular� loops, a novel method is presented based on recurrence chains. The scheme organizes non-uniformly dependent iterations into lexicographically ordered monotonic chains. While the initial and final iteration of monotonic chains form two parallel sets, the remaining iterations form an intermediate set that can be partitioned further. When there is only one pair of coupled array references, the non-uniform dependences are represented by a single recurrence equation. In that case, the chains in the intermediate set do not bifurcate and each can be executed as a WHILE loop. The independent iterations and the initial iterations of monotonic dependence chains constitute the outermost parallelism. The proposed approach compares favorably with other treatments of nonuniform dependences in the literature. When there are multiple recurrence equations, a dataflow parallel execution can be scheduled using the technique extensively to find maximum loop parallelism

Robust Region-of-Attraction Estimation

We propose a method to compute invariant subsets of the region-of-attraction for asymptotically stable equilibrium points of polynomial dynamical systems with bounded parametric uncertainty. Parameter-independent Lyapunov functions are used to characterize invariant subsets of the robust region-of-attraction. A branch-and-bound type refinement procedure reduces the conservatism. We demonstrate the method on an example from the literature and uncertain controlled short-period aircraft dynamics

On Range Searching with Semialgebraic Sets II

Let $P$ be a set of $n$ points in $\R^d$. We present a linear-size data structure for answering range queries on $P$ with constant-complexity semialgebraic sets as ranges, in time close to $O(n^{1-1/d})$. It essentially matches the performance of similar structures for simplex range searching, and, for $d\ge 5$, significantly improves earlier solutions by the first two authors obtained in~1994. This almost settles a long-standing open problem in range searching. The data structure is based on the polynomial-partitioning technique of Guth and Katz [arXiv:1011.4105], which shows that for a parameter $r$, $1 < r \le n$, there exists a $d$-variate polynomial $f$ of degree $O(r^{1/d})$ such that each connected component of $\R^d\setminus Z(f)$ contains at most $n/r$ points of $P$, where $Z(f)$ is the zero set of $f$. We present an efficient randomized algorithm for computing such a polynomial partition, which is of independent interest and is likely to have additional applications

Deforming glassy polystyrene: Influence of pressure, thermal history, and deformation mode on yielding and hardening

The toughness of a polymer glass is determined by the interplay of yielding, strain softening, and strain hardening. Molecular-dynamics simulations of a typical polymer glass, atactic polystyrene, under the influence of active deformation have been carried out to enlighten these processes. It is observed that the dominant interaction for the yield peak is of interchain nature and for the strain hardening of intrachain nature. A connection is made with the microscopic cage-to-cage motion. It is found that the deformation does not lead to complete erasure of the thermal history but that differences persist at large length scales. Also we find that the strain-hardening modulus increases with increasing external pressure. This new observation cannot be explained by current theories such as the one based on the entanglement picture and the inclusion of this effect will lead to an improvement in constitutive modeling