A Parallelizable Acceleration Framework for Packing Linear Programs

This paper presents an acceleration framework for packing linear programming problems where the amount of data available is limited, i.e., where the number of constraints m is small compared to the variable dimension n. The framework can be used as a black box to speed up linear programming solvers dramatically, by two orders of magnitude in our experiments. We present worst-case guarantees on the quality of the solution and the speedup provided by the algorithm, showing that the framework provides an approximately optimal solution while running the original solver on a much smaller problem. The framework can be used to accelerate exact solvers, approximate solvers, and parallel/distributed solvers. Further, it can be used for both linear programs and integer linear programs

GPU acceleration for statistical gene classification

The use of Bioinformatic tools in routine clinical diagnostics is still facing a number of issues. The more complex and advanced bioinformatic tools become, the more performance is required by the computing platforms. Unfortunately, the cost of parallel computing platforms is usually prohibitive for both public and small private medical practices. This paper presents a successful experience in using the parallel processing capabilities of Graphical Processing Units (GPU) to speed up bioinformatic tasks such as statistical classification of gene expression profiles. The results show that using open source CUDA programming libraries allows to obtain a significant increase in performances and therefore to shorten the gap between advanced bioinformatic tools and real medical practic

VHDL-AMS based genetic optimisation of fuzzy logic controllers

Purpose – This paper presents a VHDL-AMS based genetic optimisation methodology for fuzzy logic controllers (FLCs) used in complex automotive systems and modelled in mixed physical domains. A case study applying this novel method to an active suspension system has been investigated to obtain a new type of fuzzy logic membership function with irregular shapes optimised for best performance. Design/methodology/approach – The geometrical shapes of the fuzzy logic membership functions are irregular and optimised using a genetic algorithm (GA). In this optimisation technique, VHDL-AMS is used not only for the modelling and simulation of the FLC and its underlying active suspension system but also for the implementation of a parallel GA directly in the system testbench. Findings – Simulation results show that the proposed FLC has superior performance in all test cases to that of existing FLCs that use regular-shape, triangular or trapezoidal membership functions. Research limitations – The test of the FLC has only been done in the simulation stage, no physical prototype has been made. Originality/value – This paper proposes a novel way of improving the FLC’s performance and a new application area for VHDL-AMS

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin