Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids

Towards Ultra-High Performance and Energy Efficiency of Deep Learning Systems: An Algorithm-Hardware Co-Optimization Framework

Hardware accelerations of deep learning systems have been extensively investigated in industry and academia. The aim of this paper is to achieve ultra-high energy efficiency and performance for hardware implementations of deep neural networks (DNNs). An algorithm-hardware co-optimization framework is developed, which is applicable to different DNN types, sizes, and application scenarios. The algorithm part adopts the general block-circulant matrices to achieve a fine-grained tradeoff between accuracy and compression ratio. It applies to both fully-connected and convolutional layers and contains a mathematically rigorous proof of the effectiveness of the method. The proposed algorithm reduces computational complexity per layer from O($n^2$) to O($n\log n$) and storage complexity from O($n^2$) to O($n$), both for training and inference. The hardware part consists of highly efficient Field Programmable Gate Array (FPGA)-based implementations using effective reconfiguration, batch processing, deep pipelining, resource re-using, and hierarchical control. Experimental results demonstrate that the proposed framework achieves at least 152X speedup and 71X energy efficiency gain compared with IBM TrueNorth processor under the same test accuracy. It achieves at least 31X energy efficiency gain compared with the reference FPGA-based work.Comment: 6 figures, AAAI Conference on Artificial Intelligence, 201

Inner product computation for sparse iterative solvers on\ud distributed supercomputer

Recent years have witnessed that iterative Krylov methods without re-designing are not suitable for distribute supercomputers because of intensive global communications. It is well accepted that re-engineering Krylov methods for prescribed computer architecture is necessary and important to achieve higher performance and scalability. The paper focuses on simple and practical ways to re-organize Krylov methods and improve their performance for current heterogeneous distributed supercomputers. In construct with most of current software development of Krylov methods which usually focuses on efficient matrix vector multiplications, the paper focuses on the way to compute inner products on supercomputers and explains why inner product computation on current heterogeneous distributed supercomputers is crucial for scalable Krylov methods. Communication complexity analysis shows that how the inner product computation can be the bottleneck of performance of (inner) product-type iterative solvers on distributed supercomputers due to global communications. Principles of reducing such global communications are discussed. The importance of minimizing communications is demonstrated by experiments using up to 900 processors. The experiments were carried on a Dawning 5000A, one of the fastest and earliest heterogeneous supercomputers in the world. Both the analysis and experiments indicates that inner product computation is very likely to be the most challenging kernel for inner product-based iterative solvers to achieve exascale

Learning to infer: RL-based search for DNN primitive selection on Heterogeneous Embedded Systems

Deep Learning is increasingly being adopted by industry for computer vision applications running on embedded devices. While Convolutional Neural Networks' accuracy has achieved a mature and remarkable state, inference latency and throughput are a major concern especially when targeting low-cost and low-power embedded platforms. CNNs' inference latency may become a bottleneck for Deep Learning adoption by industry, as it is a crucial specification for many real-time processes. Furthermore, deployment of CNNs across heterogeneous platforms presents major compatibility issues due to vendor-specific technology and acceleration libraries. In this work, we present QS-DNN, a fully automatic search based on Reinforcement Learning which, combined with an inference engine optimizer, efficiently explores through the design space and empirically finds the optimal combinations of libraries and primitives to speed up the inference of CNNs on heterogeneous embedded devices. We show that, an optimized combination can achieve 45x speedup in inference latency on CPU compared to a dependency-free baseline and 2x on average on GPGPU compared to the best vendor library. Further, we demonstrate that, the quality of results and time "to-solution" is much better than with Random Search and achieves up to 15x better results for a short-time search

Distributed computing methodology for training neural networks in an image-guided diagnostic application

Distributed computing is a process through which a set of computers connected by a network is used collectively to solve a single problem. In this paper, we propose a distributed computing methodology for training neural networks for the detection of lesions in colonoscopy. Our approach is based on partitioning the training set across multiple processors using a parallel virtual machine. In this way, interconnected computers of varied architectures can be used for the distributed evaluation of the error function and gradient values, and, thus, training neural networks utilizing various learning methods. The proposed methodology has large granularity and low synchronization, and has been implemented and tested. Our results indicate that the parallel virtual machine implementation of the training algorithms developed leads to considerable speedup, especially when large network architectures and training sets are used