Efficient mining of discriminative molecular fragments

Frequent pattern discovery in structured data is receiving an increasing attention in many application areas of sciences. However, the computational complexity and the large amount of data to be explored often make the sequential algorithms unsuitable. In this context high performance distributed computing becomes a very interesting and promising approach. In this paper we present a parallel formulation of the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The application is characterized by a highly irregular tree-structured computation. No estimation is available for task workloads, which show a power-law distribution in a wide range. The proposed approach allows dynamic resource aggregation and provides fault and latency tolerance. These features make the distributed application suitable for multi-domain heterogeneous environments, such as computational Grids. The distributed application has been evaluated on the well known National Cancer Institute’s HIV-screening dataset

AutoAccel: Automated Accelerator Generation and Optimization with Composable, Parallel and Pipeline Architecture

CPU-FPGA heterogeneous architectures are attracting ever-increasing attention in an attempt to advance computational capabilities and energy efficiency in today's datacenters. These architectures provide programmers with the ability to reprogram the FPGAs for flexible acceleration of many workloads. Nonetheless, this advantage is often overshadowed by the poor programmability of FPGAs whose programming is conventionally a RTL design practice. Although recent advances in high-level synthesis (HLS) significantly improve the FPGA programmability, it still leaves programmers facing the challenge of identifying the optimal design configuration in a tremendous design space. This paper aims to address this challenge and pave the path from software programs towards high-quality FPGA accelerators. Specifically, we first propose the composable, parallel and pipeline (CPP) microarchitecture as a template of accelerator designs. Such a well-defined template is able to support efficient accelerator designs for a broad class of computation kernels, and more importantly, drastically reduce the design space. Also, we introduce an analytical model to capture the performance and resource trade-offs among different design configurations of the CPP microarchitecture, which lays the foundation for fast design space exploration. On top of the CPP microarchitecture and its analytical model, we develop the AutoAccel framework to make the entire accelerator generation automated. AutoAccel accepts a software program as an input and performs a series of code transformations based on the result of the analytical-model-based design space exploration to construct the desired CPP microarchitecture. Our experiments show that the AutoAccel-generated accelerators outperform their corresponding software implementations by an average of 72x for a broad class of computation kernels

High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The 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 receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations

Improving the scalability of parallel N-body applications with an event driven constraint based execution model

The scalability and efficiency of graph applications are significantly constrained by conventional systems and their supporting programming models. Technology trends like multicore, manycore, and heterogeneous system architectures are introducing further challenges and possibilities for emerging application domains such as graph applications. This paper explores the space of effective parallel execution of ephemeral graphs that are dynamically generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The workloads are expressed using the semantics of an Exascale computing execution model called ParalleX. For comparison, results using conventional execution model semantics are also presented. We find improved load balancing during runtime and automatic parallelism discovery improving efficiency using the advanced semantics for Exascale computing.Comment: 11 figure