Dynamic load balancing in parallel KD-tree k-means

One among the most influential and popular data mining methods is the k-Means algorithm for cluster analysis. Techniques for improving the efficiency of k-Means have been largely explored in two main directions. The amount of computation can be significantly reduced by adopting geometrical constraints and an efficient data structure, notably a multidimensional binary search tree (KD-Tree). These techniques allow to reduce the number of distance computations the algorithm performs at each iteration. A second direction is parallel processing, where data and computation loads are distributed over many processing nodes. However, little work has been done to provide a parallel formulation of the efficient sequential techniques based on KD-Trees. Such approaches are expected to have an irregular distribution of computation load and can suffer from load imbalance. This issue has so far limited the adoption of these efficient k-Means variants in parallel computing environments. In this work, we provide a parallel formulation of the KD-Tree based k-Means algorithm for distributed memory systems and address its load balancing issue. Three solutions have been developed and tested. Two approaches are based on a static partitioning of the data set and a third solution incorporates a dynamic load balancing policy

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

The Potential of Synergistic Static, Dynamic and Speculative Loop Nest Optimizations for Automatic Parallelization

Research in automatic parallelization of loop-centric programs started with static analysis, then broadened its arsenal to include dynamic inspection-execution and speculative execution, the best results involving hybrid static-dynamic schemes. Beyond the detection of parallelism in a sequential program, scalable parallelization on many-core processors involves hard and interesting parallelism adaptation and mapping challenges. These challenges include tailoring data locality to the memory hierarchy, structuring independent tasks hierarchically to exploit multiple levels of parallelism, tuning the synchronization grain, balancing the execution load, decoupling the execution into thread-level pipelines, and leveraging heterogeneous hardware with specialized accelerators. The polyhedral framework allows to model, construct and apply very complex loop nest transformations addressing most of the parallelism adaptation and mapping challenges. But apart from hardware-specific, back-end oriented transformations (if-conversion, trace scheduling, value prediction), loop nest optimization has essentially ignored dynamic and speculative techniques. Research in polyhedral compilation recently reached a significant milestone towards the support of dynamic, data-dependent control flow. This opens a large avenue for blending dynamic analyses and speculative techniques with advanced loop nest optimizations. Selecting real-world examples from SPEC benchmarks and numerical kernels, we make a case for the design of synergistic static, dynamic and speculative loop transformation techniques. We also sketch the embedding of dynamic information, including speculative assumptions, in the heart of affine transformation search spaces