DINO: Divergent node cloning for sustained redundancy in HPC

Complexity and scale of next generation HPC systems pose significant challenges in fault resilience methods such that contemporary checkpoint/restart (C/R) methods that address fail-stop behavior may be insufficient. Redundant computing has been proposed as an alternative at extreme scale. Triple redundancy has an advantage over C/R in that it can also detect silent data corruption (SDC) and then correct results via voting. However, current redundant computing approaches do not repair failed or corrupted replicas. Consequently, SDCs can no longer be detected after a replica failure since the system has been degraded to dual redundancy without voting capability. Hence, a job may have to be aborted if voting uncovers mismatching results between the remaining two replicas. And while replicas are logically equivalent, they may have divergent runtime states during job execution, which presents a challenge to simply creating new replicas dynamically. This problem is addressed by, DIvergent NOde cloning (DINO), a redundant execution environment that quickly recovers from hard failures. DINO consists of a novel node cloning service integrated into the MPI runtime system that solves the problem of consolidating divergent states among replicas on-the-fly. With DINO, after degradation to dual redundancy, a good replica can be quickly cloned so that triple redundancy is restored. We present experimental results over 9 NAS Parallel Benchmarks (NPB), Sweep3D and LULESH. Results confirm the applicability of the approach and the correctness of the recovery process and indicate that DINO can recover from failures nearly instantly. The cloning overhead depends on the process image size that needs to be transferred between source and destination of the clone operation and varies between 5.60 to 90.48 s. Simulation results with our model show that dual redundancy with DINO recovery always outperforms 2x and surpasses 3x redundancy on up to 1 million nodes. To the best of our knowledge, the design and implementation for repairing failed replicas in redundant MPI computing is unprecedented

Large-Scale Multi-Dimensional Document Clustering on GPU Clusters

Document clustering plays an important role in data mining systems. Recently, a flocking-based document clustering algorithm has been proposed to solve the problem through simulation resembling the flocking behavior of birds in nature. This method is superior to other clustering algorithms, including k-means, in the sense that the outcome is not sensitive to the initial state. One limitation of this approach is that the algorithmic complexity is inherently quadratic in the number of documents. As a result, execution time becomes a bottleneck with large number of documents. In this paper, we assess the benefits of exploiting the computational power of Beowulf-like clusters equipped with contemporary Graphics Processing Units (GPUs) as a means to significantly reduce the runtime of flocking-based document clustering. Our framework scales up to over one million documents processed simultaneously in a sixteen-node moderate GPU cluster. Results are also compared to a four-node cluster with higher-end GPUs. On these clusters, we observe 30X-50X speedups, which demonstrate the potential of GPU clusters to efficiently solve massive data mining problems. Such speedups combined with the scalability potential and accelerator-based parallelization are unique in the domain of document-based data mining, to the best of our knowledge. 1

Efficient distributed load balancing for parallel algorithms

2009 - 2010With the advent of massive parallel processing technology, exploiting the power offered by hundreds, or even thousands of processors is all but a trivial task. Computing by using multi-processor, multi-core or many-core adds a number of additional challenges related to the cooperation and communication of multiple processing units. The uneven distribution of data among the various processors, i.e. the load imbalance, represents one of the major problems in data parallel applications. Without good load distribution strategies, we cannot reach good speedup, thus good efficiency. Load balancing strategies can be classified in several ways, according to the methods used to balance workload. For instance, dynamic load balancing algorithms make scheduling decisions during the execution and commonly results in better performance compared to static approaches, where task assignment is done before the execution. Even more important is the difference between centralized and distributed load balancing approaches. In fact, despite that centralized algorithms have a wider vision of the computation, hence may exploit smarter balancing techniques, they expose global synchronization and communication bottlenecks involving the master node. This definitely does not assure scalability with the number of processors. This dissertation studies the impact of different load balancing strategies. In particular, one of the key observations driving our work is that distributed algorithms work better than centralized ones in the context of load balancing for multi-processors (alike for multi-cores and many-cores as well). We first show a centralized approach for load balancing, then we propose several distributed approaches for problems having different parallelization, workload distribution and communication pattern. We try to efficiently combine several approaches to improve performance, in particular using predictive metrics to obtain a per task compute-time estimation, using adaptive subdivision, improving dynamic load balancing and addressing distributed balancing schemas. The main challenge tackled on this thesis has been to combine all these approaches together in new and efficient load balancing schemas. We assess the proposed balancing techniques, starting from centralized approaches to distributed ones, in distinctive real case scenarios: Mesh-like computation, Parallel Ray Tracing, and Agent-based Simulations. Moreover, we test our algorithms with parallel hardware such has cluster of workstations, multi-core processors and exploiting SIMD vectorial instruction set. Finally, we conclude the thesis with several remarks, about the impact of distributed techniques, the effect of the communication pattern and workload distribution, the use of cost estimation for adaptive partitioning, the trade-off fast versus accuracy in prediction-based approaches, the effectiveness of work stealing combined with sorting, and a non-trivial way to exploit hybrid CPUGPU computations. [edited by author]IX n.s

Semantically enhanced document clustering

This thesis advocates the view that traditional document clustering could be significantly improved by representing documents at different levels of abstraction at which the similarity between documents is considered. The improvement is with regard to the alignment of the clustering solutions to human judgement. The proposed methodology employs semantics with which the conceptual similarity be-tween documents is measured. The goal is to design algorithms which implement the meth-odology, in order to solve the following research problems: (i) how to obtain multiple deter-ministic clustering solutions; (ii) how to produce coherent large-scale clustering solutions across domains, regardless of the number of clusters; (iii) how to obtain clustering solutions which align well with human judgement; and (iv) how to produce specific clustering solu-tions from the perspective of the user’s understanding for the domain of interest. The developed clustering methodology enhances separation between and improved coher-ence within clusters generated across several domains by using levels of abstraction. The methodology employs a semantically enhanced text stemmer, which is developed for the pur-pose of producing coherent clustering, and a concept index that provides generic document representation and reduced dimensionality of document representation. These characteristics of the methodology enable addressing the limitations of traditional text document clustering by employing computationally expensive similarity measures such as Earth Mover’s Distance (EMD), which theoretically aligns the clustering solutions closer to human judgement. A threshold for similarity between documents that employs many-to-many similarity matching is proposed and experimentally proven to benefit the traditional clustering algorithms in pro-ducing clustering solutions aligned closer to human judgement. 4 The experimental validation demonstrates the scalability of the semantically enhanced document clustering methodology and supports the contributions: (i) multiple deterministic clustering solutions and different viewpoints to a document collection are obtained; (ii) the use of concept indexing as a document representation technique in the domain of document clustering is beneficial for producing coherent clusters across domains; (ii) SETS algorithm provides an improved text normalisation by using external knowledge; (iv) a method for measuring similarity between documents on a large scale by using many-to-many matching; (v) a semantically enhanced methodology that employs levels of abstraction that correspond to a user’s background, understanding and motivation. The achieved results will benefit the research community working in the area of document management, information retrieval, data mining and knowledge management