Parallelization of a Dynamic Monte Carlo Algorithm: a Partially Rejection-Free Conservative Approach

We experiment with a massively parallel implementation of an algorithm for simulating the dynamics of metastable decay in kinetic Ising models. The parallel scheme is directly applicable to a wide range of stochastic cellular automata where the discrete events (updates) are Poisson arrivals. For high performance, we utilize a continuous-time, asynchronous parallel version of the n-fold way rejection-free algorithm. Each processing element carries an lxl block of spins, and we employ the fast SHMEM-library routines on the Cray T3E distributed-memory parallel architecture. Different processing elements have different local simulated times. To ensure causality, the algorithm handles the asynchrony in a conservative fashion. Despite relatively low utilization and an intricate relationship between the average time increment and the size of the spin blocks, we find that for sufficiently large l the algorithm outperforms its corresponding parallel Metropolis (non-rejection-free) counterpart. As an example application, we present results for metastable decay in a model ferromagnetic or ferroelectric film, observed with a probe of area smaller than the total system.Comment: 17 pages, 7 figures, RevTex; submitted to the Journal of Computational Physic

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Dependability in Aggregation by Averaging

Aggregation is an important building block of modern distributed applications, allowing the determination of meaningful properties (e.g. network size, total storage capacity, average load, majorities, etc.) that are used to direct the execution of the system. However, the majority of the existing aggregation algorithms exhibit relevant dependability issues, when prospecting their use in real application environments. In this paper, we reveal some dependability issues of aggregation algorithms based on iterative averaging techniques, giving some directions to solve them. This class of algorithms is considered robust (when compared to common tree-based approaches), being independent from the used routing topology and providing an aggregation result at all nodes. However, their robustness is strongly challenged and their correctness often compromised, when changing the assumptions of their working environment to more realistic ones. The correctness of this class of algorithms relies on the maintenance of a fundamental invariant, commonly designated as "mass conservation". We will argue that this main invariant is often broken in practical settings, and that additional mechanisms and modifications are required to maintain it, incurring in some degradation of the algorithms performance. In particular, we discuss the behavior of three representative algorithms Push-Sum Protocol, Push-Pull Gossip protocol and Distributed Random Grouping under asynchronous and faulty (with message loss and node crashes) environments. More specifically, we propose and evaluate two new versions of the Push-Pull Gossip protocol, which solve its message interleaving problem (evidenced even in a synchronous operation mode).Comment: 14 pages. Presented in Inforum 200