Community Detection via Semi-Synchronous Label Propagation Algorithms

A recently introduced novel community detection strategy is based on a label propagation algorithm (LPA) which uses the diffusion of information in the network to identify communities. Studies of LPAs showed that the strategy is effective in finding a good community structure. Label propagation step can be performed in parallel on all nodes (synchronous model) or sequentially (asynchronous model); both models present some drawback, e.g., algorithm termination is nor granted in the first case, performances can be worst in the second case. In this paper, we present a semi-synchronous version of LPA which aims to combine the advantages of both synchronous and asynchronous models. We prove that our models always converge to a stable labeling. Moreover, we experimentally investigate the effectiveness of the proposed strategy comparing its performance with the asynchronous model both in terms of quality, efficiency and stability. Tests show that the proposed protocol does not harm the quality of the partitioning. Moreover it is quite efficient; each propagation step is extremely parallelizable and it is more stable than the asynchronous model, thanks to the fact that only a small amount of randomization is used by our proposal.Comment: In Proc. of The International Workshop on Business Applications of Social Network Analysis (BASNA '10

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

CRAFT: A library for easier application-level Checkpoint/Restart and Automatic Fault Tolerance

In order to efficiently use the future generations of supercomputers, fault tolerance and power consumption are two of the prime challenges anticipated by the High Performance Computing (HPC) community. Checkpoint/Restart (CR) has been and still is the most widely used technique to deal with hard failures. Application-level CR is the most effective CR technique in terms of overhead efficiency but it takes a lot of implementation effort. This work presents the implementation of our C++ based library CRAFT (Checkpoint-Restart and Automatic Fault Tolerance), which serves two purposes. First, it provides an extendable library that significantly eases the implementation of application-level checkpointing. The most basic and frequently used checkpoint data types are already part of CRAFT and can be directly used out of the box. The library can be easily extended to add more data types. As means of overhead reduction, the library offers a build-in asynchronous checkpointing mechanism and also supports the Scalable Checkpoint/Restart (SCR) library for node level checkpointing. Second, CRAFT provides an easier interface for User-Level Failure Mitigation (ULFM) based dynamic process recovery, which significantly reduces the complexity and effort of failure detection and communication recovery mechanism. By utilizing both functionalities together, applications can write application-level checkpoints and recover dynamically from process failures with very limited programming effort. This work presents the design and use of our library in detail. The associated overheads are thoroughly analyzed using several benchmarks