A Scalable Scheme for Counting Linear Extensions

Peer reviewe

Algorithm-Directed Crash Consistence in Non-Volatile Memory for HPC

Fault tolerance is one of the major design goals for HPC. The emergence of non-volatile memories (NVM) provides a solution to build fault tolerant HPC. Data in NVM-based main memory are not lost when the system crashes because of the non-volatility nature of NVM. However, because of volatile caches, data must be logged and explicitly flushed from caches into NVM to ensure consistence and correctness before crashes, which can cause large runtime overhead. In this paper, we introduce an algorithm-based method to establish crash consistence in NVM for HPC applications. We slightly extend application data structures or sparsely flush cache blocks, which introduce ignorable runtime overhead. Such extension or cache flushing allows us to use algorithm knowledge to \textit{reason} data consistence or correct inconsistent data when the application crashes. We demonstrate the effectiveness of our method for three algorithms, including an iterative solver, dense matrix multiplication, and Monte-Carlo simulation. Based on comprehensive performance evaluation on a variety of test environments, we demonstrate that our approach has very small runtime overhead (at most 8.2\% and less than 3\% in most cases), much smaller than that of traditional checkpoint, while having the same or less recomputation cost.Comment: 12 page

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