514517
Efficient data access for parallel BLAST
Searching biological sequence databases is one of the most routine tasks in computational biology. This task is significantly hampered by the exponential growth in sequence database sizes. Recent advances in parallelization of biological sequence search applications have enabled bioinformatics researchers to utilize high-performance computing platforms and, as a result, greatly reduce the execution time of their sequence database searches. However, existing parallel sequence search tools have been focusing mostly on parallelizing the sequence alignment engine. While the computation-intensive alignment tasks become cheaper with larger machines, data-intensive initial preparation and result merging tasks become more expensive. Inefficient handling of input and output data can easily create performance bottlenecks even on supercomputers. It also causes a considerable data management overhead. In this paper, we present a set of techniques for efficient and flexible data handling in parallel sequence search applications. We demonstrate our optimizations through improving mpiBLAST, an open-source parallel BLAST tool rapidly gaining popularity. These optimization techniques aim at enabling flexible database partitioning, reducing I/O by caching small auxiliary files and results, enabling parallel I/O on shared files, and performing scalable result processing protocols. As a result, we reduce mpiBLAST users' operational overhead by removing the requirement of pre-partitioning databases. Meanwhile, our experiments show that these techniques can bring by an order of magnitude improvement to both the overall performance and scalability of mpiBLAST.
10862904
Improving MPI-IO output performance with active buffering plus threads
Efficient collective output of intermediate results to secondary storage becomes more and more important for scientific simulations as the gap between processing power/interconnection bandwidth and the I/O system bandwidth enlarges. Dedicated servers can offload I/O from compute processors and shorten the execution time, but it is not always possible or easy for an application to use them. We propose the use of active buffering with threads (ABT) for overlapping I/O with computation efficiently and flexibly without dedicated I/O servers. We show that the implementation of ABT in ROMIO, a popular implementation of MPI-IO, greatly reduces the application-visible cost of ROMIO's collective write calls, and improves an application's overall performance by hiding I/O cost and saving implicit synchronization overhead from collective write operations. Further, ABT is high-level, platform-independent, and transparent to users, giving users the benefit of overlapping I/O with other processing tasks even when the file system or parallel I/O library does not support asynchronous I/O.
2357877
Edge-based rich representation for vehicle classification
In this paper, we propose an approach to vehicle classification under a mid-field surveillance framework. We develop a repeatable and discriminative feature based on edge points and modified SIFT descriptors, and introduce a rich representation for object classes. Experimental results show the proposed approach is promising for vehicle classification in surveillance videos despite great challenges such as limited image size and quality and large intra-class variations. Comparisons demonstrate the proposed approach outperforms other methods
12219640
Maximum-diversity transmissions over doubly selective wireless channels
High data rates and multipath propagation give rise to frequency-selectivity of wireless channels, while carrier frequency offsets and mobility-induced Doppler shifts introduce time-selectivity in wireless links. The resulting time- and frequency-selective (or doubly selective) channels offer joint multipath-Doppler diversity gains. Relying on a basis expansion model of the doubly selective channel, we prove that the maximum achievable multipath-Doppler diversity order is determined by the rank of the correlation matrix of the channel's expansion coefficients, and is multiplicative in the effective degrees of freedom that the channel exhibits in the time and frequency dimensions. Interestingly, it turns out that time-frequency reception alone does not guarantee maximum diversity, unless the transmission is also designed judiciously. We design such block precoded transmissions. The corresponding designs for frequency-selective or time-selective channels follow as special cases, and thorough simulations are provided to corroborate our theoretical findings.