Engineering Parallel String Sorting

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we first propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Then we focus on NUMA architectures, and develop parallel multiway LCP-merge and -mergesort to reduce the number of random memory accesses to remote nodes. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations. Comprehensive experiments on five current multi-core platforms are then reported and discussed. The experiments show that our implementations scale very well on real-world inputs and modern machines.Comment: 46 pages, extension of "Parallel String Sample Sort" arXiv:1305.115

khmer: Working with Big Data in Bioinformatics

We introduce design and optimization considerations for the 'khmer' package.Comment: Invited chapter for forthcoming book on Performance of Open Source Application

Parallel String Sample Sort

We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we propose string sample sort. The algorithm makes effective use of the memory hierarchy, uses additional word level parallelism, and largely avoids branch mispredictions. Additionally, we parallelize variants of multikey quicksort and radix sort that are also useful in certain situations.Comment: 34 pages, 7 figures and 12 table

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize the multiple processors, available memory, high-bandwidth of storage, and hardware compression accelerators if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting the input data are provided by {\it plug-in} tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of NGS data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime for whole-genome sequencing data from about 20 hours to about nine minutes on the same system using up to 711 GB of memory

Vector Quantization Video Encoder Using Hierarchical Cache Memory Scheme

A system compresses image blocks via successive hierarchical stages and motion encoders which employ caches updated by stack replacement algorithms. Initially, a background detector compares the present image block with a corresponding previously encoded image block and if similar, the background detector terminates the encoding procedure by setting a flag bit. Otherwise, the image block is decomposed into smaller present image subblocks. The smaller present image subblocks are each compared with a corresponding previously encoded image subblock of comparable size within the present image block. When a present image subblock is similar to a corresponding previously encoded image subblock, then the procedure is terminated by setting a flag bit. Alternatively, the present image subblock is forwarded to a motion encoder where it is compared with displaced image subblocks, which are formed by displacing previously encoded image subblocks by motion vectors that are stored in a cache, to derive a first distortion vector. When the first distortion vector is below a first threshold TM, the procedure is terminated and the present image subblock is encoded by setting flag bit and a cache index corresponding to the first distortion vector. Alternatively, the present image subblock is passed to a block matching encoder where it is compared with other previously encoded image subblocks to derive a second distortion vector. When the second distortion vector is below a second threshold Tm, the procedure is terminated by setting a flag bit, by generating the second distortion vector, and by updating the cache.Georgia Tech Research Corporatio

ret2spec: Speculative Execution Using Return Stack Buffers

Speculative execution is an optimization technique that has been part of CPUs for over a decade. It predicts the outcome and target of branch instructions to avoid stalling the execution pipeline. However, until recently, the security implications of speculative code execution have not been studied. In this paper, we investigate a special type of branch predictor that is responsible for predicting return addresses. To the best of our knowledge, we are the first to study return address predictors and their consequences for the security of modern software. In our work, we show how return stack buffers (RSBs), the core unit of return address predictors, can be used to trigger misspeculations. Based on this knowledge, we propose two new attack variants using RSBs that give attackers similar capabilities as the documented Spectre attacks. We show how local attackers can gain arbitrary speculative code execution across processes, e.g., to leak passwords another user enters on a shared system. Our evaluation showed that the recent Spectre countermeasures deployed in operating systems can also cover such RSB-based cross-process attacks. Yet we then demonstrate that attackers can trigger misspeculation in JIT environments in order to leak arbitrary memory content of browser processes. Reading outside the sandboxed memory region with JIT-compiled code is still possible with 80\% accuracy on average.Comment: Updating to the cam-ready version and adding reference to the original pape