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  1. Free, publicly-accessible full text available May 30, 2023
  2. The Internet has become a critical component of modern civilization requiring scientific exploration akin to endeavors to understand the land, sea, air, and space environments. Understanding the baseline statistical distributions of traffic are essential to the scientific understanding of the Internet. Correlating data from different Internet observatories and outposts can be a useful tool for gaining insights into these distributions. This work compares observed sources from the largest Internet telescope (the CAIDA darknet telescope) with those from a commercial outpost (the GreyNoise honeyfarm). Neither of these locations actively emit Internet traffic and provide distinct observations of unsolicited Internet traffic (primarily botnets and scanners). Newly developed GraphBLAS hyperspace matrices and D4M associative array technologies enable the efficient analysis of these data on significant scales. The CAIDA sources are well approximated by a Zipf-Mandelbrot distribution. Over a 6-month period 70% of the brightest (highest frequency) sources in the CAIDA telescope are consistently detected by coeval observations in the GreyNoise honeyfarm. This overlap drops as the sources dim (reduce frequency) and as the time difference between the observations grows. The probability of seeing a CAIDA source is proportional to the logarithm of the brightness. The temporal correlations are well described by a modifiedmore »Cauchy distribution. These observations are consistent with a correlated high frequency beam of sources that drifts on a time scale of a month.« less
    Free, publicly-accessible full text available May 30, 2023
  3. Abstract Background Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. Results In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies asmore »well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. Conclusions ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.« less
  4. The Internet has never been more important to our society, and understanding the behavior of the Internet is essential. The Center for Applied Internet Data Analysis (CAIDA) Telescope observes a continuous stream of packets from an unsolicited darkspace representing 1/256 of the Internet. During 2019 and 2020 over 40,000,000,000,000 unique packets were collected representing the largest ever assembled public corpus of Internet traffic. Using the combined resources of the Supercomputing Centers at UC San Diego, Lawrence Berkeley National Laboratory, and MIT, the spatial temporal structure of anonymized source-destination pairs from the CAIDA Telescope data has been analyzed with GraphBLAS hierarchical hyper-sparse matrices. These analyses provide unique insight on this unsolicited Internet darkspace traffic with the discovery of many previously unseen scaling relations. The data show a significant sustained increase in unsolicited traffic corresponding to the start of the COVID19 pandemic, but relatively little change in the underlying scaling relations associated with unique sources, source fan-outs, unique links, destination fan-ins, and unique destinations. This work provides a demonstration of the practical feasibility and benefit of the safe collection and analysis of significant quantities of anonymized Internet traffic.
  5. The GraphBLAS are building blocks for expressing graph algorithms in terms of linear algebra. Currently, the GraphBLAS are defined as a C API. Implementations of the GraphBLAS have exposed limitations in expressiveness and performance due to limitations in C. A move to C++ should address many of these limitations while providing a simpler API. Furthermore, for methods based on user-defined types and operators, the performance should be significantly better. C++has grown into a pervasive programming language across many domains. We see a compelling argument to define a GraphBLAS C++ API. This paper presents our roadmap for the development of a GraphBLAS C++ API. Open issues are highlighted with the goal of fostering discussion and generating feedback within the GraphBLAS user community to guide us as we develop the GraphBLAS C++ API.
  6. The GraphBLAS emerged from an international effort to standardize linear-algebraic building blocks for computing on graphs and graph-structured data. The GraphBLAS is expressed as a C API and has paved the way for multiple implementations. The GraphBLAS C API, however, does not define how distributed-memory parallelism should be handled. This paper reviews various approaches for a GraphBLAS API for distributed computing. This work is guided by our experience with existing distributed memory libraries. Our goal for this paper is to highlight the pros and cons of different approaches rather than to advocate for one particular choice.
  7. Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for third generation sequences due to the high computational cost of analyzing sequences of length between 1Kb and 1Mb. Given the quadratic overhead of exact pairwise algorithms for long alignments, the community primarily relies on approximate algorithms that search only for high-quality alignments and stop early when one is not found. In this work, we present the first GPU optimization of the popular X-drop alignment algorithm, that we named LOGAN. Results show that our high performance multi-GPU implementation achieves up to 181.6 GCUPS and speed-ups up to 6.6 and 30.7 using 1 and 6 NVIDIA Tesla V100, respectively, over the state-of-the-art software running on two IBM Power9 processors using 168 CPU threads, with equivalent accuracy. We also demonstrate a 2.3 LOGAN speed-up versus ksw2, a state-of-art vectorized algorithm for sequence alignment implemented in minimap2, a long-read mapping software. To highlight the impact of our work on a real-world application, we couple LOGAN with a many-to-many long-read alignment software called BELLA, and demonstrate that our implementation improves the overallmore »BELLA runtime by up to 10.6. Finally, we adapt the Roofline model for LOGAN and demonstrate that our implementation is near optimal on the NVIDIA Tesla V100s.« less