SUMMARY: Recent advances in long-read sequencing and genome assembly techniques have enabled the generation of high-quality assemblies, often comprising megabase-scale sequences that span entire chromosomes. This results in longer but fewer sequences per genome, which affects the parallelization efficiency of whole-genome alignment tools. Current methods that assign one thread per query sequence now face suboptimal CPU use and longer runtimes because the processing of fewer sequences leaves many threads idle. We present mm2-plus, a fast and efficient method for whole-genome alignment, built upon the commonly used minimap2 aligner. Our improvements include a fine-grained parallel chaining algorithm and a fast method for differentiating primary and secondary chains. These optimizations accelerate the alignment of human, plant, and primate genomes by 1.6× to 7.2× without compromising accuracy. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/at-cg/mm2-plus and https://doi.org/10.5281/zenodo.18220923.

Genomics is playing an important role in transforming healthcare. Genetic data, however, is being produced at a rate that far outpaces Moore's Law. Many efforts have been made to accelerate genomics kernels on modern commodity hardware such as CPUs and GPUs, as well as custom accelerators (ASICs) for specific genomics kernels. While ASICs provide higher performance and energy efficiency than general-purpose hardware, they incur a high hardware design cost. Moreover, in order to extract the best performance, ASICs tend to have significantly different architectures for different kernels. The divergence of ASIC designs makes it difficult to run commonly used modern sequencing analysis pipelines due to software integration and programming challenges.

Over the last decade, advances in high-throughput sequencing and the availability of portable sequencers have enabled fast and cheap access to genetic data. For a given sample, sequencers typically output fragments of the DNA in the sample. Depending on the sequencing technology, the fragments range from a length of 150-250 at high accuracy to lengths in few tens of thousands but at much lower accuracy. Sequencing data is now being produced at a rate that far outpaces Moore's law and poses significant computational challenges on commodity hardware. To meet this demand, software tools have been extensively redesigned and new algorithms and custom hardware have been developed to deal with the diversity in sequencing data. However, a standard set of benchmarks that captures the diverse behaviors of these recent algorithms and can facilitate future architectural exploration is lacking. To that end, we present the GenomicsBench benchmark suite which contains 12 computationally intensive data-parallel kernels drawn from popular bioinformatics software tools. It covers the major steps in short and long-read genome sequence analysis pipelines such as basecalling, sequence mapping, de-novo assembly, variant calling and polishing. We observe that while these genomics kernels have abundant data level parallelism, it is often hard to exploit on commodity processors because of input-dependent irregularities. We also perform a detailed microarchitectural characterization of these kernels and identify their bottlenecks. GenomicsBench includes parallel versions of the source code with CPU and GPU implementations as applicable along with representative input datasets of two sizes - small and large.

During the past decade, novel Deep Learning (DL) algorithms, workloads and hardware have been developed to tackle a wide range of problems. Despite the advances in workload and hardware ecosystems, the programming methodology of DL systems is stagnant. DL workloads leverage either highly-optimized, yet platform-specific and inflexible kernels from DL libraries, or in the case of novel operators, reference implementations are built via DL framework primitives with underwhelming performance. This work introduces the Tensor Processing Primitives (TPP), a programming abstraction striving for efficient, portable implementation of DL workloads with high-productivity. TPPs define a compact, yet versatile set of 2D-tensor operators (or a virtual Tensor ISA), which subsequently can be utilized as building-blocks to construct complex operators on high-dimensional tensors. The TPP specification is platform-agnostic, thus code expressed via TPPs is portable, whereas the TPP implementation is highly-optimized and platform-specific. We demonstrate the efficacy and viability of our approach using standalone kernels and end-to-end DL & HPC workloads expressed entirely via TPPs that outperform state-of-the-art implementations on multiple platforms.

Full-batch training on Graph Neural Networks (GNN) to learn the structure of large graphs is a critical problem that needs to scale to hundreds of compute nodes to be feasible. It is challenging due to large memory capacity and bandwidth requirements on a single compute node and high communication volumes across multiple nodes. In this paper, we present DistGNN that optimizes the well-known Deep Graph Library (DGL) for full-batch training on CPU clusters via an efficient shared memory implementation, communication reduction using a minimum vertex-cut graph partitioning algorithm and communication avoidance using a family of delayed-update algorithms. Our results on four common GNN benchmark datasets: Reddit, OGB-Products, OGB-Papers and Proteins, show up to 3.7× speed-up using a single CPU socket and up to 97× speed-up using 128 CPU sockets, respectively, over baseline DGL implementations running on a single CPU socket.

Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer can generate 6 Terabases of data in less than two days, sequencing nearly 20 Billion short DNA fragments called reads at the low cost of $1000 per human genome. Large sequencing centers typically employ hundreds of such systems. Such highthroughput and low-cost generation of data underscores the need for commensurate acceleration in downstream computational analysis of the sequencing data. A fundamental step in downstream analysis is mapping of the reads to a long reference DNA sequence, such as a reference human genome. Sequence mapping is a compute-intensive step that accounts for more than 30% of the overall time of the GATK (Genome Analysis ToolKit) best practices workflow. BWA-MEM is one of the most widely used tools for sequence mapping and has tens of thousands of users. In this work, we focus on accelerating BWA-MEM through an efficient architecture aware implementation, while maintaining identical output. The volume of data requires distributed computing and is usually processed on clusters or cloud deployments with multicore processors usually being the platform of choice. Since the application can be easily parallelized across multiple sockets (even across distributed memory systems) by simply distributing the reads equally, we focus on performance improvements on a single socket multicore processor. BWA-MEM run time is dominated by three kernels, collectively responsible for more than 85% of the overall compute time. We improved the performance of the three kernels by 1) using techniques to improve cache reuse, 2) simplifying the algorithms, 3) replacing many small memory allocations with a few large contiguous ones to improve hardware prefetching of data, 4) software prefetching of data, and 5) utilization of SIMD wherever applicable and massive reorganization of the source code to enable these improvements. As a result, we achieved nearly 2x, 183x, and 8x speedups on the three kernels, respectively, resulting in up to 3.5x and 2.4x speedups on end-to-end compute time over the original BWA-MEM on single thread and single socket of Intel Xeon Skylake processor. To the best of our knowledge, this is the highest reported speedup over BWA-MEM (running on a single CPU) while using a single CPU or a single CPU-single GPGPU/FPGA combination.

High-throughput next generation sequencers (NGS) can rapidly read billions of short DNA fragments, called reads, at low cost. Moreover, their throughput is increasing and cost is decreasing at rates much faster than the Moore's law. This demands commensurate acceleration for NGS secondary analysis that process the reads to identify variations between genomes. Conventional architectural improvements can at best improve performance at the rate of Moore's law even if the software tools efficiently utilize the underlying architecture. Unfortunately, most of the dozens of software products developed for this purpose fail to exploit the underlying architecture well. Therefore, to match the pace of development of the sequencers, we will need architecture that is more tailored for the computational requirements of NGS secondary analysis as well as software that uses the architecture optimally.

Exact inference in Bayesian networks is NP-Hard. While many parallel algorithms have been proposed for this irregular problem, none have been shown to scale to even hundreds of processors. In this paper, we present a scalable distributed-memory parallel algorithm for exact inference based on Darwiche's approach, which poses inference as upward and downward accumulation of values computed at the nodes of an arithmetic circuit, a rooted directed acyclic graph. Our work includes parallel algorithms for both construction of the arithmetic circuit as well as inference using the circuit. We demonstrate the scalability of our algorithms for up to 1,536 cores on synthetic as well as real datasets, whose corresponding arithmetic circuits contain up to billions of nodes. The runtime for inference is only a small fraction of the runtime for circuit construction, providing the ability to quickly perform multiple inferences once the circuit is constructed.

Learning the structure of Bayesian networks, even in the static case, is NP-hard, compelling much of the research to focus on heuristic-based approaches. However, there are instances where exact solutions are desirable especially for small network sizes. In this work, we present a dynamic programming based exact solution to learn dynamic Bayesian network structure. Our method simultaneously learns intra- as well as higher order inter-time-slice interactions in the network. For n variables, our exact solution requires O(n2.2n(M+1)) computations to learn M-th order network. To handle such high computational requirements, we present a parallel exact solution to push the limit on the size of the networks that can be learned. Given p = 2kprocessors, the parallel algorithm runs in O(n2.2nM.(2n-k+ k)) time and achieves optimal parallel efficiency when 2n-k> k. Using MPI+X parallel programming model, the parallel algorithm linearly scales to 1,024 cores of a 64-node Intel Xeon InfiniBand cluster, sustaining >99% of parallel efficiency. We also show that the learned networks on gene network datasets are of high fidelity compared to heuristic-based techniques.

Learning Bayesian networks is NP-hard. Even with recent progress in heuristic and parallel algorithms, modeling capabilities still fall short of the scale of the problems encountered. In this paper, we present a massively parallel method for Bayesian network structure learning, and demonstrate its capability by constructing genome-scale gene networks of the model plant Arabidopsis thaliana from over 168.5 million gene expression values. We report strong scaling efficiency of 75% and demonstrate scaling to 1.57 million cores of the Tianhe-2 supercomputer. Our results constitute three and five orders of magnitude increase over previously published results in the scale of data analyzed and computations performed, respectively. We achieve this through algorithmic innovations, using efficient techniques to distribute work across all compute nodes, all available processors and coprocessors on each node, all available threads on each processor and coprocessor, and vectorization techniques to maximize single thread performance.