General-purpose compilers abstract away parallelism, locality, and synchronization, limiting their effectiveness on modern spatial architectures. As modern computing architectures increasingly rely on fine-grained control over data movement, execution order, and compute placement for performance, compiler infrastructure must provide explicit mechanisms for orchestrating compute and data to fully exploit such architectures. We introduce MLIR-AIR, a novel, open source compiler stack built on MLIR that bridges the semantic gap between high-level workloads and fine-grained spatial architectures such as AMD’s NPUs. MLIR-AIR defines the AIR dialect, which provides structured representations for asynchronous and hierarchical operations across compute and memory resources. AIR primitives allow the compiler to orchestrate spatial scheduling, distribute computation across hardware regions, and overlap communication with computation without relying on ad hoc runtime coordination or manual scheduling. We demonstrate MLIR-AIR’s capabilities through two case studies: matrix multiplication and the multi-head attention block from the LLaMA 2 model. For matrix multiplication, MLIR-AIR achieves up to 78.7% compute efficiency and generates implementations with performance almost identical to state-of-the-art, hand-optimized matrix multiplication written using the lower-level, close-to-metal MLIR-AIE framework. For multi-head attention, we demonstrate that the AIR interface supports fused implementations using approximately 150 lines of code, enabling tractable expression of complex workloads with efficient mapping to spatial hardware. MLIR-AIR transforms high-level structured control flow into spatial programs that efficiently utilize the compute fabric and memory hierarchy of an NPU, leveraging asynchronous execution, tiling, and communication overlap through compiler-managed scheduling.

Arm usage has substantially grown in the High-Performance Computing (HPC) community. Japanese supercomputer Fugaku, powered by Arm-based A64FX processors, held the top position on the Top500 list between June 2020 and June 2022, currently sitting in the fourth position. The recently released 7th generation of Amazon EC2 instances for compute-intensive workloads (C7 g) is also powered by Arm Graviton3 processors. Projects like European Mont-Blanc and U.S. DOE/NNSA Astra are further examples of Arm irruption in HPC. In parallel, over the last decade, the rapid improvement of genomic sequencing technologies and the exponential growth of sequencing data has placed a significant bottleneck on the computational side. While most genomics applications have been thoroughly tested and optimized for x86 systems, just a few are prepared to perform efficiently on Arm machines. Moreover, these applications do not exploit the newly introduced Scalable Vector Extensions (SVE). This paper presents GenArchBench, the first genome analysis benchmark suite targeting Arm architectures. We have selected computationally demanding kernels from the most widely used tools in genome data analysis and ported them to Arm-based A64FX and Graviton3 processors. Overall, the GenArch benchmark suite comprises 13 multi-core kernels from critical stages of widely-used genome analysis pipelines, including base-calling, read mapping, variant calling, and genome assembly. Our benchmark suite includes different input data sets per kernel (small and large), each with a corresponding regression test to verify the correctness of each execution automatically. Moreover, the porting features the usage of the novel Arm SVE instructions, algorithmic and code optimizations, and the exploitation of Arm-optimized libraries. We present the optimizations implemented in each kernel and a detailed performance evaluation and comparison of their performance on four different HPC machines (i.e., A64FX, Graviton3, Intel Xeon Skylake Platinum, and AMD EPYC Rome). Overall, the experimental evaluation shows that Graviton3 outperforms other machines on average. Moreover, we observed that the performance of the A64FX is significantly constrained by its small memory hierarchy and latencies. Additionally, as proof of concept, we study the performance of a production-ready tool that exploits two of the ported and optimized genomic kernels.

The FM-index is a data structure used in genomics for exact search of input sequences over large reference genomes. Algorithms based on the FM-index show an irregular memory access pattern, resulting in a memory bound problem. We analyze a recent implementation of the FM-index and highlight existing throughput-memory trade-offs, showing that memory requirements limit implementation of large k-steps. We propose COFI, a COmpressed FM-Index for large K-steps. COFI enables a 15-step FM-index using less than 16 GB for a human genome reference of 3 giga base pairs. An algorithm based on this new layout is evaluated on both a Knights Landing (KNL) and an Skylake-based system (SKX). We achieve average speed-ups of 1.46× and 1.39×, respectively, with respect to an state-of-the-art FM-index implementation that is already well optimized.

SVE (Scalable Vector Extension) is Arm's new vector instruction extension targeting high performance workloads. SVE offers many opportunities to optimise compute intensive workloads but, with the availability of SVE-enabled hardware still years away, we have to rely on simulation techniques in order to evaluate our implementations. Working with simulators can be tricky and it comes with many limitations but, used properly, a simulator like Gem5 is a valuable tool that can provide an opportunity to explore the possibilities opened by this new extension. As a use case, we focus our attention on the field of genomics, where the recent advent of high-throughput sequencing machines producing big amounts of genomic data has boosted the interest in efficient approximate string matching and alignment techniques. Genomics algorithms are the key computational building blocks for the downstream data analysis on resequencing projects where hundreds of GBytes of sequenced data are analysed against a reference genome in order to filter sequencing errors and detect potential genomic variation events. The computational requirements and sheer size of the input data used by these applications make them a challenging problem. Fortunately, they also exhibit a high degree of data parallelism, making them good candidates for vectorisation techniques. In this work we explore the unique opportunities that SVE provides in order to exploit the parallelism present in genomics algorithms. We discuss preliminary results, our simulation strategy, some of the obstacles and limitations we faced, and how to work around them in order to obtain meaningful results.

UNLABELLED: From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. AVAILABILITY AND IMPLEMENTATION: MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: In the last few years, the Non-negative Matrix Factorization ( NMF ) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. In this paper, we present NMF-mGPU, an efficient and easy-to-use implementation of the NMF algorithm that takes advantage of the high computing performance delivered by Graphics-Processing Units ( GPUs ). Driven by the ever-growing demands from the video-games industry, graphics cards usually provided in PCs and laptops have evolved from simple graphics-drawing platforms into high-performance programmable systems that can be used as coprocessors for linear-algebra operations. However, these devices may have a limited amount of on-board memory, which is not considered by other NMF implementations on GPU. RESULTS: NMF-mGPU is based on CUDA ( Compute Unified Device Architecture ), the NVIDIA's framework for GPU computing. On devices with low memory available, large input matrices are blockwise transferred from the system's main memory to the GPU's memory, and processed accordingly. In addition, NMF-mGPU has been explicitly optimized for the different CUDA architectures. Finally, platforms with multiple GPUs can be synchronized through MPI ( Message Passing Interface ). In a four-GPU system, this implementation is about 120 times faster than a single conventional processor, and more than four times faster than a single GPU device (i.e., a super-linear speedup). CONCLUSIONS: Applications of GPUs in Bioinformatics are getting more and more attention due to their outstanding performance when compared to traditional processors. In addition, their relatively low price represents a highly cost-effective alternative to conventional clusters. In life sciences, this results in an excellent opportunity to facilitate the daily work of bioinformaticians that are trying to extract biological meaning out of hundreds of gigabytes of experimental information. NMF-mGPU can be used "out of the box" by researchers with little or no expertise in GPU programming in a variety of platforms, such as PCs, laptops, or high-end GPU clusters. NMF-mGPU is freely available at https://github.com/bioinfo-cnb/bionmf-gpu .

We have explored in this paper a framework to test in a quantitative manner the stability of different endmember extraction and spectral unmixing algorithms based on the concept of Consensus Clustering. The idea is to investigate if the sensibility of those algorithms to the number of endmembers can be used to estimate this parameter itself. Preliminary results on synthetic data reveal that the proposed scheme, which can be implemented efficiently in parallel, can compete with state-of-the-art schemes.

The widespread usage of the DiscreteWaveletTransform (DWT) has motivated the development of fastDWT algorithms and their tuning on all sorts of computersystems. Several studies have compared the performanceof the most popular schemes, known as Filter Bank(FBS) and Lifting (LS), and have always concluded thatLifting is the most efficient option. However, there isno such study on streaming processors such as modernGraphic Processing Units (GPUs). Current trends havetransformed these devices into powerful stream processorswith enough flexibility to perform intensive and complexfloating-point calculations. The opportunities opened upby these platforms, as well as the growing popularityof the DWT within the computer graphics field, make anew performance comparison of great practical interest.Our study indicates that FBS outperforms LS in currentgeneration GPUs. In our experiments, the actual FBS gainsrange between 10% and 140%, depending on the problemsize and the type and length of the wavelet filter. Moreover,design trends suggest higher gains in future generationGPUs.

Spatial/spectral algorithms have been shown in previous work to be a promising approach to the problem of extracting image end members from remotely sensed hyperspectral data. Such algorithms map nicely on high-performance systems such as massively parallel clusters and networks of computers. Unfortunately, these systems are generally expensive and difficult to adapt to onboard data processing scenarios, in which low-weight and low-power integrated components are highly desirable to reduce mission payload. An exciting new development in this context is the emergence of graphics processing units (GPUs), which can now satisfy extremely high computational requirements at low cost. In this letter, we propose a GPU-based implementation of the automated morphological end member extraction algorithm, which is used in this letter as a representative case study of joint spatial/spectral techniques for hyperspectral image processing. The proposed implementation is quantitatively assessed in terms of both end member extraction accuracy and parallel efficiency, using two generations of commercial GPUs from NVidia. Combined, these parts offer a thoughtful perspective on the potential and emerging challenges of implementing hyperspectral imaging algorithms on commodity graphics hardware.