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The end of Moore’s Law and Dennard scaling has driven the proliferation of heterogeneous systems with accelerators, including CPUs, GPUs, and FPGAs, each with distinct architectures, compilers, and programming environments. GPUs excel at massively parallel processing for tasks like deep learning training and graphics rendering, while FPGAs offer hardware-level flexibility and energy efficiency for low-latency, high-throughput applications. In contrast, CPUs, while general-purpose, often fall short in high-parallelism or power-constrained applications. This architectural diversity makes it challenging to compare these accelerators effectively, leading to uncertainty in selecting optimal hardware and software tools for specific applications. To address this challenge, we introduce HeteroBench, a versatile benchmark suite for heterogeneous systems. HeteroBench allows users to evaluate multi-compute kernel applications across various accelerators, including CPUs, GPUs (from NVIDIA, AMD, Intel), and FPGAs (AMD), supporting programming environments of Python, Numba-accelerated Python, serial C++, OpenMP (both CPUs and GPUs), OpenACC and CUDA for GPUs, and Vitis HLS for FPGAs. This setup enables users to assign kernels to suitable hardware platforms, ensuring comprehensive device comparisons. What makes HeteroBench unique is its vendor-agnostic, cross-platform approach, spanning diverse domains such as image processing, machine learning, numerical computation, and physical simulation, ensuring deeper insights for HPC optimization. Extensive testing across multiple systems provides practical reference points for HPC practitioners, simplifying hardware selection and performance tuning for both developers and end-users alike. This suite may assist to make more informed decision on AI/ML deployment and HPC development, making it an invaluable resource for advancing academic research and industrial applications. 

The HPC industry is inexorably moving towards an era of extremely heterogeneous architectures, with more devices configured on any given HPC platform and potentially more kinds of devices, some of them highly specialized. Writing a separate code suitable for each target system for a given HPC application is not practical. The better solution is to use directive-based parallel programming models such as OpenMP. OpenMP provides a number of options for offloading a piece of code to devices like GPUs. To select the best option from such options during compilation, most modern compilers use analytical models to estimate the cost of executing the original code and the different offloading code variants. Building such an analytical model for compilers is a difficult task that necessitates a lot of effort on the part of a compiler engineer. Recently, machine learning techniques have been successfully applied to build cost models for a variety of compiler optimization problems. In this paper, we present COMPOFF, a cost model which uses the multi-layer perceptrons to statically estimates the Cost of OpenMP OFFloading. We used six different transformations on a parallel code of Wilson Dslash Operator to support GPU offloading, and we predicted their cost of execution on different GPUs using COMPOFF during compile time. Our results show that this model can predict offloading costs with a root mean squared error in prediction of less than 0.5 seconds. Our preliminary findings indicate that this work will make it much easier and faster for scientists and compiler developers to port legacy HPC applications that use OpenMP to new heterogeneous computing environments. 

OpenMP is one of the most popular programming models to exploit node-level parallelism of supercomputers. Many researchers are interested in developing OpenMP compilers or extending existing standard for new capabilities. However, there is a lack of training resources for researchers who are involved in the compiler and language development around OpenMP, making learning curve in this area steep. In this paper, we introduce an ongoing effort, FreeCompilerCamp.org, a free and open online learning platform aimed to train researchers to quickly develop OpenMP compilers. The platform is built on top of Play-With-Docker, a docker playground for users to conduct experiments in an online terminal sandbox. It provides a live training website that is set up on cloud, so anyone with internet access and a web browser will be able to take the training. It also enables developers with relevant skills to contribute new tutorials. The entire training system is open-source and can be deployed on a private server, workstation or even laptop for personal use. We have created some initial tutorials to train users to learn how to extend the Clang/LLVM and ROSE compiler to support new OpenMP features. We welcome anyone to try out our system, give us feedback, contribute new training courses, or enhance the training platform to make it an effective learning resource for the HPC community. 

Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website (https://www.uniprot.org/), designed to enhance our users’ experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins. 

Abstract The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.