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Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial…
We explored the possible benefits of integrating quantum simulators in a "hybrid" quantum machine learning (QML) workflow that uses both classical and quantum computations in a high-performance computing (HPC) environment. Here, we used two…
Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…
This paper presents the Parallel Coupler for Multimodel Simulations (PCMS), a new GPU accelerated generalized coupling framework for coupling simulation codes on leadership class supercomputers. PCMS includes distributed control and field…
The ongoing convergence of HPC and cloud computing presents a fundamental challenge: HPC applications, designed for static and homogeneous supercomputers, are ill-suited for the dynamic, heterogeneous, and volatile nature of the cloud.…
Heterogeneous nodes that combine multi-core CPUs with diverse accelerators are rapidly becoming the norm in both high-performance computing (HPC) and AI infrastructures. Exploiting these platforms, however, requires orchestrating several…
We propose a novel computing runtime that exposes remote compute devices via the cross-vendor open heterogeneous computing standard OpenCL and can execute compute tasks on the MEC cluster side across multiple servers in a scalable manner.…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
The considerable impact of Convolutional Neural Networks on many Artificial Intelligence tasks has led to the development of various high performance algorithms for the convolution operator present in this type of networks. One of these…
We detail the performance optimizations made in rocHPL, AMD's open-source implementation of the High-Performance Linpack (HPL) benchmark targeting accelerated node architectures designed for exascale systems such as the Frontier…
We explore the performance and portability of the high-level programming models: the LLVM-based Julia and Python/Numba, and Kokkos on high-performance computing (HPC) nodes: AMD Epyc CPUs and MI250X graphical processing units (GPUs) on…
This paper discusses the challenges encountered when analyzing the energy efficiency of synthetic benchmarks and the Gromacs package on the Fritz and Alex HPC clusters. Experiments were conducted using MPI parallelism on full sockets of…
Despite the increasing adoption of Field-Programmable Gate Arrays (FPGAs) in compute clouds, there remains a significant gap in programming tools and abstractions which can leverage network-connected, cloud-scale, multi-die FPGAs to…
Recent trends in the HPC field have introduced new CPU architectures with improved vectorization capabilities that require optimization to achieve peak performance and thus pose challenges for performance portability. The deployment of…
Learning-based lossless compressors play a crucial role in large-scale genomic database backup, storage, transmission, and management. However, their 1) inadequate compression ratio, 2) low compression \& decompression throughput, and 3)…
This monograph presents the design, implementation, and evaluation of Pyroclast, a modular high-performance Python framework for large-scale geodynamic simulations. Pyroclast addresses limitations of legacy geodynamics solvers, often…
OCaml is an industrial-strength, multi-paradigm programming language, widely used in industry and academia. OCaml was developed for solving numerical and scientific problems involving large scale data-intensive operations and one such…
The dynamic load-balancing framework in Charm++/AMPI, developed at the University of Illinois, is based on using processor virtualization to allow thread migration across processors. This framework has been successfully applied to many…
There are a number of different phenomena in the early universe that have to be studied numerically with lattice simulations. This paper presents a graphics processing unit (GPU) accelerated Python program called PyCOOL that solves the…
Automatically tuning parallel compute kernels allows libraries and frameworks to achieve performance on a wide range of hardware, however these techniques are typically focused on finding optimal kernel parameters for particular input sizes…