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Energy efficiency is a growing concern for modern computing, especially for HPC due to operational costs and the environmental impact. We propose a methodology to find energy-optimal frequency and number of active cores to run single-node…
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…
The adoption of hybrid GPU-CPU nodes in traditional supercomputing platforms opens acceleration opportunities for electronic structure calculations in materials science and chemistry applications, where medium sized Hermitian generalized…
Computer simulations have become a very powerful tool for scientific research. In order to facilitate research in computational biology, the BioDynaMo project aims at a general platform for biological computer simulations, which should be…
We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU…
We have developed GPU versions for two major high-performance-computing (HPC) applications originating from two different scientific domains. GENE is a plasma microturbulence code which is employed for simulations of nuclear fusion plasmas.…
Earth system models (ESM) demand significant hardware resources and energy consumption to solve atmospheric chemistry processes. Recent studies have shown improved performance from running these models on GPU accelerators. Nonetheless,…
Current computational systems are heterogeneous by nature, featuring a combination of CPUs and GPUs. As the latter are becoming an established platform for high-performance computing, the focus is shifting towards the seamless programming…
Due to decelerating gains in single-core CPU performance, computationally expensive simulations are increasingly executed on highly parallel hardware platforms. Agent-based simulations, where simulated entities act with a certain degree of…
Integrating quantum mechanics into drug discovery marks a decisive shift from empirical trial-and-error toward quantitative precision. However, the prohibitive cost of ab initio molecular dynamics has historically forced a compromise…
Agent-based cellular models simulate tissue evolution by capturing the behavior of individual cells, their interactions with neighboring cells, and their responses to the surrounding microenvironment. An important challenge in the field is…
This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in…
Model Predictive Control (MPC) is a computationally demanding control technique that allows dealing with multiple-input and multiple-output systems, while handling constraints in a systematic way. The necessity of solving an optimization…
The rapid development in scientific research provides a need for more compute power, which is partly being solved by GPUs. This paper presents a microarchitectural analysis of the modern NVIDIA Blackwell architecture by studying GPU…
Machine learning based on neural networks has advanced rapidly, but the high energy consumption required for training and inference remains a major challenge. Hyperdimensional Computing (HDC) offers a lightweight, brain-inspired alternative…
Quantum computers can in principle solve certain problems exponentially more quickly than their classical counterparts. We have not yet reached the advent of useful quantum computation, but when we do, it will affect nearly all scientific…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
High-performance computing systems are more and more often based on accelerators. Computing applications targeting those systems often follow a host-driven approach in which hosts offload almost all compute-intensive sections of the code…