Related papers: MD-Bench: A generic proxy-app toolbox for state-of…
With the increasing maturity and scale of quantum hardware and its integration into HPC systems, there is a need to develop robust techniques for developing, characterizing, and benchmarking quantum-HPC applications and middleware systems.…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
Benchmarking is crucial for testing and validating any system, even more so in real-time systems. Typical real-time applications adhere to well-understood abstractions: they exhibit a periodic behavior, operate on a well-defined working…
The Lattice Boltzmann Method (LBM) is a computational technique of Computational Fluid Dynamics (CFD) that has gained popularity due to its high parallelism and ability to handle complex geometries with minimal effort. Although LBM…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
Obtaining standardized crowdsourced benchmark of computational methods is a major issue in data science communities. Dedicated frameworks enabling fair benchmarking in a unified environment are yet to be developed. Here we introduce…
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase…
Comprehending the performance bottlenecks at the core of the intricate hardware-software interactions exhibited by highly parallel programs on HPC clusters is crucial. This paper sheds light on the issue of automatically asynchronous MPI…
Workflow and serverless frameworks have empowered new approaches to distributed application design by abstracting compute resources. However, their typically limited or one-size-fits-all support for advanced data flow patterns leaves…
The design of low-power wearables for the biomedical domain has received a lot of attention in recent decades, as technological advances in chip manufacturing have allowed real-time monitoring of patients using low-complexity ML within the…
The use of disaggregated or far memory systems such as CXL memory pools has renewed interest in Near-Data Processing (NDP): situating cores close to memory to reduce bandwidth requirements to and from the CPU. Hardware designs for such…
With the rapid advancement of Large Language Models (LLMs) in code generation, human-AI interaction is evolving from static text responses to dynamic, interactive HTML-based applications, which we term MiniApps. These applications require…
Motivated by the need to emulate workload execution characteristics on high-performance and distributed heterogeneous resources, we introduce Synapse. Synapse is used as a proxy application (or "representative application") for real…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
The aim of parallel computing is to increase an application performance by executing the application on multiple processors. OpenMP is an API that supports multi platform shared memory programming model and shared-memory programs are…
As we rapidly approach the frontiers of ultra large computing resources, software optimization is becoming of paramount interest to scientific application developers interested in efficiently leveraging all available on-Node computing…
The rapid growth of microcontroller-based IoT devices has opened up numerous applications, from smart manufacturing to personalized healthcare. Despite the widespread adoption of energy-efficient microcontroller units (MCUs) in the Tiny…
In recent years, machine learning potentials (MLPs) have become indispensable tools in physics, chemistry, and materials science, driving the development of software packages for molecular dynamics (MD) simulations and related applications.…
Continuous dynamical systems, characterized by differential equations, are ubiquitously used to model several important problems: plasma dynamics, flow through porous media, weather forecasting, and epidemic dynamics. Recently, a wide range…
Design-to-code translates high-fidelity UI designs into executable front-end implementations, but progress remains hard to compare due to inconsistent datasets, toolchains, and evaluation protocols. We introduce 1D-Bench, a benchmark…