Related papers: Redesigning GROMACS Halo Exchange: Improving Stron…

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…

The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…

Distributed GPU applications increasingly rely on kernel-level, cross-node coordination to reduce launch overheads and improve compute-communication overlap, but such support is lacking. On OFI-based interconnects such as HPE Slingshot,…

Molecular dynamics simulations are essential tools in computational biophysics, but their performance depend heavily on hardware choices and configuration. In this work, we presents a comprehensive performance analysis of four NVIDIA GPU…

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…

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…

Static resource allocations in high-performance computing (HPC) lead to inefficiencies for time-varying workloads, causing idle resources, queue delays, and higher node-hour costs. The Dynamic Management of Resources (DMR) middleware…

GROMACS is a de-facto standard for classical Molecular Dynamics (MD). The rise of AI-driven interatomic potentials that pursue near-quantum accuracy at MD throughput now poses a significant challenge: embedding neural-network inference into…

Sparse General Matrix Multiply (SpGEMM) is key for various High-Performance Computing (HPC) applications such as genomics and graph analytics. Using the semiring abstraction, many algorithms can be formulated as SpGEMM, allowing…

GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…

Large deep learning models have demonstrated strong ability to solve many tasks across a wide range of applications. Those large models typically require training and inference to be distributed. Tensor parallelism is a common technique…

In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit…

Large language models (LLMs) have been widely deployed for online generative services, where numerous LLM instances jointly handle workloads with fluctuating request arrival rates and variable request lengths. To efficiently execute…

One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…

We present a parallel implementation of the particle-particle/particle-mesh (P3M) algorithm for distributed memory clusters. The GRACOS (GRAvitational COSmology) code uses a hybrid method for both computation and domain decomposition.…

Sparse Matrix-Matrix Multiplication (SpMM) is a fundamental operation in graph computing and analytics. However, the irregularity of real-world graphs poses significant challenges to achieving efficient SpMM operation for graph data on…

For many years, systems running Nvidia-based GPU architectures have dominated the heterogeneous supercomputer landscape. However, recently GPU chipsets manufactured by Intel and AMD have cut into this market and can now be found in some of…

High-performance computing is used for diverse simulations, some of which parallelize over the Message Passing Interface (MPI) with ease, whilst others may have challenges related to uniform balancing of computational load and communication…

This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…

As large language models (LLMs) continue to grow in size, distributed inference has become increasingly important. Model-parallel strategies must now efficiently scale not only across multiple GPUs but also across multiple nodes. In this…