Related papers: Performance metrics in a hybrid MPI-OpenMP based m…

We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…

With multi-core processors a ubiquitous building block of modern supercomputers, it is now past time to enable applications to embrace these developments in processor design. To achieve exascale performance, applications will need ways of…

Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…

As fusion energy devices advance, plasma simulations are crucial for reactor design. Our work extends BIT1 hybrid parallelization by integrating MPI with OpenMP and OpenACC, focusing on asynchronous multi-GPU programming. Results show…

Modern OpenMP threading techniques are used to convert the MPI-only Hartree-Fock code in the GAMESS program to a hybrid MPI/OpenMP algorithm. Two separate implementations that differ by the sharing or replication of key data structures…

Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…

The increasing number of processing elements and decreas- ing memory to core ratio in modern high-performance platforms makes efficient strong scaling a key requirement for numerical algorithms. In order to achieve efficient scalability on…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

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…

We evaluate optimized parallel sparse matrix-vector operations for several representative application areas on widespread multicore-based cluster configurations. First the single-socket baseline performance is analyzed and modeled with…

Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…

Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…

Optimizing metamaterials with complex geometries is a big challenge. Although an active learning algorithm, combining machine learning (ML), quantum computing, and optical simulation, has emerged as an efficient optimization tool, it still…

Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…

Upcoming HPC clusters will feature hybrid memories and storage devices per compute node. In this work, we propose to use the MPI one-sided communication model and MPI windows as unique interface for programming memory and storage. We…

Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…

Message Passing Interface (MPI) is a foundational programming model for high-performance computing. MPI libraries traditionally employ network interconnects (e.g., Ethernet and InfiniBand) and network protocols (e.g., TCP and RoCE) with…

We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…

With the increasing number of Quad-Core-based clusters and the introduction of compute nodes designed with large memory capacity shared by multiple cores, new problems related to scalability arise. In this paper, we analyze the overall…