Related papers: Breaking Down the Parallel Performance of GROMACS,…
With large-scale Integral Field Spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data.…
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 describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
Efficient hybrid DFT simulations of solid state materials would be extremely beneficial for computational chemistry and materials science, but is presently bottlenecked by difficulties in computing Hartree-Fock (HF) exchange with plane wave…
Large-scale plasma simulations are critical for designing and developing next-generation fusion energy devices and modeling industrial plasmas. BIT1 is a massively parallel Particle-in-Cell code designed for specifically studying plasma…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
Real-time simulation enables the understanding of system operating conditions by evaluating simulation models of physical components running synchronized at the real-time wall clock. Leveraging the real-time measurements of comprehensive…
Energy efficiency is becoming increasingly important for computing systems, in particular for large scale HPC facilities. In this work we evaluate, from an user perspective, the use of Dynamic Voltage and Frequency Scaling (DVFS)…
LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids 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…
Large-scale HPC simulations of plasma dynamics in fusion devices require efficient parallel I/O to avoid slowing down the simulation and to enable the post-processing of critical information. Such complex simulations lacking parallel I/O…
This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on gpu hardware using single precision. The simulations use a vortex particle method…
The CP-PACS is a massively parallel MIMD computer with the theoretical peak speed of 614 GFLOPS which has been developed for computational physics applications at the University of Tsukuba, Japan. We report on the performance of the CP-PACS…
Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles…
In the recent years it can be observed increasing popularity of parallel processing using multi-core processors, local clusters, GPU and others. Moreover, currently one of the main requirements the IT users is the reduction of maintaining…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
Since its inception in 1995, LAMMPS has grown to be a world-class molecular dynamics code, with thousands of users, over one million lines of code, and multi-scale simulation capabilities. We discuss how LAMMPS has adapted to the modern…
In atomistic spin dynamics simulations, the time cost of constructing the space- and time-displaced pair correlation function in real space increases quadratically as the number of spins $N$, leading to significant computational effort. The…
As the sophistication of Machine Learning Force Fields (MLFF) increases to match the complexity of extended molecules and materials, so does the need for tools to properly analyze and assess the practical performance of MLFFs. To go beyond…