Related papers: Code modernization strategies for short-range non-…
We present our experience with the modernization on the GR-MHD code BHAC, aimed at improving its novel hybrid (MPI+OpenMP) parallelization scheme. In doing so, we showcase the use of performance profiling tools usable on x86 (Intel-based)…
Traditional heterogeneous parallel algorithms, designed for heterogeneous clusters of workstations, are based on the assumption that the absolute speed of the processors does not depend on the size of the computational task. This assumption…
Balancing the workload of sophisticated simulations is inherently difficult, since we have to balance both computational workload and memory footprint over meshes that can change any time or yield unpredictable cost per mesh entity, while…
Clusters of SMP nodes provide support for a wide diversity of parallel programming paradigms. Combining both shared memory and message passing parallelizations within the same application, the hybrid MPI-OpenMP paradigm is an emerging trend…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
The increasing use of heterogeneous embedded systems with multi-core CPUs and Graphics Processing Units (GPUs) presents important challenges in effectively exploiting pipeline, task and data-level parallelism to meet throughput requirements…
High-energy physics (HEP) experiments have developed millions of lines of code over decades that are optimized to run on traditional x86 CPU systems. However, we are seeing a rapidly increasing fraction of floating point computing power in…
Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
Using a realistic molecular catalyst system, we conduct scaling studies of ab initio molecular dynamics simulations using the CP2K code on both Intel Xeon CPU and NVIDIA V100 GPU architectures. We explore using process placement and…
Simulations based on particle methods, such as Smoothed Particle Hydrodynamics (SPH), are known to be computationally demanding. While such methods have for long been executed in parallel on multi-core CPUs, in recent years the increasing…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
Atomistic simulation drives scientific advances in modern material science and accounts for a significant proportion of wall time on High Performance Computing facilities. It is important that algorithms are efficient and implementations…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
The Simplex tableau has been broadly used and investigated in the industry and academia. With the advent of the big data era, ever larger problems are posed to be solved in ever larger machines whose architecture type did not exist in the…
Computation of a signal's estimated covariance matrix is an important building block in signal processing, e.g., for spectral estimation. Each matrix element is a sum of products of elements in the input matrix taken over a sliding window.…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Heterogeneous memory technologies are increasingly important instruments in addressing the memory wall in HPC systems. While most are deployed in single node setups, CXL.mem is a technology that implements memories that can be attached to…