Related papers: Optimizing the Performance of Reactive Molecular D…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. RE simulations involve the concurrent execution of independent simulations which infrequently interact and exchange information. The…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
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…
Nowadays, latency-critical, high-performance applications are parallelized even on power-constrained client systems to improve performance. However, an important scenario of fine-grained tasking on simultaneous multithreading CPU cores in…
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…
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)…
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…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
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…
The exascale race is at an end with the announcement of the Aurora and Frontier machines. This next generation of supercomputers utilize diverse hardware architectures to achieve their compute performance, providing an added onus on the…
Parallel processing is considered as todays and future trend for improving performance of computers. Computing devices ranging from small embedded systems to big clusters of computers rely on parallelizing applications to reduce execution…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
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…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
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…
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample the highly informative but highly unlikely reactive…
Scientific computing in the exascale era demands increased computational power to solve complex problems across various domains. With the rise of heterogeneous computing architectures the need for vendor-agnostic, performance portability…