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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 present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
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…
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…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
Computational biology has increasingly turned to agent-based modeling to explore complex biological systems. Biological diffusion (diffusion, decay, secretion, and uptake) is a key driver of biological tissues. GPU computing can vastly…
In drug discovery, molecular docking is the task in charge of estimating the position of a molecule when interacting with the docking site. This task is usually used to perform screening of a large library of molecules, in the early phase…
In recent years, it has become increasingly common for high performance computers (HPC) to possess some level of heterogeneous architecture - typically in the form of GPU accelerators. In some machines these are isolated within a dedicated…
The high energy consumption of electronic data processors, together with physical challenges limiting their further improvement, has triggered intensive interest in alternative computation paradigms. Here we focus on network-based…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
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…
Portability is critical to ensuring high productivity in developing and maintaining scientific software as the diversity in on-node hardware architectures increases. While several programming models provide portability for diverse GPU…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…
Accelerated computing is widely used in high-performance computing. Therefore, it is crucial to experiment and discover how to better utilize GPUGPUs latest generations on relevant applications. In this paper, we present results and share…
Robustly estimating energy consumption in High-Performance Computing (HPC) is essential for assessing the energy footprint of modern workloads, particularly in fields such as Artificial Intelligence (AI) research, development, and…
This paper assesses and reports the experience of ten teams working to port,validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC…
New challenges in Astronomy and Astrophysics (AA) are urging the need for a large number of exceptionally computationally intensive simulations. "Exascale" (and beyond) computational facilities are mandatory to address the size of…