Related papers: Towards High-Performance and Portable Molecular Do…
A current trend in HPC systems is the utilization of architectures with SIMD or vector extensions to exploit data parallelism. There are several ways to take advantage of such modern vector architectures, each with a different impact on the…
Most modern processors contain vector units that simultaneously perform the same arithmetic operation over multiple sets of operands. The ability of compilers to automatically vectorize code is critical to effectively using these units.…
This living paper reviews the present High Performance Computing (HPC) capabilities of the Tinker-HP molecular modeling package. We focus here on the reference, double precision, massively parallel molecular dynamics engine present in…
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…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
The complexity of combustion simulations demands the latest high-performance computing tools to accelerate its time-to-solution results. A current trend on HPC systems is the utilization of CPUs with SIMD or vector extensions to exploit…
Much of the current focus in high-performance computing is on multi-threading, multi-computing, and graphics processing unit (GPU) computing. However, vectorization and non-parallel optimization techniques, which can often be employed…
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…
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…
Computed Tomography (CT) is a key 3D imaging technology that fundamentally relies on the compute-intense back-projection operation to generate 3D volumes. GPUs are typically used for back-projection in production CT devices. However, with…
We present a technique for automatically transforming kernel-based computations in disparate, nested loops into a fused, vectorized form that can reduce intermediate storage needs and lead to improved performance on contemporary hardware.…
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…
Resource-limited robots face significant challenges in executing computationally intensive tasks, such as locomotion and manipulation, particularly for real-time optimal control algorithms like Model Predictive Control (MPC). This paper…
High Performance Computing (HPC) platforms allow scientists to model computationally intensive algorithms. HPC clusters increasingly use General-Purpose Graphics Processing Units (GPGPUs) as accelerators; FPGAs provide an attractive…
As an important goal of high-performance computing, the concept of performance portability has been around for many years. As the failure of Moore's Law, it is no longer feasible to improve computer performance by simply increasing the…
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materials science and computational chemistry. We present…
Virtual screening (VS) is a computationally intensive process crucial for drug discovery, often requiring significant resources to analyze large chemical libraries and predict ligand-protein interactions. This study evaluates the…
Traditionally, high energy physics (HEP) experiments have relied on x86 CPUs for the majority of their significant computing needs. As the field looks ahead to the next generation of experiments such as DUNE and the High-Luminosity LHC, the…
For years, SIMD/vector units have enhanced the capabilities of modern CPUs in High-Performance Computing (HPC) and mobile technology. Typical commercially-available SIMD units process up to 8 double-precision elements with one instruction.…
QMCPACK has enabled cutting-edge materials research on supercomputers for over a decade. It scales nearly ideally but has low single-node efficiency due to the physics-based abstractions using array-of-structures objects, causing…