Related papers: Acceleration of a QM/MM-QMC simulation using GPU
This dissertation presents the design, implementation and evaluation of GPU-accelerated simulation frameworks for Evolutionary Spatial Cyclic Games (ESCGs), a class of agent-based models used to study ecological and evolutionary dynamics.…
Radiation Treatment Planning (RTP) is the process of planning the appropriate external beam radiotherapy to combat cancer in human patients. RTP is a complex and compute-intensive task, which often takes a long time (several hours) to…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…
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…
Energy system optimization models are increasing in scope and resolution, yielding large and challenging linear programs. For a long time, the standard way to address such problems has relied on shared-memory interior-point methods (IPM),…
In this paper, we develop a new parallel auxiliary grid algebraic multigrid (AMG) method to leverage the power of graphic processing units (GPUs). In the construction of the hierarchical coarse grid, we use a simple and fixed coarsening…
Usage of GPUs as co-processors is a well-established approach to accelerate costly algorithms operating on matrices and vectors. We aim to further improve the performance of the Global Neutrino Analysis framework (GNA) by adding GPU support…
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.…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
Process mapping asks to assign vertices of a task graph to processing elements of a supercomputer such that the computational workload is balanced while the communication cost is minimized. Motivated by the recent success of GPU-based graph…
Modern computing platforms tend to deploy multiple GPUs (2, 4, or more) on a single node to boost system performance, with each GPU having a large capacity of global memory and streaming multiprocessors (SMs). GPUs are an expensive…
We present qrpca, a fast and scalable QR-decomposition principal component analysis package. The software, written in both R and python languages, makes use of torch for internal matrix computations, and enables GPU acceleration, when…
At high energy physics experiments, processing billions of records of structured numerical data from collider events to a few statistical summaries is a common task. The data processing is typically more complex than standard query…
Graphics processing units (GPUs) are recently being used to an increasing degree for general computational purposes. This development is motivated by their theoretical peak performance, which significantly exceeds that of broadly available…
We created an efficient algorithm suitable for graphics processing units (GPUs) to perform Monte Carlo simulations of a subset of reaction-diffusion models. The algorithm uses techniques that are specific to GPU programming, and combines…
The accuracy of phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) can be systematically improved with better trial states. Using multi-Slater determinant trial states, ph-AFQMC has the potential to faithfully treat strongly…
Matrix-accelerated stencil computation is a hot research topic, yet its application to three-dimensional (3D) high-order stencils and HPC remains underexplored. With the emergence of matrix units on multicore CPUs, we analyze matrix-based…
Support for lower precision computation is becoming more common in accelerator hardware due to lower power usage, reduced data movement and increased computational performance. However, computational science and engineering (CSE) problems…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
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…