Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond

In this and a set of companion whitepapers, the USQCD Collaboration lays out a program of science and computing for lattice gauge theory. These whitepapers describe how calculation using lattice QCD (and other gauge theories) can aid the interpretation of ongoing and upcoming experiments in particle and nuclear physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers

A Streaming Multi-GPU Implementation of Image Simulation Algorithms for Scanning Transmission Electron Microscopy

Simulation of atomic resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods. By distributing the workload between multiple CUDA-enabled GPUs and multicore processors, accelerations as high as 1000x for PRISM and 30x for multislice are achieved relative to traditional multislice implementations using a single 4-GPU machine. We demonstrate a potentially important application of Prismatic, using it to compute images for atomic electron tomography at sufficient speeds to include in the reconstruction pipeline. Prismatic is freely available both as an open-source CUDA/C++ package with a graphical user interface and as a Python package, PyPrismatic

Multi­-Scattering: Computational light transport in turbid media

This thesis presents and describes the development of an online freely accessible software called Multi-Scattering for the computational modeling of light propagation in scattering and absorbing media. The model is based on the use of the Monte Carlo method, where billions of photon packets are being launched and tracked through simulated cubic volumes. The software also includes features for modeling image formation by inserting a virtual collecting lens and a detection matrix which simulate a camera objective and a sensor array respectively. In addition, the Lorenz-Mie theory is integrated to generate the scattering phase functions from spherical particles. The model has been accelerated by means of general-purpose computing on graphics processing units, reducing the computation time by a factor up to 200x in comparison with a single CPU thread. By using four graphic cards on a single computer, the simulation speed increases by a factor of 800x. With an anisotropy factor g= 0.86, the transport path of one billion photons can be computed in 10 seconds for optical depth OD=10 and in 20 minutes for OD=500.The simulations are running from a computer server at Lund University, allowing researchers to login and use it freely without any need for programming skills or specific software/hardware installations. There are countless types of scattering media in which this model can be used to predict photon transport, including medical tissues, blood samples, clouds, smoke, fog, turbid liquids, spray systems, etc. In this thesis, the software has been used for a variety of scattering situations and to simulate photon transport: 1) inside a portion of a human head, 2) within atomizing spray systems, 3) in controlled aqueous dispersion of polystyren spheres, 4) for time-of-flight measurements in intralipid solutions and 5) for Diffuse Correlation Spectroscopy applications.Finally, the numerical results have been validated by rigorously comparing the simulated results with experimental data. The user interface for both setting-up a simulation and displaying the corresponding results is found at: https://multi-scattering.co

Highly parallel Monte-Carlo simulations of the acousto-optic effect in heterogeneous turbid media

The development of a highly parallel simulation of the acousto-optic effect is detailed. The simulation supports optically heterogeneous simulation domains under insonification by arbitrary monochromatic ultrasound fields. An adjoint method for acousto-optics is proposed to permit point-source/point-detector simulations. The flexibility and efficiency of this simulation code is demonstrated in the development of spatial absorption sensitivity maps which are in broad agreement with current experimental investigations. The simulation code has the potential to provide guidance in the feasibility and optimization of future studies of the acousto-optic technique, and its speed may permit its use as part of an iterative inversion model

ValoMC: a Monte Carlo software and MATLAB toolbox for simulating light transport in biological tissue

A Monte Carlo method for photon transport has gained wide popularity in biomedical optics for studying light behaviour in tissue. Nowadays, typical computation times range from a few minutes to hours. Although various implementations of the Monte Carlo algorithm exist, there is only a limited number of free software available. In addition, these packages may require substantial learning efforts. To address these issues, we present a new Monte Carlo software with a user-friendly interface. The simulation geometry is defined using an unstructured (triangular or tetrahedral) mesh. The program solves the photon fluence in the computation domain and the exitance at the domain boundary. It is capable of simulating complex measurement geometries with spatially varying optical parameter distributions and supports several types of light sources as well as intensity modulated light. Furthermore, attention is given to ease of use and fast problem set up with a MATLAB (The MathWorks Inc., Natick, MA) interface. The simulation code is written in C++ and parallelized using OpenMP. The simulation code has been validated against analytical and numerical solutions of radiative transfer equation and other Monte Carlo software in good agreement. The software is available for download from the homepage https://inverselight.github.io/ValoMC/ and the source code from GitHub https://github.com/InverseLight/ValoMC