The Scientific Computing seminar series usually takes place on Wednesdays at 15:00. Join on zoom or in person in room RH001. There will be coffee available after the seminar.
To sign up for the seminar mailing list please email [email protected]
Contact: [email protected]
- Wednesday, Nov 17, 15:00, Hermann Haverkort, University of Bonn, TBA
- Wednesday, Nov 3, 2021 15:00, Joseph Schuchart, University of Tennessee, Knoxville, TBA
- Wednesday, Oct 27, 2021 15:00, Nicole Beisiegel, TU Dublin, TBA
- Wednesday, Oct 6, 2021 15:00, Edmond Chow, Georgia Tech, Introduction to Asynchronous Iterative Solvers
Abstract: The standard iterative methods for solving linear and nonlinear systems of equations are all synchronous, meaning that in the parallel execution of these methods where some processors may complete an iteration before other processors (for example, due to load imbalance), the fastest processors must wait for the slowest processors before continuing to the next iteration. This talk will discuss parallel iterative methods that operate asynchronously, meaning that the processors never wait for each other, but instead proceed using whatever iterate values are already available from other processors. Processor idle time is thus eliminated, but questions arise about the convergence of these methods. Asynchronous iterative methods will be introduced using simple fixed-point iterative methods for linear systems, before discussing asynchronous versions of rapidly converging methods, in particular, second order Richardson, and multigrid methods.
- Friday, Aug 27, 2021 13:00, Adam Tuft, Durham University, A Tour of OMPT and Otter for Tracing Task-Centric OpenMP Programs
Abstract: Reasoning about the structure of task-based programs, while vital for understanding their performance, is challenging for complex programs exhibiting irregular or nested tasking. The new OpenMP Tools (OMPT) interface defines event-driven callbacks allowing tools to gather rich runtime data on task creation and synchronisation. An example of such a tool is Otter (https://github.com/adamtuft/otter) which performs event-based tracing of OpenMP programs through OMPT, allowing the task-based structure of a target program to be recovered. This 30-minute presentation will give a brief tour of OMPT and will demonstrate its utility with examples provided by Otter.
- Thursday, Jul 15, 2021 09:30, Georg Hager, Performance counter analysis with Likwid and single node performance assessment
- Friday, Jun 25, 2021 13:00, Thomas Weinhart, University of Twente, Automated calibration for discrete particle simulations
Abstract: The Discrete Particle Method (DPM) captures the collective behaviour of a granular material by simulating the kinematics of the individual grains. DPM can provide valuable insights that are difficult to obtain with either experiments or continuum models. However, calibrating the parameters of a DPM model against experimental measurements often takes significant effort and expertise, since automated and systematic calibration techniques are lacking.I will present an automated calibration technique, based on Bayesian filtering: We conduct experimental measurements to determine the material response, then simulate the same process in MercuryDPM, our open-source DPM solver , and measure the response of the simulated process. Then we apply a numerical optimisation algorithm to find the DPM parameters for which the response of the experiments and simulations match. This optimisation is done using a probabilistic optimisation technique called GrainLearning . The technique can find local optima in only two to three iterations, even for complex contact models with many microscopic parameters.The technique has already been used in several projects, yielding good results. We present two test cases, one for calibrating a sintering model for 3D printing processes and one for calibrating the bulk response of a sheared granular material, and discuss the results.References: Weinhart, T., Orefice, L., Post, M., et al, Fast, flexible particle simulations – An introduction to MercuryDPM, Computer Physics Communications, 249, 107129 (2020).  Cheng, H., Shuku, T., Thoeni, K. et al. Probabilistic calibration of discrete element simulations using the sequential quasi-Monte Carlo filter. Granular Matter 20, 11 (2018).
- Friday, Jun 18, 2021 13:00, Alexander Moskovsky, Moscow State University, RSC Group, Energy efficiency in HPC
Abstract: High performance computing (HPC) is a pinnacle of modern computer engineering both regarding software and hardware components. Nowadays, they aggregate a large number of components: nodes, accelerators, storage devices and so on. One of the most acute problems on the hardware side is a rapid growth of energy dissipation and density: modern supercomputers consume megawatts of electric power. On the software side, the system software has to support the configuration of multiple components in concert.The RSC Group is a pioneer in liquid cooling for HPC solutions since the beginning of 2010. Liquid cooling enables 30-40% percent reduction of total supercomputer power consumption in comparison to forced airflow cooling. At the same time, liquid cooled HPC systems can be much more compact. RSC also develops a software stack that enables on-demand configurations for the both computational and storage systems, with support of Lustre and Intel DAOS and other filesystems. Such hyperconverged systems in HPC offer compactness and uniformity in hardware, but they require a software orchestrator to support it’s disaggregated architecture.RSC develops systems in close collaboration with it’s academic partners that inspire and motivate many solutions implemented in production. End-users from Russian Academy of Sciences, major Russian universities and research organisations tackle a wide spectrum of problems ranging from high energy physics to life sciences. RSC systems are present in supercomputer ratings like Top500, Green500, HPCG , IO500 and occupy 25% of Russian Top50 list of the most powerful computing systems.
- Friday, Jun 4, 2021 13:00, Benjamin Uekermann, University of Stuttgart, preCICE 2 – A Sustainable and User-Friendly Coupling Library
Abstract: In the last five years, we have turned the coupling library preCICE from a working prototype to a sustainable and user-friendly community software project.In this presentation, I want to tell you about the challenges, success stories, and struggles of this endeavor, besides a brief introduction to the software itself. In particular, I cover documentation, tutorials, testing, integration with external simulation software, funding, and community building. Read more on https://precice.org/.
- Friday, May 14, 2021 13:00, Nicole Aretz, RWTH Aachen , Title: Sensor selection for linear Bayesian inverse problems with variable model configurations
Abstract: In numerical simulations, mathematical models such as partial differential equations are widely used to predict the behavior of a physical system. The uncertainty in the prediction caused by unknown parameters can be decreased by incorporating measurement data: by means of Bayesian inversion a posterior probability distribution can be obtained that updates prior information on the uncertain parameters. As experimental data can be expensive, sensor positions need to be chosen carefully to obtain informative data despite a limited budget.In this talk we consider a group of forward models which are characterized through different configurations of the physical system. The configuration is a non-linear influence on the solution, e.g. the geometry or material of an individual work piece in a production chain. Our goal is to choose one set of sensors for the estimation of an uncertain linear influence whose measurement data is informative for all possible configurations. To this end, we identify an observability coefficient that links the experimental design to the covariance of the posterior. We then present a sequential sensor selection algorithm that improves the observability coefficient uniformly for all configurations. Computational feasibility is achieved through model order reduction. In particular, we discuss opportunities and challenges to decrease the computational cost of the inverse problem via the reduced basis method. We demonstrate our results on steady-state heat conduction problems for a thermal block and a geothermal model of the Perth Basin in Western Australia.
- Thursday, Apr 8, 2021 13:00, Jochim Protze, Title: Asynchronous MPI communication with OpenMP tasks
Abstract: Your communication depends on computation results as input? Your computation task depends on data to arrive from a different process? OpenMP task dependencies should allow to express such dependencies. OpenMP 5.0 introduced detached tasks. In combination with MPI detached communication , this allows to build task dependency graphs across MPI processes. In this short presentation you will learn how you can integrate MPI detached communication into your project and profit from real asynchronous communication. If you don’t want to use OpenMP tasks, the same approach will also work with C++ futures/promises.
Zoom link for this session: https://durhamuniversity.zoom.us/j/97425330730?pwd=Ti92aXRKSXRmN2FPZmNTazdoVEl0QT09
- Friday, Mar 12, 2021 13:00, Tim Dodwell, Alan Turing Institute, University of Exeter, Title: Adaptive Multilevel Delayed Acceptance
Abstract: Uncertainty Quantification through Markov Chain Monte Carlo (MCMC) can be prohibitively expensive for target probability densities with expensive likelihood functions, for instance when the evaluation involves solving a Partial Differential Equation (PDE), as is the case in a wide range of engineering applications. Multilevel Delayed Acceptance (MLDA) with an Adaptive Error Model (AEM) is a novel approach, which alleviates this problem by exploiting a hierarchy of models, with increasing complexity and cost, and correcting the inexpensive models on-the-fly. The method has been integrated within the open-source probabilistic programming package PyMC3 and is available in the latest development version
- Friday, Feb 5, 2021 13:00, Andy Davis, Courant Institute, Title: Super-parameterized numerical methods for the Boltzmann equation modeling Arctic sea ice dynamics
Abstract: We devise a super-parameterized sea ice model that captures dynamics at multiple spatial and temporal scales. Arctic sea ice contains many ice floes—chunks of ice—whose macro-scale behavior is driven by oceanic/atmospheric currents and floe-floe interaction. There is no characteristic floe size and, therefore, accurately modeling sea ice dynamics requires a multi-scale approach. Our two-tiered model couples basin-scale conservation equations with small-scale particle methods. Unlike many other sea ice models, we do not average quantities of interest (e.g., mass/momentum) over a representative volume element. Instead, we explicitly model small-scale dynamics using the Boltzmann equation, which evolves a probability distribution over position and velocity. In practice, existing numerical methods approximating the Boltzmann equation are computationally intractable when modeling Arctic basin scale dynamics. Our approach decomposes the density function into a mass density that models how ice is distributed in the spatial domain and a velocity density that models the small-scale variation in velocity at a given location. The mass density and macro-scale expected velocity evolve according to a hyperbolic conservation equation. However, the flux term depends on expectations with respect to the velocity density at each spatial point. We, therefore, use particle methods to simulate the conditional density at key locations. We make each particle method independent using a local change of variables that defines micro-scale coordinates. We model small-scale ice dynamics (e.g., collision) in this transformed domain.