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Snapshot: Guest talk by HLRS scientist Johannes Gebert

Today on 6th May 2025, Johannes Gebert of the High-Performance Computing Center Stuttgart ( HRLS) visited us at the HPSC Lab at the University of Augsburg. He gave a guest talk as part of the Advanced Analytics and Predictive Sciences Seminar, titled "Enabling Massively Parallel Simulations of Directly Discretized CT Scans of Human Bones" (see abstract below). Furthermore, we had some interesting discussions on future computing in the HPC context and on the direction of the German and European HPC landscape. Thanks a lot for your visit, Johannes!

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Abstract

Quantifying the patient-specific elastic behavior of human bone can improve the design of implants, for example in total hip- or knee replacements. We calculate the mechanical stiffness tensor of human bone by direct discretization of computed tomography (CT) scans with more than 18 billion voxels. The software started as a serial implementation but now requires different massively parallel parameterizations, which poses significant challenges. Many computations may run ideally parallel; one computation may be a single large-scale job or any other variant. We solved the challenge with MPI and PETSc to distribute the linear algebraic system, allowing for computing large volumes of interest (VoIs) in bone. At the same time, pre- and post-processing are still serially implemented.
We will examine the challenges in the software's legacy components and its performance bottlenecks. Furthermore, we will show the perspective of the high-performance computing center in which the user deploys the simulation and measures to, e.g., optimize for short turnaround times.

Using p4est meshes for our simulations we implemented flexible multiphysics coupling across interface boundaries in Trixi.jl. Unlike structured meshes, p4est meshes can be much more flexible. They do not require to be rectangular or even simply connected. As a test case we show here two meshes. One writes the word "Trixi.jl" and the other is its complement. We couple an MHD system with an Euler system and initialize the domain with a linear pressure wave that travels to the left.
mhd_euler_t0
Coupled Euler-Mhd system using two p4est meshes. Shown is the gas density at time t = 0. ? University of Augsburg
mhd_euler_t34
Coupled Euler-Mhd system using two p4est meshes. Shown is the gas density at time t = 34. ? University of Augsburg

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