Leinen, Willi Günter

In the scope of the dtec.bw project hpc.bw, innovative HPC hardware resources were procured to investigate their performance for HSU-relevant compute-intensive software. Benchmarks for different software packages were conducted, and respective results are reported and documented in the following, considering the Intel Xeon architecture used in the HPC cluster HSUper, AMD EPYC 7763 and ARM FX700.

Increasing amounts of data and simulations in scientific areas enforce the need of improved software performance. The maintaining scientific staff is often not primarily trained for this purpose or lacks personnel and time to address software performance issues. A particular aim of the dtec.bw-funded project hpc.bw is to tackle some of these shortcomings. A pillar of the hpc.bw agenda is the offer of a low-threshold consultancy and development support focused on performance engineering. This paper provides an insight on our related activities. We illustrate the structure of our annual calls for short-term performance engineering projects, we outline our results at the example of the performance engineering project “benEFIT - Numerical simulation of non-destructive testing in concrete”, and we draw a first conclusion on the current procedure.

Benchmarking the performance of one’s application in high performance computing (HPC) systems is critically important for reducing runtime and energy costs. Yet, accessing the plethora of relevant metrics that impact performance is often challenging, particularly for users without hardware experience. In this paper, we introduce the novel benchmarking tool xbat developed by MEGWARE GmbH. xbat requires no setup from the user side, and it allows the user to run, monitor and evaluate their application from the tool’s web interface, consolidating the entire benchmarking process in an approachable, intuitive workflow. We demonstrate the capabilities of the tool using benchmark applications of varying complexity and show that it can manage all aspects of the benchmarking workflow in a seamless manner. In particular, we focus on the open-source molecular dynamics research software ls1 mardyn, and the closed-source optimisation package Gurobi. Both packages present unique challenges. Mixed-integer programming solvers, such as those integrated in the Gurobi software, exhibit significant performance variability, so that seemingly innocuous parameter changes and machine characteristics can affect the runtime drastically, and ls1 mardyn comes with an auto-tuning library AutoPas, that enables the selection of various node-level algorithms to compute molecular trajectories. Focusing on these two packages, we showcase the practicality, versatility and utility of xbat, and share its current and future developments.

Radial basis function finite difference (RBF-FD) discretization has recently emerged as an alternative to classical finite difference or finite element discretization of (systems) of partial differential equations. In this paper, we focus on the construction of preconditioners for the iterative solution of the resulting linear systems of equations. In RBF-FD, a higher discretization accuracy may be obtained by increasing the stencil size. This, however, leads to a less sparse and often also worse conditioned stiffness matrix which are both challenges for subsequent iterative solvers. We propose to construct preconditioners based on stiffness matrices resulting from RBF-FD discretization with smaller stencil sizes compared to the one for the actual system to be solved. In our numerical results, we focus on RBF-FD discretizations based on polyharmonic splines (PHS) with polynomial augmentation. We illustrate the performance of smaller stencil preconditioners in the solution of the three-dimensional convection-diffusion equation.