Numerical models of complex real-world phenomena often necessitate High Performance Computing (HPC). Uncertainties increase problem dimensionality further and pose even greater challenges.

SIMD vectorization has lately become a key challenge in high-performance computing. However, hand-written explicitly vectorized code often poses a threat to the software’s sustainability. In this publication, we solve this sustainability and performance portability issue by enriching the simulation framework dune-pdelab with a code generation approach. The approach is based on the well-known domain-specific language UFL but combines it with loopy, a more powerful intermediate representation for the computational kernel. Given this flexible tool, we present and implement a new class of vectorization strategies for the assembly of Discontinuous Galerkin methods on hexahedral meshes exploiting the finite element’s tensor product structure. The performance-optimal variant from this class is chosen by the code generator through an auto-tuning approach. The implementation is done within the open source PDE software framework Dune and the discretization module dune-pdelab. The strength of the proposed approach is illustrated with performance measurements for DG schemes for a scalar diffusion reaction equation and the Stokes equation. In our measurements, we utilize both the AVX2 and the AVX512 instruction set, achieving 30% to 40% of the machine’s theoretical peak performance for one matrix-free application of the operator.

Coordination of fate transition and cell division is crucial to maintain the plant architecture and to achieve efficient production of plant organs. In this paper, we analysed the stem cell dynamics at the shoot apical meristem (SAM) that is one of the plant stem cells locations. We designed a mathematical model to elucidate the impact of hormonal signaling on the fate transition rates between different zones corresponding to slowly dividing stem cells and fast dividing transit amplifying cells. The model is based on a simplified two-dimensional disc geometry of the SAM and accounts for a continuous displacement towards the periphery of cells produced in the central zone. Coupling growth and hormonal signaling results in a nonlinear system of reaction-diffusion equations on a growing domain with the growth rate depending on the model components. The model is tested by simulating perturbations in the level of key transcription factors that maintain SAM homeostasis. The model provides new insights on how the transcription factor HECATE is integrated in the regulatory network that governs stem cell differentiation.