64 research outputs found
Hydrodynamic turbulence in quasi-Keplerian rotating flows
No full textWe report a direct-numerical-simulation study of the Taylor-Couette flow in the quasi-Keplerian regime at shear Reynolds numbers up to O(10(5)). Quasi-Keplerian rotating flow has been investigated for decades as a simplified model system to study the origin of turbulence in accretion disks that is not fully understood. The flow in this study is axially periodic and thus the experimental end-wall effects on the stability of the flow are avoided. Using optimal linear perturbations as initial conditions, our simulations find no sustained turbulence: the strong initial perturbations distort the velocity profile and trigger turbulence that eventually decays. Published by AIP Publishing
A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor–Couette flow
No full textA hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes
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Pre-exascale computing of protein–ligand binding free energies with open source software for drug design
No full textNowadays, drug design projects benefit from highly accurate protein–ligand binding free energy predictions based on molecular dynamics simulations. While such calculations have been computationally expensive in the past, we now demonstrate that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days. We report our results of free energy calculations on a large set of pharmaceutically relevant targets assembled to reflect industrial drug discovery projects
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster
No full textABSTRACT We benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high‐performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel‐MPI and Open‐MPI. The largest system showed near‐perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687 ns/d for the 82k atom system, 116 ns/d for the 53M atom system, and about 35 ns/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state‐of‐the‐art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.Bundesministerium für Bildung und Forschung https://doi.org/10.13039/501100002347European Commission https://doi.org/10.13039/50110000078
Neutrino-Strahlungshydrodynamik: Stellarer Kollaps und der Explosionsmechanismus von Typ II Supernovae
No full textAccording to the current standard picture supernova explosions of evolved massive stars are mediated by the deposition of neutrino energy in the stellar medium. Detailed numerical simulations, however, have so far not been able to demonstrate the viability of this mechanism convincingly. The aim of this thesis was to overcome a fundamental deficiency inherent to current supernova models namely the treatment of the neutrino transport. Using a newly developed numerical method based on the Boltzmann transport equation the transport and interaction of neutrinos in the dense medium of the nascent neutron star could be computed with high accuracy. Compared to previous models enhanced neutrino energy deposition was found in our supernova simulation. This, however, turns out to be not sufficient to cause healthy supernova explosions in spherically symmetric models, which underlines the importance of convective phenomena in the early phases of a supernova.Nach heutiger gültiger Standardvorstellung verursacht der Energieübertrag von Neutrinos auf das stellare Medium die Supernovaexplosion massereicher Sterne. Die dabei ablaufenden Prozesse, insbesondere der Transport und die Wechselwirkung von Neutrinos im dichten Medium des entstehenden Neutronensterns, wurden mit Hilfe eines neuentwickelten numerischen Verfahrens mit hoher Genauigkeit berechnet. Der damit gefundene erhöhte Energieübertrag allein reicht jedoch in sphärisch symmetrischen Modellen nicht aus, um die Explosion zu verursachen, wodurch die Bedeutung konvektiver Phänomene in der Frühphase der Supernovaentwicklung unterstrichen wird
Radiation hydrodynamics with neutrinos stellar core collapse and the explosion mechanism of type II supernovae
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Evaluation of performance portability frameworks for the implementation of a particle‐in‐cell code
No full textExplosion mechanisms of massive stars : a critical review of possibilities and perspectives
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