PetaFLOP Molecular Dynamics for Engineering Applications

Molecular dynamics (MD) simulations enable the investigation of multicomponent and multiphase processes relevant to engineering applications, such as droplet coalescence or bubble formation. These scenarios require the simulation of ensembles containing a large number of molecules. We present recent advances within the MD framework ls1 mardyn which is being developed with particular regard to this class of problems. We discuss several OpenMP schemes that deliver optimal performance at node-level. We have further introduced nonblocking communication and communication hiding for global collective operations. Together with revised data structures and vectorization, these improvements unleash PetaFLOP performance and enable multi-trillion atom simulations on the HLRS supercomputer Hazel Hen. We further present preliminary results achieved for droplet coalescence scenarios at a smaller scale.BMBF, 01IH16008, Verbundprojekt: TaLPas - Task-basierte Lastverteilung und Auto-Tuning in der Partikelsimulatio

Proton Spin-Lattice Relaxation in Organic Molecular Solids: Polymorphism and the Dependence on Sample Preparation

We report solid‐state nuclear magnetic resonance 1H spin‐lattice relaxation, single‐crystal X‐ray diffraction, powder X‐ray diffraction, field emission scanning electron microscopy, and differential scanning calorimetry in solid samples of 2‐ethylanthracene (EA) and 2‐ethylanthraquinone (EAQ) that have been physically purified in different ways from the same commercial starting compounds. The solid‐state 1H spin‐lattice relaxation is always non‐exponential at high temperatures as expected when CH3 rotation is responsible for the relaxation. The 1H spin‐lattice relaxation experiments are very sensitive to the “several‐molecule” (clusters) structure of these van der Waals molecular solids. In the three differently prepared samples of EAQ, the relaxation also becomes very non‐exponential at low temperatures. This is very unusual and the decay of the nuclear magnetization can be fitted with both a stretched exponential and a double exponential. This unusual result correlates with the powder X‐ray diffractometry results and suggests that the anomalous relaxation is due to crystallites of two (or more) different polymorphs (concomitant polymorphism)

The tetanic depression in fast motor units of mammalian skeletal muscle can be evoked by lengthening of one initial interpulse interval

A lower than expected tetanic force (the tetanic depression) is regularly observed in fast motor units (MUs) when a higher stimulation frequency immediately follows a lower one. The aim of the present study was to determine whether prolongation of only the first interpulse interval (IPI) resulted in tetanic depression. The experiments were carried out on fast MUs of the medial gastrocnemius muscle in cats and rats. The tetanic depression was measured in each case as the force decrease of a tetanus with one IPI prolonged in relation to the tetanic force at the respective constant stimulation frequency. Force depression was observed in all cases studied and was considerably greater in cats. For cats, the mean values of force depression amounted to 28.64% for FR and 10.86% for FF MUs whereas for rats 9.30 and 7.21% for FR and FF motor units, respectively. Since the phenomenon of tetanic depression in mammalian muscle is commonly observed even after a change in only the initial interpulse interval within a stimulation pattern, it can effectively influence processes of force regulation during voluntary activity of a muscle, when motoneurones progressively increase the firing rate

In situ, steerable, hardware-independent and data-structure agnostic visualization with ISAAC

The computation power of supercomputers grows faster than the bandwidth of their storage and network. In particular, applications using hardware accelerators like Nvidia GPUs cannot save enough data to be analyzed in a later step. There is a high risk of losing important scientific information. We introduce the in situ template library ISAAC which enables arbitrary applications like scientific simulations to live visualize their data without the need of deep copy operations or data transformation using the very same compute node and hardware accelerator the data is already residing on. Arbitrary meta data can be added to the renderings and user defined steering commands can be asynchronously sent back to the running application. Using an aggregating server, ISAAC streams the interactive visualization video and enables user to access their applications from everywhere