Experiences in porting mini-applications to OpenACC and OpenMP on heterogeneous systems

This article studies mini-applications—Minisweep, GenASiS, GPP, and FF—that use computational methods commonly encountered in HPC. We have ported these applications to develop OpenACC and OpenMP versions, and evaluated their performance on Titan (Cray XK7 with K20x GPUs), Cori (Cray XC40 with Intel KNL), Summit (IBM AC922 with Volta GPUs), and Cori-GPU (Cray CS-Storm 500NX with Intel Skylake and Volta GPUs). Our goals are for these new ports to be useful to both application and compiler developers, to document and describe the lessons learned and the methodology to create optimized OpenMP and OpenACC versions, and to provide a description of possible migration paths between the two specifications. Cases where specific directives or code patterns result in improved performance for a given architecture are highlighted. We also include discussions of the functionality and maturity of the latest compilers available on the above platforms with respect to OpenACC or OpenMP implementations

Large Area Crop Inventory Experiment (LACIE). Intensive test site assessment report

There are no author-identified significant results in this report

Ocean spectra for the high-frequency waves as determined from airborne radar measurements

The possibilities of using radar to obtain oceanographic information are described. Ocean spectra for the short gravity and gravity-capillary waves have been derived from radar crosssection measurements for vertical polarization at 428 MHz, 1228 MHz, 4455 MHz, and 8910 MHz...

Efficient dynamical downscaling of general circulation models using continuous data assimilation

Continuous data assimilation (CDA) is successfully implemented for the first time for efficient dynamical downscaling of a global atmospheric reanalysis. A comparison of the performance of CDA with the standard grid and spectral nudging techniques for representing long- and short-scale features in the downscaled fields using the Weather Research and Forecast (WRF) model is further presented and analyzed. The WRF model is configured at 25km horizontal resolution and is driven by 250km initial and boundary conditions from NCEP/NCAR reanalysis fields. Downscaling experiments are performed over a one-month period in January, 2016. The similarity metric is used to evaluate the performance of the downscaling methods for large and small scales. Similarity results are compared for the outputs of the WRF model with different downscaling techniques, NCEP reanalysis, and Final Analysis. Both spectral nudging and CDA describe better the small-scale features compared to grid nudging. The choice of the wave number is critical in spectral nudging; increasing the number of retained frequencies generally produced better small-scale features, but only up to a certain threshold after which its solution gradually became closer to grid nudging. CDA maintains the balance of the large- and small-scale features similar to that of the best simulation achieved by the best spectral nudging configuration, without the need of a spectral decomposition. The different downscaled atmospheric variables, including rainfall distribution, with CDA is most consistent with the observations. The Brier skill score values further indicate that the added value of CDA is distributed over the entire model domain. The overall results clearly suggest that CDA provides an efficient new approach for dynamical downscaling by maintaining better balance between the global model and the downscaled fields

Creating artificial magnetic fields for cold atoms by photon-assisted tunneling

This paper proposes a simple setup for introducing an artificial magnetic field for neutral atoms in 2D optical lattices. This setup is based on the phenomenon of photon-assisted tunneling and involves a low-frequency periodic driving of the optical lattice. This low-frequency driving does not affect the electronic structure of the atom and can be easily realized by the same means which employed to create the lattice. We also address the problem of detecting this effective magnetic field. In particular, we study the center of mass wave-packet dynamics, which is shown to exhibit certain features of cyclotron dynamics of a classical charged particle.Comment: EPL-style, 8 pages, 4 figure

Computer Simulation of Transverse Ship-Ice Collisions

NRC publication: Ye

Gut-seeded α-synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice

Parkinson’s disease is a synucleinopathy that is characterized by motor dysfunction, death of midbrain dopaminergic neurons and accumulation of α-synuclein (α-Syn) aggregates. Evidence suggests that α-Syn aggregation can originate in peripheral tissues and progress to the brain via autonomic fibers. We tested this by inoculating the duodenal wall of mice with α-Syn preformed fibrils. Following inoculation, we observed gastrointestinal deficits and physiological changes to the enteric nervous system. Using the AAV-PHP.S capsid to target the lysosomal enzyme glucocerebrosidase for peripheral gene transfer, we found that α-Syn pathology is reduced due to the increased expression of this protein. Lastly, inoculation of α-Syn fibrils in aged mice, but not younger mice, resulted in progression of α-Syn histopathology to the midbrain and subsequent motor defects. Our results characterize peripheral synucleinopathy in prodromal Parkinson’s disease and explore cellular mechanisms for the gut-to-brain progression of α-Syn pathology

Coherent matter waves emerging from Mott-insulators

We study the formation of (quasi-)coherent matter waves emerging from a Mott insulator for strongly interacting bosons on a one-dimensional lattice. It has been shown previously that a quasi-condensate emerges at momentum k=\pi/2a, where a is the lattice constant, in the limit of infinitely strong repulsion (hard-core bosons). Here we show that this phenomenon persists for all values of the repulsive interaction that lead to a Mott insulator at a commensurate filling. The non-equilibrium dynamics of hard-core bosons is treated exactly by means of a Jordan-Wigner transformation, and the generic case is studied using a time-dependent density matrix renormalization group technique. Different methods for controlling the emerging matter wave are discussed.Comment: 20 pages, 11 figures. Published versio

Transport of interface states in the Heisenberg chain

We demonstrate the transport of interface states in the one-dimensional ferromagnetic Heisenberg model by a time dependent magnetic field. Our analysis is based on the standard Adiabatic Theorem. This is supplemented by a numerical analysis via the recently developed time dependent DMRG method, where we calculate the adiabatic constant as a function of the strength of the magnetic field and the anisotropy of the interaction.Comment: minor revision, final version; 13 pages, 4 figure