TensorFlow Doing HPC

TensorFlow is a popular emerging open-source programming framework supporting the execution of distributed applications on heterogeneous hardware. While TensorFlow has been initially designed for developing Machine Learning (ML) applications, in fact TensorFlow aims at supporting the development of a much broader range of application kinds that are outside the ML domain and can possibly include HPC applications. However, very few experiments have been conducted to evaluate TensorFlow performance when running HPC workloads on supercomputers. This work addresses this lack by designing four traditional HPC benchmark applications: STREAM, matrix-matrix multiply, Conjugate Gradient (CG) solver and Fast Fourier Transform (FFT). We analyze their performance on two supercomputers with accelerators and evaluate the potential of TensorFlow for developing HPC applications. Our tests show that TensorFlow can fully take advantage of high performance networks and accelerators on supercomputers. Running our TensorFlow STREAM benchmark, we obtain over 50% of theoretical communication bandwidth on our testing platform. We find an approximately 2x, 1.7x and 1.8x performance improvement when increasing the number of GPUs from two to four in the matrix-matrix multiply, CG and FFT applications respectively. All our performance results demonstrate that TensorFlow has high potential of emerging also as HPC programming framework for heterogeneous supercomputers.Comment: Accepted for publication at The Ninth International Workshop on Accelerators and Hybrid Exascale Systems (AsHES'19

Characterization of a broad-based mosquito yeast interfering RNA larvicide with a conserved target site in mosquito semaphorin-1a genes

BACKGROUND: RNA interference (RNAi), which has facilitated functional characterization of mosquito neural development genes such as the axon guidance regulator semaphorin-1a (sema1a), could one day be applied as a new means of vector control. Saccharomyces cerevisiae (baker's yeast) may represent an effective interfering RNA expression system that could be used directly for delivery of RNA pesticides to mosquito larvae. Here we describe characterization of a yeast larvicide developed through bioengineering of S. cerevisiae to express a short hairpin RNA (shRNA) targeting a conserved site in mosquito sema1a genes. RESULTS: Experiments conducted on Aedes aegypti larvae demonstrated that the yeast larvicide effectively silences sema1a expression, generates severe neural defects, and induces high levels of larval mortality in laboratory, simulated-field, and semi-field experiments. The larvicide was also found to induce high levels of Aedes albopictus, Anopheles gambiae and Culex quinquefasciatus mortality. CONCLUSIONS: The results of these studies indicate that use of yeast interfering RNA larvicides targeting mosquito sema1a genes may represent a new biorational tool for mosquito control

Sum rule for the optical Hall angle

We consider the optical Hall conductivity of a general electronic medium and prove that the optical Hall angle obeys a new sum rule. This sum rule governs the response of an electronic fluid to a Lorentz electric field and can thought of as the transverse counterpart to the f-sum rule in optical conductivity. The physical meaning of this sum rule is discussed, giving a number of examples of its application to a variety of of electronic media.Comment: Four pages. Latex file with two postscript figure

Laminar flow of two miscible fluids in a simple network

When a fluid comprised of multiple phases or constituents flows through a network, non-linear phenomena such as multiple stable equilibrium states and spontaneous oscillations can occur. Such behavior has been observed or predicted in a number of networks including the flow of blood through the microcirculation, the flow of picoliter droplets through microfluidic devices, the flow of magma through lava tubes, and two-phase flow in refrigeration systems. While the existence of non-linear phenomena in a network with many inter-connections containing fluids with complex rheology may seem unsurprising, this paper demonstrates that even simple networks containing Newtonian fluids in laminar flow can demonstrate multiple equilibria. The paper describes a theoretical and experimental investigation of the laminar flow of two miscible Newtonian fluids of different density and viscosity through a simple network. The fluids stratify due to gravity and remain as nearly distinct phases with some mixing occurring only by diffusion. This fluid system has the advantage that it is easily controlled and modeled, yet contains the key ingredients for network non-linearities. Experiments and 3D simulations are first used to explore how phases distribute at a single T-junction. Once the phase separation at a single junction is known, a network model is developed which predicts multiple equilibria in the simplest of networks. The existence of multiple stable equilibria is confirmed experimentally and a criteria for their existence is developed. The network results are generic and could be applied to or found in different physical systems

Quantum rotor theory of spinor condensates in tight traps

In this work, we theoretically construct exact mappings of many-particle bosonic systems onto quantum rotor models. In particular, we analyze the rotor representation of spinor Bose-Einstein condensates. In a previous work it was shown that there is an exact mapping of a spin-one condensate of fixed particle number with quadratic Zeeman interaction onto a quantum rotor model. Since the rotor model has an unbounded spectrum from above, it has many more eigenstates than the original bosonic model. Here we show that for each subset of states with fixed spin F_z, the physical rotor eigenstates are always those with lowest energy. We classify three distinct physical limits of the rotor model: the Rabi, Josephson, and Fock regimes. The last regime corresponds to a fragmented condensate and is thus not captured by the Bogoliubov theory. We next consider the semiclassical limit of the rotor problem and make connections with the quantum wave functions through use of the Husimi distribution function. Finally, we describe how to extend the analysis to higher-spin systems and derive a rotor model for the spin-two condensate. Theoretical details of the rotor mapping are also provided here.Comment: 10 pages, 2 figure

Localization and Anomalous Transport in a 1-D Soft Boson Optical Lattice

We study the dynamics of Bose-Einstein condensed atoms in a 1-D optical lattice potential in a regime where the collective (Josephson) tunneling energy is comparable with the on-site interaction energy, and the number of particles per lattice site is mesoscopically large. By directly imaging the motion of atoms in the lattice, we observe an abrupt suppression of atom transport through the array for a critical ratio of these energies, consistent with quantum fluctuation induced localization. Directly below the onset of localization, the frequency of the observed superfluid transport can be explained by a phonon excitation but deviates substantially from that predicted by the hydrodynamic/Gross-Pitaevskii equations.Comment: 14 pages, 5 figure

Infrared Hall effect in high Tc superconductors: Evidence for non-Fermi liquid Hall scattering

Infrared (20-120 cm-1 and 900-1100 cm-1) Faraday rotation and circular dichroism are measured in high Tc superconductors using sensitive polarization modulation techniques. Optimally doped YBCO thin films are studied at temperatures down to 15 K and magnetic fields up to 8 T. At 1000 cm-1 the Hall conductivity varies strongly with temperature in contrast to the longitudinal conductivity which is nearly independent of temperature. The Hall scattering rate has a T^2 temperature dependence but, unlike a Fermi liquid, depends only weakly on frequency. The experiment puts severe constraints on theories of transport in the normal state of high Tc superconductors.Comment: 8 pages, 3 figure