MILC Code Performance on High End CPU and GPU Supercomputer Clusters

With recent developments in parallel supercomputing architecture, many core, multi-core, and GPU processors are now commonplace, resulting in more levels of parallelism, memory hierarchy, and programming complexity. It has been necessary to adapt the MILC code to these new processors starting with NVIDIA GPUs, and more recently, the Intel Xeon Phi processors. We report on our efforts to port and optimize our code for the Intel Knights Landing architecture. We consider performance of the MILC code with MPI and OpenMP, and optimizations with QOPQDP and QPhiX. For the latter approach, we concentrate on the staggered conjugate gradient and gauge force. We also consider performance on recent NVIDIA GPUs using the QUDA library

Free to Air? Legal Protection for TV Program Formats

Television is only as strong as its programming. The use of program formats has slowly but surely developed into an important component of the television industry. This paper examines the surprising gap between the constantly growing, multi-billion-dollar trade of program formats and their unclear and contradictory legal treatment. Using an interdisciplinary approach, I look at the characteristics of both the product at hand and the markets it serves to examine possible justification for legal protection. I argue that the use of the term TV format is misleading and that a clear separation between the unpublished and published stages of the format creation process is necessary. Next, I show that contract law and internal industry mechanisms create an overall efficient, unpublished format market where no additional legal protection is needed. In the international trade market of published program formats, however, I conclude that a clearer legal approach offering better protection is justified

MILC staggered conjugate gradient performance on Intel KNL

We review our work done to optimize the staggered conjugate gradient (CG) algorithm in the MILC code for use with the Intel Knights Landing (KNL) architecture. KNL is the second gener- ation Intel Xeon Phi processor. It is capable of massive thread parallelism, data parallelism, and high on-board memory bandwidth and is being adopted in supercomputing centers for scientific research. The CG solver consumes the majority of time in production running, so we have spent most of our effort on it. We compare performance of an MPI+OpenMP baseline version of the MILC code with a version incorporating the QPhiX staggered CG solver, for both one-node and multi-node runs.Comment: 8 pages, 4 figure

Modeling cancer metabolism on a genome scale

Cancer cells have fundamentally altered cellular metabolism that is associated with their tumorigenicity and malignancy. In addition to the widely studied Warburg effect, several new key metabolic alterations in cancer have been established over the last decade, leading to the recognition that altered tumor metabolism is one of the hallmarks of cancer. Deciphering the full scope and functional implications of the dysregulated metabolism in cancer requires both the advancement of a variety of omics measurements and the advancement of computational approaches for the analysis and contextualization of the accumulated data. Encouragingly, while the metabolic network is highly interconnected and complex, it is at the same time probably the best characterized cellular network. Following, this review discusses the challenges that genome‐scale modeling of cancer metabolism has been facing. We survey several recent studies demonstrating the first strides that have been done, testifying to the value of this approach in portraying a network‐level view of the cancer metabolism and in identifying novel drug targets and biomarkers. Finally, we outline a few new steps that may further advance this field

Properties of N∗N^*(1535) at Finite Density in the Extended Parity-Doublet Models

We improve so called ``naive'' and ``mirror'' models for the positive and negative parity nucleons, $N$ and $N^{*}$, by introducing nonlinear terms allowed by chiral symmetry. Both models in this improvement reproduce the observed nucleon axial charge in free space and reveal interesting density dependence of the axial charges for $N$ and $N^*$, and the doublet masses. A remarkable difference between the two models is found in the off-diagonal axial charge, $g_{ANN^*}$, which could appear either as suppression or as enhancement of $N^* \to \pi N$ decay in the medium.Comment: 14 pages (including two postscript figures), revte

Computing Nearly Singular Solutions Using Pseudo-Spectral Methods

In this paper, we investigate the performance of pseudo-spectral methods in computing nearly singular solutions of fluid dynamics equations. We consider two different ways of removing the aliasing errors in a pseudo-spectral method. The first one is the traditional 2/3 dealiasing rule. The second one is a high (36th) order Fourier smoothing which keeps a significant portion of the Fourier modes beyond the 2/3 cut-off point in the Fourier spectrum for the 2/3 dealiasing method. Both the 1D Burgers equation and the 3D incompressible Euler equations are considered. We demonstrate that the pseudo-spectral method with the high order Fourier smoothing gives a much better performance than the pseudo-spectral method with the 2/3 dealiasing rule. Moreover, we show that the high order Fourier smoothing method captures about $12 \sim 15$ more effective Fourier modes in each dimension than the 2/3 dealiasing method. For the 3D Euler equations, the gain in the effective Fourier codes for the high order Fourier smoothing method can be as large as 20% over the 2/3 dealiasing method. Another interesting observation is that the error produced by the high order Fourier smoothing method is highly localized near the region where the solution is most singular, while the 2/3 dealiasing method tends to produce oscillations in the entire domain. The high order Fourier smoothing method is also found be very stable dynamically. No high frequency instability has been observed.Comment: 26 pages, 23 figure

Real-time pion propagation in finite-temperature QCD

We argue that in QCD near the chiral limit, at all temperatures below the chiral phase transition, the dispersion relation of soft pions can be expressed entirely in terms of three temperature-dependent quantities: the pion screening mass, a pion decay constant, and the axial isospin susceptibility. The definitions of these quantities are given in terms of equal-time (static) correlation functions. Thus, all three quantities can be determined directly by lattice methods. The precise meaning of the Gell-Mann--Oakes--Renner relation at finite temperature is given.Comment: 25 pages, 2 figures; v2: discussion on the region of applicability expanded, to be published in PR

A Mean Field Theory of the Chiral Phase Transition

The recent discussions by Koci\'c and Kogut on the nature of the chiral phase transition are reviewed. The mean-field nature of the transition suggested by these authors is supported in random matrix theory by Verbaarschot and Jackson which reproduces many aspects of QCD lattice simulations. In this paper, we point out physical arguments that favor a mean-field transition, not only for zero density and high temperature, but also for finite density. We show, using the Gross-Neveu model in 3 spatial dimensions in mean-field approximation, how the phase transition is constructed. In order to reproduce the lowering of the $\rho=0$, $T=0$ vacuum evaluated in lattice calculations, we introduce {nucleons} rather than constituent quarks in negative energy states, down to a momentum cut-off of $\Lambda$. We also discuss Brown-Rho scaling of the hadron masses in relation to the QCD phase transition, and how this scaling affects the CERES and HELIOS-3 dilepton experiments.Comment: 23 pages, Latex, no figure

Lattice Calculation of Glueball Matrix Elements

Matrix elements of the form $$ are calculated using the lattice QCD Monte Carlo method. Here, $|G>$ is a glueball state with quantum numbers $0^{++}$, $2^{++}$, $0^{-+}$ and $G$ is the gluon field strength operator. The matrix elements are obtained from the hybrid correlation functions of the fuzzy and plaquette operators performed on the $12^{4}$ and $14^{4}$ lattices at $\beta = 5.9$ and $5.96$ respectively. These matrix elements are compared with those from the QCD sum rules and the tensor meson dominance model. They are the non-perturbative matrix elements needed in the calculation of the partial widths of $J/\Psi$ radiative decays into glueballs.Comment: 12 pages, UK/92-0