Performance Analysis of the Lattice Boltzmann Model Beyond Navier-Stokes

The lattice Boltzmann method is increasingly important in facilitating large-scale fluid dynamics simulations. To date, these simulations have been built on discretized velocity models of up to 27 neighbors. Recent work has shown that higher order approximations of the continuum Boltzmann equation enable not only recovery of the Navier-Stokes hydrodynamics, but also simulations for a wider range of Knudsen numbers, which is especially important in micro- and nanoscale flows. These higher-order models have significant impact on both the communication and computational complexity of the application. We present a performance study of the higherorder models as compared to the traditional ones, on both the IBM Blue Gene/P and Blue Gene/Q architectures. We study the tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of extended models and enable efficient modeling of extreme regimes of computational fluid dynamics.Physic

G254 undergraduate experiment

This paper describes the experiments on payload G254. Each experiment is accommodated in a spacepak and six experiments fly in a full canister. One of the experiments will be housed in a new Isospacepak structure, which will be described briefly. Five of the six experiments have dedicated controllers. The objective of each experiment is discussed. In addition, the operational scenario is provided

Dynamic Adaptable Asynchronous Progress Model for MPI RMA Multiphase Applications

Casper is a process-based asynchronous progress model for MPI one-sided communication on multi- and many-core architectures. The one-sided communication is not truly one-sided in most MPI implementations: the target process still relies on software progress to complete incoming operations. Casper allows the user to specify an arbitrary number of cores dedicated to background ghost processes and transparently redirects the RMA operations to ghost processes by utilizing the PMPI redirection and MPI-3 shared-memory technologies. Although Casper benefits applications that suffer from lack of asynchronous progress, the operation redirection design might not support complex multiphase applications effectively, which often involve dynamically changing communication density and computing workloads. In this paper, we present an adaptive mechanism in Casper to address the limitation of static asynchronous progress in multiphase applications. We exploit two adaptive strategies, a user-guided strategy and a fully transparent and automatic strategy based on self-profiling and prediction, to dynamically reconfigure the asynchronous progress in Casper according to real-time performance characteristics during multiphase execution. We evaluate the adaptive approaches in both microbenchmarks and a real quantum chemistry application suite, NWChem, on the Cray XC30 supercomputer and an Intel Omni-Path cluster.This material was based upon work supported by the U.S. Dept. of Energy, Office of Science, Advanced Scientific Computing Research (SC-21), under contract DE-AC02- 06CH11357. The experimental resources for this paper were provided by the National Energy Research Scientific Computing Center (NERSC) on the Edison Cray XC30 supercomputer and by the Laboratory Computing Resource Center on the Bebop cluster at Argonne National Laboratory. Antonio J. Peña is co-financed by the Spanish Ministry of Economy and Competitiveness under Juan de la Cierva fellowship number IJCI-2015-23266.Peer ReviewedPostprint (author's final draft

Endothelin-B Receptor Activation in Astrocytes Regulates the Rate of Oligodendrocyte Regeneration during Remyelination.

Reactive astrogliosis is an essential and ubiquitous response to CNS injury, but in some cases, aberrant activation of astrocytes and their release of inhibitory signaling molecules can impair endogenous neural repair processes. Our lab previously identified a secreted intercellular signaling molecule, called endothelin-1 (ET-1), which is expressed at high levels by reactive astrocytes in multiple sclerosis (MS) lesions and limits repair by delaying oligodendrocyte progenitor cell (OPC) maturation. However, as ET receptors are widely expressed on neural cells, the cell- and receptor-specific mechanisms of OPC inhibition by ET-1 action remain undefined. Using pharmacological approaches and cell-specific endothelin receptor (EDNR) ablation, we show that ET-1 acts selectively through EDNRB on astrocytes-and not OPCs-to indirectly inhibit remyelination. These results demonstrate that targeting specific pathways in reactive astrocytes represents a promising therapeutic target in diseases with extensive reactive astrogliosis, including MS

Exploring the Impact of Efficacy Messages on Cessation-Related Outcomes Using Ecological Momentary Assessment

Introduction:Observational studies indicate that cigarette package inserts with efficacy messages about the benefits of quitting (i.e. response efficacy) and recommendations for successful cessation increase smokers’ self-efficacy to quit and promote sustained cessation. However, the effects of inserts with such efficacy messages have not been studied using experimental designs. This study used ecological momentary assessment (EMA) to assess smokers’ responses to efficacy inserts.Material and Methods:In a randomized case-crossover study among smokers from the United States (n=23), participants received a one-week supply of cigarettes with efficacy inserts and a one-week supply without any inserts, and were randomized to use the packs with inserts on either the first or second week of the study. For 14 consecutive days, participants used a smartphone to answer brief surveys on cessation-related variables during smoking sessions and at the beginning of each day. Multilevel mixed-effects linear and logistic regression models compared responses during the insert period to those of the non-insert period.Results:The insert period was associated with greater desire to quit (b=0.21, p=0.012), motivation to quit (b=0.18, p=0.001), self-efficacy to cut down (b=0.26, p\u3c0.001) and to quit (b=0.28, p\u3c0.000), and response efficacy/ perceived benefits of quitting (b=0.13, p=0.012). Insert exposure was not significantly associated with forgoing cigarettes (OR=1.9, p=0.2).Conclusions:Results from this EMA study suggest that inserts with efficacy messages may promote determinants of smoking cessation. This is consistent with observational research in Canada, which is the only country to use inserts with efficacy messages as well as pictorial warnings about smoking risks on the outside of packs. Future studies should assess the extent to which efficacy inserts can not only be used to communicate health information to smokers but also work in synergy with pictorial warnings

The 'Diverse, Dynamic New World of Global Tobacco Control'?:An Analysis of Participation in the Conference of the Parties to the WHO Framework Convention on Tobacco Control

INTRODUCTION: The increasingly inequitable impacts of tobacco use highlight the importance of ensuring developing countries’ ongoing participation in global tobacco control. The WHO Framework Convention on Tobacco Control (FCTC) has been widely regarded as reflecting the high engagement and effective influence of developing countries. METHODS: We examined participation in FCTC governance based on records from the first four meetings of the Conference of the Parties (COP), comparing representation and delegate diversity across income levels and WHO regions. RESULTS: While attendance at the COP sessions is high, there are substantial disparities in the relative representation of different income levels and regions, with lower middle and low income countries contributing only 18% and 10% of total meeting delegates, respectively. In regional terms, Europe provided the single largest share of delegates at all except the Durban (2008) meeting. Thirty-nine percent of low income countries and 27% of those from Africa were only ever represented by a single person delegation compared with 10% for high income countries and 11% for Europe. Rotation of the COP meeting location outside of Europe is associated with better representation of other regions and a stronger presence of delegates from national ministries of health and focal points for tobacco control. CONCLUSIONS: Developing countries face particular barriers to participating in the COP process, and their engagement in global tobacco control is likely to diminish in the absence of specific measures to support their effective participation

Antioxidant protection from HIV-1 gp120-induced neuroglial toxicity

BACKGROUND: The pathogenesis of HIV-1 glycoprotein 120 (gp120) associated neuroglial toxicity remains unresolved, but oxidative injury has been widely implicated as a contributing factor. In previous studies, exposure of primary human central nervous system tissue cultures to gp120 led to a simplification of neuronal dendritic elements as well as astrocytic hypertrophy and hyperplasia; neuropathological features of HIV-1-associated dementia. Gp120 and proinflammatory cytokines upregulate inducible nitric oxide synthase (iNOS), an important source of nitric oxide (NO) and nitrosative stress. Because ascorbate scavenges reactive nitrogen and oxygen species, we studied the effect of ascorbate supplementation on iNOS expression as well as the neuronal and glial structural changes associated with gp120 exposure. METHODS: Human CNS cultures were derived from 16–18 week gestation post-mortem fetal brain. Cultures were incubated with 400 μM ascorbate-2-O-phosphate (Asc-p) or vehicle for 18 hours then exposed to 1 nM gp120 for 24 hours. The expression of iNOS and neuronal (MAP2) and astrocytic (GFAP) structural proteins was examined by immunohistochemistry and immunofluorescence using confocal scanning laser microscopy (CSLM). RESULTS: Following gp120 exposure iNOS was markedly upregulated from undetectable levels at baseline. Double label CSLM studies revealed astrocytes to be the prime source of iNOS with rare neurons expressing iNOS. This upregulation was attenuated by the preincubation with Asc-p, which raised the intracellular concentration of ascorbate. Astrocytic hypertrophy and neuronal injury caused by gp120 were also prevented by preincubation with ascorbate. CONCLUSIONS: Ascorbate supplementation prevents the deleterious upregulation of iNOS and associated neuronal and astrocytic protein expression and structural changes caused by gp120 in human brain cell cultures

MPI Application Binary Interface Standardization

MPI is the most widely used interface for high-performance computing (HPC) workloads. Its success lies in its embrace of libraries and ability to evolve while maintaining backward compatibility for older codes, enabling them to run on new architectures for many years. In this paper, we propose a new level of MPI compatibility: a standard Application Binary Interface (ABI). We review the history of MPI implementation ABIs, identify the constraints from the MPI standard and ISO C, and summarize recent efforts to develop a standard ABI for MPI. We provide the current proposal from the MPI Forum's ABI working group, which has been prototyped both within MPICH and as an independent abstraction layer called Mukautuva. We also list several use cases that would benefit from the definition of an ABI while outlining the remaining constraints

Elemental: A new framework for distributed memory dense matrix computations

Abstract Parallelizing dense matrix computations to distributed memory architectures is a well-studied subject and generally considered to be among the best understood domains of parallel computing. Two packages, developed in the mid 1990s, still enjoy regular use: ScaLAPACK and PLAPACK. With the advent of many-core architectures, which may very well take the shape of distributed memory architectures within a single processor, these packages must be revisited since it will likely not be practical to use MPI-based implementations. Thus, this is a good time to review lessons learned since the introduction of these two packages and to propose a simple yet effective alternative. Preliminary performance results show the new solution achieves competitive, if not superior, performance on large clusters (i.e., on two racks o