Hierarchical multithreading: programming model and system software

This paper addresses the underlying sources of performance degradation (e.g. latency, overhead, and starvation) and the difficulties of programmer productivity (e.g. explicit locality management and scheduling, performance tuning, fragmented memory, and synchronous global barriers) to dramatically enhance the broad effectiveness of parallel processing for high end computing. We are developing a hierarchical threaded virtual machine (HTVM) that defines a dynamic, multithreaded execution model and programming model, providing an architecture abstraction for HEC system software and tools development. We are working on a prototype language, LITL-X (pronounced "little-X") for latency intrinsic-tolerant language, which provides the application programmers with a powerful set of semantic constructs to organize parallel computations in a way that hides/manages latency and limits the effects of overhead. This is quite different from locality management, although the intent of both strategies is to minimize the effect of latency on the efficiency of computation. We work on a dynamic compilation and runtime model to achieve efficient LITL-X program execution. Several adaptive optimizations were studied. A methodology of incorporating domain-specific knowledge in program optimization was studied. Finally, we plan to implement our method in an experimental testbed for a HEC architecture and perform a qualitative and quantitative evaluation on selected applications

AI-based analysis of super-resolution microscopy: Biological discovery in the absence of ground truth

The nanoscale resolution of super-resolution microscopy has now enabled the use of fluorescent based molecular localization tools to study whole cell structural biology. Machine learning based analysis of super-resolution data offers tremendous potential for discovery of new biology, that by definition is not known and lacks ground truth. Herein, we describe the application of weakly supervised learning paradigms to super-resolution microscopy and its potential to enable the accelerated exploration of the molecular architecture of subcellular macromolecules and organelles.Comment: 14 pages, 3 figure

Towards an Integrated Multiscale Simulation of Turbulent Clouds on PetaScale Computers

The development of precipitating warm clouds is affected by several effects of small-scale air turbulence including enhancement of droplet-droplet collision rate by turbulence, entrainment and mixing at the cloud edges, and coupling of mechanical and thermal energies at various scales. Large-scale computation is a viable research tool for quantifying these multiscale processes. Specifically, top-down large-eddy simulations (LES) of shallow convective clouds typically resolve scales of turbulent energy-containing eddies while the effects of turbulent cascade toward viscous dissipation are parameterized. Bottom-up hybrid direct numerical simulations (HDNS) of cloud microphysical processes resolve fully the dissipation-range flow scales but only partially the inertial subrange scales. it is desirable to systematically decrease the grid length in LES and increase the domain size in HDNS so that they can be better integrated to address the full range of scales and their coupling. In this paper, we discuss computational issues and physical modeling questions in expanding the ranges of scales realizable in LES and HDNS, and in bridging LES and HDNS. We review our on-going efforts in transforming our simulation codes towards PetaScale computing, in improving physical representations in LES and HDNS, and in developing better methods to analyze and interpret the simulation results

Automatic Program Segment Similarity Detection in Targeted Program Performance Improvement

Targeted optimization of program segments can provide an additional program speedup over the highest default op-timization level, such as-O3 in GCC. The key challenge is how to automatically search for performance sensitive pro-gram segments in a given code, to which a customized set of optimization compiler options could be applied. In this paper we propose a method for automatic detec-tion of performance sensitive program segments based on program segment similarity. First we create a proxy seg-ment template database trained over a set of random in-put programs. The compiler identifies program segments by correlating them to the pre-build proxy segment templates using the syntax structure and architecture-dependent be-havior similarity. We argue that the identified program seg-ments can be custom optimized to improve the overall pro-gram performance. The method is evaluated on the Intel XScale PXA255 platform using randomly selected benchmarks. The experi-mental results show that our method can provide additional speedups over the highest optimization level in GCC 3.3 (-O3) for an arbitrary set of applications.

Statistical Properties of Charmonium Spectrum and a New Mechanism of J/\psi Suppression

The statistical properties of Charmonium energy spectrum determined by the Bethe-Salpeter equation are investigated. It is found that the regular motion of the $c\bar{c}$ system can be expected at a small value of color screening mass but the chaotic motion at a large one. It is shown that the level mixing due to color screening serves as a new mechanism resulting in the J/$\psi$ suppression. Moreover, this kind of suppression can occur before the color screening mass reaches its critical value for J/$\psi$ dissociation. It implies that a strong J/$\psi$ suppression is possible in the absence of dissociation of J/$\psi$.Comment: 13 latex pages, 2 figures. Phys. Rev. C in pres

A simulation study on the measurement of D0-D0bar mixing parameter y at BES-III

We established a method on measuring the \dzdzb mixing parameter $y$ for BESIII experiment at the BEPCII $e^+e^-$ collider. In this method, the doubly tagged $\psi(3770) \to D^0 \overline{D^0}$ events, with one $D$ decays to CP-eigenstates and the other $D$ decays semileptonically, are used to reconstruct the signals. Since this analysis requires good $e/\pi$ separation, a likelihood approach, which combines the $dE/dx$, time of flight and the electromagnetic shower detectors information, is used for particle identification. We estimate the sensitivity of the measurement of $y$ to be 0.007 based on a $20fb^{-1}$ fully simulated MC sample.Comment: 6 pages, 7 figure

A novel absorptive/reflective solar concentrator for heat and electricity generation: an optical and thermal analysis.

The crossed compound parabolic concentrator (CCPC) is one of the most efficient non-imaging solar concentrators used as a stationary solar concentrator or as a second stage solar concentrator. In this study, the CCPC is modified to demonstrate for the first time a new generation of solar concentrators working simultaneously as an electricity generator and thermal collector. The CCPC is designed to have two complementary surfaces, one reflective and one absorptive, and is named as an absorptive/reflective CCPC (AR-CCPC). Usually, the height of the CCPC is truncated with a minor sacrifice of the geometric concentration. These truncated surfaces rather than being eliminated are instead replaced with absorbent surfaces to collect heat from solar radiation. The optical efficiency including absorptive/reflective part of the AR-CCPC was simulated and compared for different geometric concentration ratios varying from 3.6× to 4×. It was found that the combined optical efficiency of the AR-CCPC 3.6×/4× remained constant and high all day long and that it had the highest total optical efficiency compared to other concentrators. In addition, the temperature distributions of AR-CCPC surfaces and the assembled solar cell were simulated based on those heat flux boundary conditions. It was shown that the addition of a thermal absorbent surface can increase the wall temperature. The maximum value reached 321.5 K at the front wall under 50° incidence. The experimental verification was also adopted to show the benefits of using absorbent surfaces. The initial results are very promising and significant for the enhancement of solar concentrator systems with lower concentrations

Patterns of lung cancer mortality in 23 countries: Application of the Age-Period-Cohort model

BACKGROUND: Smoking habits do not seem to be the main explanation of the epidemiological characteristics of female lung cancer mortality in Asian countries. However, Asian countries are often excluded from studies of geographical differences in trends for lung cancer mortality. We thus examined lung cancer trends from 1971 to 1995 among men and women for 23 countries, including four in Asia. METHODS: International and national data were used to analyze lung cancer mortality from 1971 to 1995 in both sexes. Age-standardized mortality rates (ASMR) were analyzed in five consecutive five-year periods and for each five-year age group in the age range 30 to 79. The age-period-cohort (APC) model was used to estimate the period effect (adjusted for age and cohort effects) for mortality from lung cancer. RESULTS: The sex ratio of the ASMR for lung cancer was lower in Asian countries, while the sex ratio of smoking prevalence was higher in Asian countries. The mean values of the sex ratio of the ASMR from lung cancer in Taiwan, Hong Kong, Singapore, and Japan for the five 5-year period were 2.10, 2.39, 3.07, and 3.55, respectively. These values not only remained quite constant over each five-year period, but were also lower than seen in the western countries. The period effect, for lung cancer mortality as derived for the 23 countries from the APC model, could be classified into seven patterns. CONCLUSION: Period effects for both men and women in 23 countries, as derived using the APC model, could be classified into seven patterns. Four Asian countries have a relatively low sex ratio in lung cancer mortality and a relatively high sex ratio in smoking prevalence. Factors other than smoking might be important, especially for women in Asian countries

Hypoglycemia and Death in Mice Following Experimental Exposure to an Extract of Trogia venenata Mushrooms

BACKGROUND: Clusters of sudden unexplained death (SUD) in Yunnan Province, China, have been linked to eating Trogia venenata mushrooms. We evaluated the toxic effect of this mushroom on mice. METHODS: We prepared extracts of fresh T. venenata and Laccaria vinaceoavellanea mushrooms collected from the environs of a village that had SUD. We randomly allocated mice into treatment groups and administered mushroom extracts at doses ranging from 500 to 3500 mg/kg and water (control) via a gavage needle. We observed mice for mortality for 7 days after a 3500 mg/kg dose and for 24 hours after doses from 500 to 3000 mg/kg. We determined biochemical markers from serum two hours after a 2000 mg/kg dose. RESULTS: Ten mice fed T. venenata extract (3500 mg/kg) died by five hours whereas all control mice (L. vinaceoavellanea extract and water) survived the seven-day observation period. All mice died by five hours after exposure to single doses of T. venenata extract ranging from 1500 to 3000 mg/kg, while the four mice exposed to a 500 mg/kg dose all survived. Mice fed 2000 mg/kg of T. venenata extract developed profound hypoglycemia (median= 0.66 mmol/L) two hours after exposure. DISCUSSION: Hypoglycemia and death within hours of exposure, a pattern unique among mushroom toxicity, characterize T. venenata poisoning

Decision Support System for the Response to Infectious Disease Emergencies Based on WebGIS and Mobile Services in China

Background: For years, emerging infectious diseases have appeared worldwide and threatened the health of people. The emergence and spread of an infectious-disease outbreak are usually unforeseen, and have the features of suddenness and uncertainty. Timely understanding of basic information in the field, and the collection and analysis of epidemiological information, is helpful in making rapid decisions and responding to an infectious-disease emergency. Therefore, it is necessary to have an unobstructed channel and convenient tool for the collection and analysis of epidemiologic information in the field. Methodology/Principal Findings: Baseline information for each county in mainland China was collected and a database was established by geo-coding information on a digital map of county boundaries throughout the country. Google Maps was used to display geographic information and to conduct calculations related to maps, and the 3G wireless network was used to transmit information collected in the field to the server. This study established a decision support system for the response to infectious-disease emergencies based on WebGIS and mobile services (DSSRIDE). The DSSRIDE provides functions including data collection, communication and analyses in real time, epidemiological detection, the provision of customized epidemiological questionnaires and guides for handling infectious disease emergencies, and the querying of professional knowledge in the field. These functions of the DSSRIDE could be helpful for epidemiological investigations in the field and the handling of infectious-disease emergencies. Conclusions/Significance: The DSSRIDE provides a geographic information platform based on the Google Maps application programming interface to display information of infectious disease emergencies, and transfers information between workers in the field and decision makers through wireless transmission based on personal computers, mobile phones and personal digital assistants. After a 2-year practice and application in infectious disease emergencies, the DSSRIDE is becoming a useful platform and is a useful tool for investigations in the field carried out by response sections and individuals. The system is suitable for use in developing countries and low-income districts