Influences on Throughput and Latency in Stream Programs

Vu Thien Nga Nguyen and Raimund Kirner, 'Influences on Throughput and Latency in Stream Programs' paper presented at the 2nd Workshop on Feedback-Directed Compiler Optimization for Multi-Core Architectures. Berlin, Germany. 22 January 2013Stream programming is a promising approach to execute programs on parallel hardware such as multi-core systems. It allows to reuse sequential code at component level and to extend such code with concurrency-handling at the communication level. In this paper we investigate in the performance of stream programs in terms of throughput and latency. We identify factors that affect these performance metrics and propose an efficient scheduling approach to obtain the maximal performance

The epidemiology of trichinellosis in northern Vietnam

Trichinellosis is a meat-borne zoonotic disease caused by nematodes of the genus Trichinella. Typically, it is acquired by eating undercooked meat from pigs that are raised in non-controlled management conditions or from wildlife. The parasite is transmitted both in the domestic and sylvatic lifecycles. In the last decade, several outbreaks of trichinellosis have been observed in Northern Vietnam, where the disease was previously practically unknown. In chapter 1 a general review of the literature is given on Trichinella spp and trichinellosis, with special focus on the epidemiology, the diagnosis and the situation in SE Asia, particularly in Vietnam. This chapter is followed by the objectives of the thesis that introduce the research chapters. The 2nd chapter describes data on trichinellosis in domestic animals. In the 1st part the seroprevalence of anti-Trichinella IgG was measured in free-roaming pigs in Son La province of NW Vietnam where an outbreak of trichinellosis occurred in 2008. Of the 1035 pigs from which serum samples were collected, 206 (19.9%) were positive in ELISA. In Muscle samples from serologically positive pigs were tested by artificial digestion. Trichinella larvae were detected in 14.5% of them and identified by multiplex PCR as T. spiralis. In the 2nd part, the seroprevalence of Trichinella infection was determined in 558 pigs, 125 dogs and 98 cats in two provinces of NW Vietnam. The overall seroprevalence was 5.6%, 4% and 0% in pigs, dogs and cats, respectively. In pigs, positive cases were distributed in 8/20 districts of the two provinces. The results indicate that pigs and dogs act as a reservoir and play an important role in the maintenance of the domestic cycle of T. spiralis in NW Vietnam. In the 3rd chapter the occurrence of trichinellosis in wild boars and synanthropic rats was studied in NW Vietnam. The results showed prevalences of T. spiralis of 3.2% and 2,8% in hunted wild boars and rats, respectively. Trichinella-infected rats were found in 7 of the 20 districts of Dien Bien and Son La provinces. These results indicate that the local population and health centers should be made aware of the risks of eating raw or undercooked meat dishes prepared from wild animals. The 4th chapter describes studies on human trichinellosis. In the 1st part an outbreak of trichinellosis in Thanh Hoa province is described (2012), involving 24 patients who consumed raw meat from a wild boar. Six of these patients were treated in hospitals in Hanoi. ELISA and muscle biopsies were positive in all six patients. Trichinella sp. larvae were identified as T. spiralis by molecular analysis of the cox3 gene. In the 2nd part a post-outbreak cross-sectional study in the same community was described. A total of 100 inhabitants were identified with suspected trichinellosis, of which, 30% had antibodies to Trichinella. Serologically confirmed cases had fever, myalgia, facial oedema, diarrhoea, and/or pain of the masseter muscles. Clinical symptoms resolved in all patients after albendazole treatment. The results suggest that only a proportion of the trichinellosis cases had sought health care during the outbreak. In the 3rd part the presence of anti-Trichinella IgG in the serum of persons from ethnic minorities from NW Vietnam with clinical signs and symptoms that are compatible with trichinellosis was assessed. A total of 645 persons were enrolled, of which 200 lived in two villages where previously outbreaks of human trichinellosis had occurred, and 445 people who were hospitalized in the provincial hospitals without a definitive diagnosis. Seven (3.5%) persons from the villages and seven (1.6%) hospitalized patients, tested positive by both ELISA and Western Blot. The concomitant occurrence of facial edema and myalgia among the enrolled persons from the villages, accounted for 75% of the positive predictive value (PPV) and 99.5% of the negative predictive value (NPV), suggesting that they could be used for suspecting trichinellosis when serology is not available. In the 5th chapter we discuss the findings of our research in the context of the emergence of trichinellosis in Northern Vietnam. The high prevalence (1.6–3.5%) of anti-Trichinella IgG in persons from Northern Vietnamese provinces where T. spiralis is circulating in pigs and wildlife strongly supports the need to develop control programs to eliminate the infection from pigs and for consumers’ education and protection. There is a need to implement surveillance and better diagnosis for trichinellosis in humans and of Trichinella infections in slaughter animals and wildlife and to set up educational programs to prevent infection in Northern Vietnam

Monitoring framework for stream-processing networks

Vu Thien Nga Nguyen, Raimund Kirner, and Frank Penczek, 'Monitoring framework for stream-processing networks'. Paper presented at the Workshop on Feedback-Directed Compiler Optimization for Multi-Core Architectures (FD-COMA 2012), Berlin, Germany. 21-23 January 2013.In this paper we present a monitoring framework that exploits special characteristics of stream-processing networks in order to reason the performance. The novelty of the framework is to trace the non-deterministic execution which is reflected in i) the dynamic mapping and scheduling of network components at the operating system level and ii) the dynamic message routing across the network at runtime. We evaluate the efficiency with an implementation for the coordination language S-Net, showing negligible overhead in most cases

Population genomics of the giant black tiger shrimp Penaeus monodon to understand wild fishery and aquaculture production

Nga Vu investigated the genetic structure of black tiger shrimp within the Indo-Pacific using genome-wide markers. She found evidence for the existence of genetic adaptation within and among populations as a consequence of geographic distance and/or environmental conditions. Her research will be used by the aquaculture industry to identify populations to use as foundation animals for genetic improvement programs

The Humoral Response against <i>Salmonella</i> Typhi Protein Antigens During Acute, Convalescent, and Chronic Typhoid Fever

Enteric (typhoid) fever is a life-threatening disease caused by the Salmonella enterica subspecies enterica serovars Typhi (S. Typhi) and Paratyphi A, B, and C (S. Paratyphi A, B, and C). The disease still causes major public health problems in low- and middle-income countries, principally in Asia and Africa. The increasing frequency of multi-drug resistant (MDR) and extended-drug resistant isolates (XDR) of S. Typhi and an increasing incidence of S. Paratyphi A mean that the international dynamics of enteric fever are changing. These changes add urgency to the demand for more efficient enteric fever control campaigns. The aim of this thesis was to assess control measures for enteric fever in Vietnam and to develop techniques that can be used as further control methods. I firstly systemically reviewed retrospective information regarding enteric fever in Vietnam and combined these data with data on economic development. This investigation revealed that national economic growth, the provision of improved quality drinking water, and better sanitation were likely the greatest contributors to the decline and ultimate elimination of enteric fever in Vietnam. My work then evaluated the serodiagnostic potential of a panel of novel S. Typhi protein antigens and the Vi capsular polysaccharide (Vi) in a group of patients with febrile diseases in Bangladesh. These data demonstrated the utility of serology for typhoid diagnostics when exploiting a combination of Vi and at least one protein antigen. I then assessed the acquisition of antibody against typhoid toxin during natural S. Typhi and S. Paratyphi A infections and measured the capability of these antibodies to neutralise the toxin. The data provided supporting evidence for generating an antitoxin treatment for enteric fever (caused by both S. Typhi and S. Paratyphi A), and potentially encourages the use of typhoid toxin in vaccine formulations. Within the scope of searching for vaccine novel candidates, my work further identified a panel of immunogenic antigens shared between S. Typhi and S. Paratyphi A that can stimulate an antibody response which can instigate bactericidal killing during natural infection. Finally, by exploiting the unique immunological profiles of S. Typhi carriers (cytokines and antibody), I developed a method of identifying S. Typhi carriers and estimating the prevalence of S. Typhi carriage in a typhoid endemic population. My findings will potentially lead to the development of novel enteric fever control strategies. I conclude that improved case detection and widespread vaccination campaigns using polyvalent Salmonella vaccines should be initiated for reducing the burden of enteric fever in endemic areas

LMI based antiswing adaptive controller for uncertain overhead cranes

This paper proposes an adaptive anti-sway controller for uncertain overhead cranes. The state-space model of the 2D overhead crane with the system parameter uncertainties is shown firstly. Next, the adaptive controller which can adapt with the system uncertainties and input disturbances is established. The proposed controller has ability to move the trolley to the destination in short time and with small oscillation of the load despite the effect of the uncertainties and disturbances. Moreover, the controller has simple structure so it is easy to execute. Also, the stability of the closed-loop system is analytically proven. The proposed algorithm is verified by using Matlab/Simulink simulation tool. The simulation results show that the presented controller gives better performances (i.e., fast transient response, position tracking, and low swing angle) than the state feedback controller when there exist system parameter variations as well as input disturbances

An Efficient Execution Model for Reactive Stream Programs

Stream programming is a paradigm where a program is structured by a set of computational nodes connected by streams. Focusing on data moving between computational nodes via streams, this programming model fits well for applications that process long sequences of data. We call such applications reactive stream programs (RSPs) to distinguish them from stream programs with rather small and finite input data. In stream programming, concurrency is expressed implicitly via communication streams. This helps to reduce the complexity of parallel programming. For this reason, stream programming has gained popularity as a programming model for parallel platforms. However, it is also challenging to analyse and improve the performance without an understanding of the program's internal behaviour. This thesis targets an effi cient execution model for deploying RSPs on parallel platforms. This execution model includes a monitoring framework to understand the internal behaviour of RSPs, scheduling strategies for RSPs on uniform shared-memory platforms; and mapping techniques for deploying RSPs on heterogeneous distributed platforms. The foundation of the execution model is based on a study of the performance of RSPs in terms of throughput and latency. This study includes quantitative formulae for throughput and latency; and the identification of factors that influence these performance metrics. Based on the study of RSP performance, this thesis exploits characteristics of RSPs to derive effective scheduling strategies on uniform shared-memory platforms. Aiming to optimise both throughput and latency, these scheduling strategies are implemented in two heuristic-based schedulers. Both of them are designed to be centralised to provide load balancing for RSPs with dynamic behaviour as well as dynamic structures. The first one uses the notion of positive and negative data demands on each stream to determine the scheduling priorities. This scheduler is independent from the runtime system. The second one requires the runtime system to provide the position information for each computational node in the RSP; and uses that to decide the scheduling priorities. Our experiments show that both schedulers provides similar performance while being significantly better than a reference implementation without dynamic load balancing. Also based on the study of RSP performance, we present in this thesis two new heuristic partitioning algorithms which are used to map RSPs onto heterogeneous distributed platforms. These are Kernighan-Lin Adaptation (KLA) and Congestion Avoidance (CA), where the main objective is to optimise the throughput. This is a multi-parameter optimisation problem where existing graph partitioning algorithms are not applicable. Compared to the generic meta-heuristic Simulated Annealing algorithm, both proposed algorithms achieve equally good or better results. KLA is faster for small benchmarks while slower for large ones. In contrast, CA is always orders of magnitudes faster even for very large benchmarks

Throughput-driven Partitioning of Stream Programs on Heterogeneous Distributed Systems

This is an Open Access article. © 2015 IEEE. Translations and content mining are permitted for academic research only. Personal use is also permitted, but republication/redistribution requires IEEE permission. See http://www.ieee.org/publications_standards/publications/rights/index.html for more information.Graph partitioning is an important problem in computer science and is of NP-hard complexity. In practice it is usually solved using heuristics. In this article we introduce the use of graph partitioning to partition the workload of stream programs to optimise the throughput on heterogeneous distributed platforms. Existing graph partitioning heuristics are not adequate for this problem domain. In this article we present two new heuristics to capture the problem space of graph partitioning for stream programs to optimise throughput. The first algorithm is an adaptation of the well-known Kernighan-Lin algorithm, called KL-Adapted (KLA), which is relatively slow. As a second algorithm we have developed the Congestion Avoidance (CA) partitioning algorithm, which performs reconfiguration moves optimised to our problem type. We compare both KLA and CA with the generic meta-heuristic Simulated Annealing (SA). All three methods achieve similar throughput results for most cases, but with significant differences in calculation time. For small graphs KLA is faster than SA, but KLA is slower for larger graphs. CA on the other hand is always orders of magnitudes faster than both KLA and SA, even for large graphs. This makes CA potentially useful for re-partitioning of systems during runtime.Peer reviewedFinal Published versio

A Power-Aware Framework for Executing Streaming Programs on Networks-on-Chip

Nilesh Karavadara, Simon Folie, Michael Zolda, Vu Thien Nga Nguyen, Raimund Kirner, 'A Power-Aware Framework for Executing Streaming Programs on Networks-on-Chip'. Paper presented at the Int'l Workshop on Performance, Power and Predictability of Many-Core Embedded Systems (3PMCES'14), Dresden, Germany, 24-28 March 2014.Software developers are discovering that practices which have successfully served single-core platforms for decades do no longer work for multi-cores. Stream processing is a parallel execution model that is well-suited for architectures with multiple computational elements that are connected by a network. We propose a power-aware streaming execution layer for network-on-chip architectures that addresses the energy constraints of embedded devices. Our proof-of-concept implementation targets the Intel SCC processor, which connects 48 cores via a network-on- chip. We motivate our design decisions and describe the status of our implementation

Trichinellosis in Vietnam

Trichinellosis is a zoonotic parasitic disease with a worldwide distribution. The aim of this work was to describe the epidemiological and clinical data of five outbreaks of trichinellosis, which affected ethnic minorities living in remote mountainous areas of northwestern Vietnam from 1970 to 2012. Trichinellosis was diagnosed in 126 patients, of which 11 (8.7%) were hospitalized and 8 (6.3%) died. All infected people had consumed raw pork from backyard and roaming pigs or wild boar at wedding, funeral, or New Year parties. The short incubation period (average of 9.5 days), the severity of the symptoms, which were characterized by diarrhea, abdominal pain, fever, myalgia, edema, weight loss, itch, and lisping, and the high mortality, suggest that patients had ingested a high number of larvae. The larval burden in pigs examined in one of the outbreaks ranged from 70 to 879 larvae/g. These larvae and those collected from a muscle biopsy taken from a patient from the 2012 outbreak were identified as Trichinella spiralis. Data presented in this work show that the northern regions of Vietnam are endemic areas for Trichinella infections in domestic pigs and humans