Nested parallelism for multi-core HPC systems using Java

Since its introduction in 1993, the Message Passing Interface (MPI) has become a de facto standard for writing High Performance Computing (HPC) applications on clusters and Massively Parallel Processors (MPPs). The recent emergence of multi-core processor systems presents a new challenge for established parallel programming paradigms, including those based on MPI. This paper presents a new Java messaging system called MPJ Express. Using this system, we exploit multiple levels of parallelism - messaging and threading - to improve application performance on multi-core processors. We refer to our approach as nested parallelism. This MPI-like Java library can support nested parallelism by using Java or Java OpenMP (JOMP) threads within an MPJ Express process. Practicality of this approach is assessed by porting to Java a massively parallel structure formation code from Cosmology called Gadget-2. We introduce nested parallelism in the Java version of the simulation code and report good speed-ups. To the best of our knowledge it is the first time this kind of hybrid parallelism is demonstrated in a high performance Java application. (C) 2009 Elsevier Inc. All rights reserved.

Exploiting Nested Parallelism on Heterogeneous Processors

Heterogeneous computing systems have become common in modern processor architectures. These systems, such as those released by AMD, Intel, and Nvidia, include both CPU and GPU cores on a single die available with reduced communication overhead compared to their discrete predecessors. Currently, discrete CPU/GPU systems are limited, requiring larger, regular, highly-parallel workloads to overcome the communication costs of the system. Without the traditional communication delay assumed between GPUs and CPUs, we believe non-traditional workloads could be targeted for GPU execution. Specifically, this thesis focuses on the execution model of nested parallel workloads on heterogeneous systems. We have designed a simulation flow which utilizes widely used CPU and GPU simulators to model heterogeneous computing architectures. We then applied this simulator to non-traditional GPU workloads using different execution models. We also have proposed a new execution model for nested parallelism allowing users to exploit these heterogeneous systems to reduce execution time.

Human Herpesvirus Infections Of The Central Nervous System: Laboratory Diagnosis Based On Dna Detection By Nested Pcr In Plasma And Cerebrospinal Fluid Samples.

Infections of the central nervous systems (CNS) present a diagnostic problem for which an accurate laboratory diagnosis is essential. Invasive practices, such as cerebral biopsy, have been replaced by obtaining a polymerase chain reaction (PCR) diagnosis using cerebral spinal fluid (CSF) as a reference method. Tests on DNA extracted from plasma are noninvasive, thus avoiding all of the collateral effects and patient risks associated with CSF collection. This study aimed to determine whether plasma can replace CSF in nested PCR analysis for the detection of CNS human herpesvirus (HHV) diseases by analysing the proportion of patients whose CSF nested PCR results were positive for CNS HHV who also had the same organism identified by plasma nested PCR. In this study, CSF DNA was used as the gold standard, and nested PCR was performed on both types of samples. Fifty-two patients with symptoms of nervous system infection were submitted to CSF and blood collection. For the eight HHV, one positive DNA result-in plasma and/or CSF nested PCR-was considered an active HHV infection, whereas the occurrence of two or more HHVs in the same sample was considered a coinfection. HHV infections were positively detected in 27/52 (51.9%) of the CSF and in 32/52 (61.5%) of the plasma, difference not significant, thus nested PCR can be performed on plasma instead of CSF. In conclusion, this findings suggest that plasma as a useful material for the diagnosis of cases where there is any difficulty to perform a CSF puncture.

Rapid detection of bovine coronavirus by a semi-nested RT-PCR

Bovine coronavirus (BCoV) is a member of the group 2 of the Coronavirus (Nidovirales: Coronaviridae) and the causative agent of enteritis in both calves and adult bovine, as well as respiratory disease in calves. The present study aimed to develop a semi-nested RT-PCR for the detection of BCoV based on representative up-to-date sequences of the nucleocapsid gene, a conserved region of coronavirus genome. Three primers were designed, the first round with a 463bp and the second (semi-nested) with a 306bp predicted fragment. The analytical sensitivity was determined by 10-fold serial dilutions of the BCoV Kakegawa strain (HA titre: 256) in DEPC treated ultra-pure water, in fetal bovine serum (FBS) and in a BCoV-free fecal suspension, when positive results were found up to the 10-2, 10-3 and 10-7 dilutions, respectively, which suggests that the total amount of RNA in the sample influence the precipitation of pellets by the method of extraction used. When fecal samples was used, a large quantity of total RNA serves as carrier of BCoV RNA, demonstrating a high analytical sensitivity and lack of possible substances inhibiting the PCR. The final semi-nested RT-PCR protocol was applied to 25 fecal samples from adult cows, previously tested by a nested RT-PCR RdRp used as a reference test, resulting in 20 and 17 positives for the first and second tests, respectively, and a substantial agreement was found by kappa statistics (0.694). The high sensitivity and specificity of the new proposed method and the fact that primers were designed based on current BCoV sequences give basis to a more accurate diagnosis of BCoV-caused diseases, as well as to further insights on protocols for the detection of other Coronavirus representatives of both Animal and Public Health importance.

Dual candidemia detected by nested polymerase chain reaction in two critically ill children

The use of improved microbiological procedures associated with molecular techniques has increased the identification of Candida bloodstream infections, even if the isolation of more than one species by culture methods remains uncommon. We report the cases of two children presenting with severe gastrointestinal disorders and other risk factors that contribute to Candida infections. In the first patient, C. albicans DNA was initially detected by a nested-amplification and C. tropicalis was found later during hospitalization, while blood cultures were persistently negative. In the second child, there was amplification of C. albicans and C. glabrata DNA in the same samples, but blood cultures yielded only C. albicans. Both patients received antifungal therapy but had unfavorable outcomes. These two cases illustrate that PCR was more successful than culture methods in detecting Candida in the bloodstream of high risk children, and was also able to detect the presence of more than one species in the same patient that might impact therapy when the fungi are resistant to azole compounds.

Multiplex semi-nested RT-PCR with exogenous internal control for simultaneous detection of bovine coronavirus and group A rotavirus

Neonatal calf diarrhea is a multi-etiology syndrome of cattle and direct detection of the two major agents of the syndrome, group A rotavirus and Bovine coronavirus (BCoV) is hampered by their fastidious growth in cell culture. This study aimed at developing a multiplex semi-nested RT-PCR for simultaneous detection of BCoV (N gene) and group A rotavirus (VP1 gene) with the addition of an internal control (mRNA ND5). The assay was tested in 75 bovine feces samples tested previously for rotavirus using PAGE and for BCoV using nested RT-PCR targeted to RdRp gene. Agreement with reference tests was optimal for BCoV (kappa = 0.833) and substantial for rotavirus detection (kappa = 0.648). the internal control, ND5 mRNA, was detected successfully in all reactions. Results demonstrated that this multiplex semi-nested RT-PCR was effective in the detection of BCoV and rotavirus, with high sensitivity and specificity for simultaneous detection of both viruses at a lower cost, providing an important tool for studies on the etiology of diarrhea in cattle. (C) 2010 Elsevier B.V. All rights reserved.

Development and validation of nested-PCR for the diagnosis of clinical and subclinical infectious laryngotracheitis

A standardised nested-PCR method that amplifies a region of the glycoprotein E gene of avian infectious laryngotracheitis virus (ILTV) has been developed for the diagnosis of infection by Gallid herpesvirus 1. The two sets of primers employed produced the expected ampIification products of 524bp(externa I primers) and 219bp (internal primers) in the presence of ILTV DNA, whereas no Such amplicons were obtained with other avian respiratory pathogens or with DNA extracted from the cells of uninfected chickens. The identity of the 219bp amplified product was con firmed by DNA sequencing. The standardised nested-PCR method detected ILTV DNA from trachea, lung, conjunctiva and trigeminal ganglia samples from flocks of birds with and without clinical signs. and showed hi.-h sensitivity (95.4%) and specificity (93.1%) when compared with the reference test involving virus isolation in specific-pathogen-free chicken embryos. The standardised nested-PCR method described may be used to detect clinical and latent ILTV infections, and will be of significant value for both diagnostic and epidemiological Studies. (c) 2008 Elsevier B.V. All rights reserved.

Influence of root parallelism on the stability of extraction-site closures

Introduction: In premolar extraction cases, root parallelism is recommended to preserve the stability of space closures. The influence of the degree of root parallelism on relapse of tooth extraction spaces has been a controversial topic in the literature. The aim of this study was to compare the angle between the long axes of the canine and the second premolarin patients with and without stability of extraction-space closures. Methods: A sample of 56 patients, treated with 4 premolar extractions, was divided into 2 groups: group 1, consisting of 25 patients with reopening of extraction spaces; and group 2, consisting of 31 patients without reopening of extraction spaces. Panoramic radiographs of each patient were analyzed at the posttreatment and 1-year posttreatment stages. The data were statistically analyzed by using chi-square tests, t tests, analysis of variance (ANOVA), and Pearson correlation coefficients. Results: The results showed that the groups did not differ regarding the angle between the canine and the second premolar, and there was no correlation between angular changes and reopening of extraction spaces, showing that dental angular changes are not determining factors for relapse, and other factors should be investigated. Conclusions: The final angle and the posttreatment changes observed in the angle between the long axes of the canine and the second premolar showed no influence on the relapse of extraction spaces. (Am J Orthod Dentofacial Orthop 2011; 139: e505-e510)

Supporting intra-task parallelism in real-time multiprocessor systems

Os sistemas de tempo real modernos geram, cada vez mais, cargas computacionais pesadas e dinâmicas, começando-se a tornar pouco expectável que sejam implementados em sistemas uniprocessador. Na verdade, a mudança de sistemas com um único processador para sistemas multi- processador pode ser vista, tanto no domínio geral, como no de sistemas embebidos, como uma forma eficiente, em termos energéticos, de melhorar a performance das aplicações. Simultaneamente, a proliferação das plataformas multi-processador transformaram a programação paralela num tópico de elevado interesse, levando o paralelismo dinâmico a ganhar rapidamente popularidade como um modelo de programação. A ideia, por detrás deste modelo, é encorajar os programadores a exporem todas as oportunidades de paralelismo através da simples indicação de potenciais regiões paralelas dentro das aplicações. Todas estas anotações são encaradas pelo sistema unicamente como sugestões, podendo estas serem ignoradas e substituídas, por construtores sequenciais equivalentes, pela própria linguagem. Assim, o modo como a computação é na realidade subdividida, e mapeada nos vários processadores, é da responsabilidade do compilador e do sistema computacional subjacente. Ao retirar este fardo do programador, a complexidade da programação é consideravelmente reduzida, o que normalmente se traduz num aumento de produtividade. Todavia, se o mecanismo de escalonamento subjacente não for simples e rápido, de modo a manter o overhead geral em níveis reduzidos, os benefícios da geração de um paralelismo com uma granularidade tão fina serão meramente hipotéticos. Nesta perspetiva de escalonamento, os algoritmos que empregam uma política de workstealing são cada vez mais populares, com uma eficiência comprovada em termos de tempo, espaço e necessidades de comunicação. Contudo, estes algoritmos não contemplam restrições temporais, nem outra qualquer forma de atribuição de prioridades às tarefas, o que impossibilita que sejam diretamente aplicados a sistemas de tempo real. Além disso, são tradicionalmente implementados no runtime da linguagem, criando assim um sistema de escalonamento com dois níveis, onde a previsibilidade, essencial a um sistema de tempo real, não pode ser assegurada. Nesta tese, é descrita a forma como a abordagem de work-stealing pode ser resenhada para cumprir os requisitos de tempo real, mantendo, ao mesmo tempo, os seus princípios fundamentais que tão bons resultados têm demonstrado. Muito resumidamente, a única fila de gestão de processos convencional (deque) é substituída por uma fila de deques, ordenada de forma crescente por prioridade das tarefas. De seguida, aplicamos por cima o conhecido algoritmo de escalonamento dinâmico G-EDF, misturamos as regras de ambos, e assim nasce a nossa proposta: o algoritmo de escalonamento RTWS. Tirando partido da modularidade oferecida pelo escalonador do Linux, o RTWS é adicionado como uma nova classe de escalonamento, de forma a avaliar na prática se o algoritmo proposto é viável, ou seja, se garante a eficiência e escalonabilidade desejadas. Modificar o núcleo do Linux é uma tarefa complicada, devido à complexidade das suas funções internas e às fortes interdependências entre os vários subsistemas. Não obstante, um dos objetivos desta tese era ter a certeza que o RTWS é mais do que um conceito interessante. Assim, uma parte significativa deste documento é dedicada à discussão sobre a implementação do RTWS e à exposição de situações problemáticas, muitas delas não consideradas em teoria, como é o caso do desfasamento entre vários mecanismo de sincronização. Os resultados experimentais mostram que o RTWS, em comparação com outro trabalho prático de escalonamento dinâmico de tarefas com restrições temporais, reduz significativamente o overhead de escalonamento através de um controlo de migrações, e mudanças de contexto, eficiente e escalável (pelo menos até 8 CPUs), ao mesmo tempo que alcança um bom balanceamento dinâmico da carga do sistema, até mesmo de uma forma não custosa. Contudo, durante a avaliação realizada foi detetada uma falha na implementação do RTWS, pela forma como facilmente desiste de roubar trabalho, o que origina períodos de inatividade, no CPU em questão, quando a utilização geral do sistema é baixa. Embora o trabalho realizado se tenha focado em manter o custo de escalonamento baixo e em alcançar boa localidade dos dados, a escalonabilidade do sistema nunca foi negligenciada. Na verdade, o algoritmo de escalonamento proposto provou ser bastante robusto, não falhando qualquer meta temporal nas experiências realizadas. Portanto, podemos afirmar que alguma inversão de prioridades, causada pela sub-política de roubo BAS, não compromete os objetivos de escalonabilidade, e até ajuda a reduzir a contenção nas estruturas de dados. Mesmo assim, o RTWS também suporta uma sub-política de roubo determinística: PAS. A avaliação experimental, porém, não ajudou a ter uma noção clara do impacto de uma e de outra. No entanto, de uma maneira geral, podemos concluir que o RTWS é uma solução promissora para um escalonamento eficiente de tarefas paralelas com restrições temporais.

Supporting parallelism in server-based multiprocessor systems

Developing an efficient server-based real-time scheduling solution that supports dynamic task-level parallelism is now relevant to even the desktop and embedded domains and no longer only to the high performance computing market niche. This paper proposes a novel approach that combines the constantbandwidth server abstraction with a work-stealing load balancing scheme which, while ensuring isolation among tasks, enables a task to be executed on more than one processor at a given time instant.

Algebraic structure for the crossing of balanced and stair nested designs

Stair nesting allows us to work with fewer observations than the most usual form of nesting, the balanced nesting. In the case of stair nesting the amount of information for the different factors is more evenly distributed. This new design leads to greater economy, because we can work with fewer observations. In this work we present the algebraic structure of the cross of balanced nested and stair nested designs, using binary operations on commutative Jordan algebras. This new cross requires fewer observations than the usual cross balanced nested designs and it is easy to carry out inference.

Crossing balanced and stair nested desings

Balanced nesting is the most usual form of nesting and originates, when used singly or with crossing of such sub-models, orthogonal models. In balanced nesting we are forced to divide repeatedly the plots and we have few degrees of freedom for the first levels. If we apply stair nesting we will have plots all of the same size rendering the designs easier to apply. The stair nested designs are a valid alternative for the balanced nested designs because we can work with fewer observations, the amount of information for the different factors is more evenly distributed and we obtain good results. The inference for models with balanced nesting is already well studied. For models with stair nesting it is easy to carry out inference because it is very similar to that for balanced nesting. Furthermore stair nested designs being unbalanced have an orthogonal structure. Other alternative to the balanced nesting is the staggered nesting that is the most popular unbalanced nested design which also has the advantage of requiring fewer observations. However staggered nested designs are not orthogonal, unlike the stair nested designs. In this work we start with the algebraic structure of the balanced, the stair and the staggered nested designs and we finish with the structure of the cross between balanced and stair nested designs.

Diagnosis of hepatitis C virus in Brazilian blood donors using a reverse transcriptase nested polymerase chain reaction: comparison with enzyme immunoassay and recombinant protein immunoblot assay

Screening blood donations for anti-HCV antibodies and alanine aminotransferase (ALT) serum levels generally prevents the transmission of hepatitis C virus (HCV) by transfusion. The aim of the present study was to evaluate the efficiency of the enzyme immunoassay (EIA) screening policy in identifying potentially infectious blood donors capable to transmit hepatitis C through blood transfusion. We have used a reverse transcriptase (RT)-nested polymerase chain reaction (PCR) to investigate the presence of HCV-RNA in blood donors. The prevalence of HCV-RNA positive individuals was compared with the recombinant immunoblot assay (RIBA-2) results in order to assess the usefulness of both tests as confirmatory assays. Both tests results were also compared with the EIA-2 OD/C ratio (optical densities of the samples divided by the cut off value). ALT results were expressed as the ALT quotient (qALT), calculated dividing the ALT value of the samples by the maximum normal value (53UI/l) for the method. Donors (n=178) were divided into five groups according to their EIA anti-HCV status and qALT: group A (EIA > or = 3, ALT<1), group B (EIA > or = 3, ALT>1), group C (1<=EIA<3, ALT<1), group D (1<=EIA<3, ALT>1) and group E (EIA<=0.7). HCV sequences were detected by RT-nested PCR, using primers for the most conserved region of viral genome. RIBA-2 was applied to the same samples. In group A (n=6), all samples were positive by RT-nested PCR and RIBA-2. Among 124 samples in group B, 120 (96.8%) were RIBA-2 positive and 4 (3.2%) were RIBA-2 indeterminate but were seropositive for antigen c22.3. In group B, 109 (87.9%) of the RIBA-2 positive samples were also RT-nested PCR positive, as well as were all RIBA-2 indeterminate samples. In group C, all samples (n=9) were RT-nested PCR negative: 4 (44.4%) were also RIBA-2 negative, 4 (44.4%) were RIBA-2 positive and 1 (11.1%) was RIBA-2 indeterminate. HCV-RNA was detected by RT-nested PCR in 3 (37.5%) out of 8 samples in group D. Only one of them was also RIBA-2 positive, all the others were RIBA-2 indeterminate. All of the group E samples (controls) were RT- nested PCR and RIBA-2 negative. Our study suggests a strong relation between anti-HCV EIA-2 ratio > or = 3 and detectable HCV-RNA by RT-nested PCR. We have also noted that blood donors with RIBA-2 indeterminate presented a high degree of detectable HCV-RNA using RT-nested PCR (75%), especially when the c22.3 band was detected.

An Execution Model for Fine-Grained Parallelism in Ada

20th International Conference on Reliable Software Technologies - Ada-Europe 2015 (Ada-Europe 2015), 25 to 29, Jun, 2015. Madrid, Spain. Best Paper Award.