Analysis and optimization of task granularity on the Java virtual machine

Task granularity, i.e., the amount of work performed by parallel tasks, is a key performance attribute of parallel applications. On the one hand, fine-grained tasks (i.e., small tasks carrying out few computations) may introduce considerable parallelization overheads. On the other hand, coarse-grained tasks (i.e., large tasks performing substantial computations) may not fully utilize the available CPU cores, leading to missed parallelization opportunities. We focus on task-parallel applications running in a single Java Virtual Machine on a shared- memory multicore. Despite their performance may considerably depend on the granularity of their tasks, this topic has received little attention in the literature. Our work fills this gap, analyzing and optimizing the task granularity of such applications. In this dissertation, we present a new methodology to accurately and efficiently collect the granularity of each executed task, implemented in a novel profiler. Our profiler collects carefully selected metrics from the whole system stack with low overhead. Our tool helps developers locate performance and scalability problems, and identifies classes and methods where optimizations related to task granularity are needed, guiding developers towards useful optimizations. Moreover, we introduce a novel technique to drastically reduce the overhead of task-granularity profiling, by reifying the class hierarchy of the target application within a separate instrumentation process. Our approach allows the instrumentation process to instrument only the classes representing tasks, inserting more efficient instrumentation code which decreases the overhead of task detection. Our technique significantly speeds up task-granularity profiling and so enables the collection of accurate metrics with low overhead.We use our novel techniques to analyze task granularity in the DaCapo, ScalaBench, and Spark Perf benchmark suites. We reveal inefficiencies related to fine-grained and coarse-grained tasks in several workloads. We demonstrate that the collected task-granularity profiles are actionable by optimizing task granularity in numerous benchmarks, performing optimizations in classes and methods indicated by our tool. Our optimizations result in significant speedups (up to a factor of 5.90x) in numerous workloads suffering from fine- and coarse-grained tasks in different environments. Our results highlight the importance of analyzing and optimizing task granularity on the Java Virtual Machine

Evaluation of Bacillus thuringiensis subsp. Israelensis and Bacillus sphaericus combination against Culex pipiens in highly vegetated ditches

9openInternationalItalian coauthor/editorAmong the few mosquito larvicides available in the market, Bacillus thuringiensis subsp. israelensis (Bti) and B. sphaericus (Bs) represent the most environmentally safe alternatives. The combination of the 2 products is known to overcome their specific limitations by producing a synergistic effect. The aim of the study was to assess the effect and persistence of a single treatment with a granular Bti + Bs formulation on highly vegetated ditches in northeastern Italy that represents the primary rural larval sites for Culex pipiens, the primary vector of the West Nile virus in Europe. The analysis takes into account the nonlinear temporal effects on the population dynamics of larvae and pupae. The results showed a dramatic reduction in mosquito larval abundance 24 h posttreatment (93%) and was effective against larvae up to 22 days (100%). The residual effect after 28 days was 99.5%, and a limited residual effect was observed after 39 days (31.2%). A reduction in pupal density was observed after 4 days (70%) and was >98% from days 14 to 28 posttreatment, persisting for up to 39 days (84% after 39 days). The results demonstrate the effective use of the Bti + Bs formulation against Cx. pipiens in vegetated ditches in rural areas. Our modeling framework provides a flexible statistical approach to predict the residual effect of the product over time, in order to plan a seasonal intervention scheme.openVirgillito, Chiara; Manica, Mattia; Marini, Giovanni; Rosà, Roberto; Della Torre, Alessandra; Martini, Simone; Drago, Andrea; Baseggio, Alberto; Caputo, BeniaminoVirgillito, C.; Manica, M.; Marini, G.; Rosà, R.; Della Torre, A.; Martini, S.; Drago, A.; Baseggio, A.; Caputo, B

West Nile Virus lineage 1 in Italy: newly introduced or a re-occurrence of a previously circulating strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008–2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory activ

West Nile Virus lineage 2 overwintering in Italy

In January 2022, West Nile virus (WNV) lineage 2 (L2) was detected in an adult female goshawk rescued near Perugia in the region of Umbria (Italy). The animal showed neurological symptoms and died 15 days after its recovery in a wildlife rescue center. This was the second case of WNV infection recorded in birds in the Umbria region during the cold season, when mosquitoes, the main WNV vectors, are usually not active. According to the National Surveillance Plan, the Umbria region is included amongst the WNV low-risk areas. The necropsy evidenced generalized pallor of the mucous membranes, mild splenomegaly, and cerebral edema. WNV L2 was detected in the brain, heart, kidney, and spleen homogenate using specific RT-PCR. Subsequently, the extracted viral RNA was sequenced. A Bayesian phylogenetic analysis performed through a maximum-likelihood tree showed that the genome sequence clustered with the Italian strains within the European WNV strains among the central-southern European WNV L2 clade. These results, on the one hand, confirmed that the WNV L2 strains circulating in Italy are genetically stable and, on the other hand, evidenced a continuous WNV circulation in Italy throughout the year. In this report case, a bird-to-bird WNV transmission was suggested to support the virus overwintering. The potential transmission through the oral route in a predatory bird may explain the relatively rapid spread of WNV, as well as other flaviviruses characterized by similar transmission patterns. However, rodent-to-bird transmission or mosquito-to-bird transmission cannot be excluded, and further research is needed to better understand WNV transmission routes during the winter season in Ital

FJProf: profiling fork/join applications on the Java virtual machine

An efficient fork/join application should maximize parallelism while minimizing overheads, and maximize locality while minimizing contention. However, there is no unique optimal implementation that best resolves such tradeoffs and failing in balancing them may lead to fork/join applications suffering from several issues (e.g., suboptimal forking, load imbalance, excessive synchronization), possibly compromising the performance gained by a task-parallel execution. Moreover, there is a lack of profilers enabling performance analysis of a fork/join application. As a result, developers are often required to implement their own tools for monitoring and collecting information and metrics on fork/join applications, which could be time-consuming, error-prone, and is often beyond the expertise of the developer. In this paper, we present FJProf, a novel profiler which accurately collects dynamic information and key metrics to facilitate characterizing several performance attributes specific to a fork/join application running on a single Java Virtual Machine (JVM) in a shared-memory multicore. FJProf reports information and graphics to developers that help them understand the details of the fork/join processing exposed by a parallel application running on the JVM. We show how FJProf supports performance analysis by characterizing a fork/join application from the Renaissance benchmark suite

Managing chamois (<em>Rupicapra rupicapra</em>) populations: a model with macroparasites infection and host dynamics

<strong>Abstract</strong> The following paper contains a mathematical model for the analysis of temporal variations of a chamois (<em>Rupicapra rupicapra</em> L.)-Trichostrongylidae free-living system in the Brenta area (Trentino, Italy) under different harvesting regimes. The numerical values of the parameters of the model were obtained through the analysis of population counts and the parasitological surveys obtained during a four year study. Different harvesting regimes could affect differently the dynamics both of the host population and its parasites. Simple demographic analysis seems to suggest that the culling of older individuals is appropriate. However, if we insert a parameter into the system which considers immunity to parasitic infection then the culling of younger individuals becomes more appropriate for the maintenance of health and population size

Exclusion and spatial segregation in the apparent competition between two hosts sharing macroparasites

42013 MANM 1reservedInternationalIn this paper we investigate the spatial dynamics of a deterministic model describing two host species that partially share a common spatial domain, experiencing apparent competition mediated by macroparasites. The aim of this work is to understand the mechanisms underlying apparent competition processes in a spatially structured environment, which have been generally overlooked up to now. First, we analyse the behaviour of a single-host macroparasite partial differential equation (PDE) model, both in the cases of uniform or spatially-dependent vital rates of the host, focusing on the role of spatial diffusion on parasite persistence and host abundance. We obtained the threshold condition for parasite persistence, and (in contrast to what occurs in reaction–diffusion models for an isolated population) we found that, in the case of spatially-dependent vital rates, increasing the host diffusion coefficient results in an increase of the overall host population. Then, a PDE model featuring spatial diffusion and apparent competition mediated via shared macroparasites between two species is analysed in order to understand the role of spatial heterogeneity in host coexistence. We assumed a partial overlap among the habitats of the two species and found that the shared parasites could cause, depending on the values of the diffusion coefficients and differences in induced mortality among host species, a decrease of the realized habitat and, eventually, the extinction of the species less tolerant to parasite infection. This shows that the presence of regulating parasites complicates the effect of dispersal on population dynamics and that the dynamics of apparent competition cannot be adequately understood from spatially-independent models.restrictedManica, M.; Rosà, R.; Pugliese, A.; Bolzoni, L.Manica, M.; Rosa', R.; Pugliese, A.; Bolzoni, L