Optimizing iterative data-flow scientific applications using directed cyclic graphs

Data-flow programming models have become a popular choice for writing parallel applications as an alternative to traditional work-sharing parallelism. They are better suited to write applications with irregular parallelism that can present load imbalance. However, these programming models suffer from overheads related to task creation, scheduling and dependency management, limiting performance and scalability when tasks become too small. At the same time, many HPC applications implement iterative methods or multi-step simulations that create the same directed acyclic graphs of tasks on each iteration. By giving application programmers a way to express that a specific loop is creating the same task pattern on each iteration, we can create a single task directed acyclic graph (DAG) once and transform it into a cyclic graph. This cyclic graph is then reused for successive iterations, minimizing task creation and dependency management overhead. This paper presents the taskiter, a new construct we propose for the OmpSs-2 and OpenMP programming models, allowing the use of directed cyclic task graphs (DCTG) to minimize runtime overheads. Moreover, we present a simple immediate successor locality-aware heuristic that minimizes task scheduling overhead by bypassing the runtime task scheduler. We evaluate the implementation of the taskiter and the immediate successor heuristic in 8 iterative benchmarks. Using small task granularities, we obtain a geometric mean speedup of 2.56x over the reference OmpSs-2 implementation, and a 3.77x and 5.2x speedup over the LLVM and GCC OpenMP runtimes, respectively.This work was supported in part by the European Union’s Horizon 2020/EuroHPC Research and Innovation Programme (DEEP-SEA) under Grant 955606; in part by the Spanish State Research Agency—Ministry of Science and Innovation, Generalitat de Catalunya, under Project PCI2021121958 and Project 2021-SGR-01007; in part by the Spanish Ministry of Science and Technology under Contract PID2019-107255GB; and in part by Severo Ochoa under Grant CEX2021-001148-S/MCIN/AEI/10.13039/501100011033.Peer ReviewedPostprint (published version

Diisopropylamide and TMP turbo-grignard reagents : a structural rationale for their contrasting reactivities

A neutral dimeric molecule in crystal form, the diisopropylamido turbo-Grignard reagent "(iPr2N)MgCl⋅LiCl" (see structure; blue N, red O, green Mg, yellow Cl, black C) separates into several charged ate species in dynamic exchange with each other in THF solution as determined by a combination of EXSY and DOSY NMR studies

Improving nanos6 dependency subsystem

El model de programació OmpSs-2 amplia el model bàsic de dependències d'OpenMP amb característiques avançades com dependències weak i en regions de memòria no contigües. Aquestes característiques també funcionen a través de diferents nivells de parentesc entre tasques, proporcionant un mecanisme de sincronització general i de gra fi. En el cas general, aquesta funcionalitat avançada simplifica la tasca de paral·lelitzar programes complexos i en millora el rendiment. No obstant això, la implementació actual del sistema de dependències a la llibreria Nanos6 és complexa i per tant difícil d'optimitzar per a certs casos. En aquest treball es dissenya, desenvolupa i avalua una nova implementació alternativa del sistema de dependències, amb l'objectiu de proporcionar un subconjunt de les característiques actual però centrant-se en el rendiment i la simplicitat. Addicionalment, s'incorpora a la llibreria un mecanisme per canviar entre ambdues implementacions en temps d'execució.The OmpSs-2 programming model extends the basic dependency model of OpenMP with advanced features such as weak dependencies and dependencies over non-contiguous memory regions. These features also work across different task-nesting levels, providing a general and fine-grained synchronization mechanism. In general, these advanced features simplify the parallelization of complex applications and also improve performance. However, the current implementation of the data dependency subsystem in the Nanos6 runtime is complex and thus difficult to optimize for certain use cases. In this work, a new alternative implementation of the dependency subsystem aiming to provide a subset of the current features but focusing instead in performance and simplicity is designed, developed and evaluated. Additionally, a mechanism to switch between both implementations at execution time is also added to Nanos6

A SLAM-based augmented reality app for the assessment of spatial short-term memory using visual and auditory stimuli

A SLAM-based Augmented Reality (AR) app has been designed, developed, and validated to assess spatial short-term memory. Our app can be used with visual and auditory stimuli and can run on mobile devices. It can be used in any indoor environment. The anchors and data of the app are persistently stored in the cloud. As an authoring tool, the type of stimulus, its number, and specific positions in the real environment can be customized for each session. A study involving 48 participants was carried out to analyze the performance outcomes comparing the location and remembering of stimuli in a real environment using visual versus auditory stimuli. The number of objects placed correctly was similar for the two different stimuli used. However, the group that used the auditory stimulus spent significantly more time completing the task and required significantly more attempts. The performance outcomes were independent of age and gender. For the auditory stimuli, correlations among all of the variables of the AR app and the variables of two other tasks (object-recall and map-pointing) were found. We also found that the greater the number of correctly placed auditory stimuli, the greater the perceived competence and the less mental effort required. The greater the number of errors, the less the perceived competence. Finally, the auditory stimuli are valid stimuli that may benefit the assessment of the memorization of spatial-auditory associations, but the memorization of spatial-visual associations is dominant, as our results suggest

Advanced synchronization techniques for task-based runtime systems

Task-based programming models like OmpSs-2 and OpenMP provide a flexible data-flow execution model to exploit dynamic, irregular and nested parallelism. Providing an efficient implementation that scales well with small granularity tasks remains a challenge, and bottlenecks can manifest in several runtime components. In this paper, we analyze the limiting factors in the scalability of a task-based runtime system and propose individual solutions for each of the challenges, including a wait-free dependency system and a novel scalable scheduler design based on delegation. We evaluate how the optimizations impact the overall performance of the runtime, both individually and in combination. We also compare the resulting runtime against state of the art OpenMP implementations, showing equivalent or better performance, especially for fine-grained tasks.This project is supported by the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No.s 754304 (DEEP-EST), by the Spanish Ministry of Science and Innovation (contract PID2019-107255GB and TIN2015-65316P) and by the Generalitat de Catalunya (2017-SGR-1414).Peer ReviewedPostprint (author's final draft

Looking back to look forward: a timeline of the Fitzroy River catchment. Report to the Australian Department of Agriculture, Water and the Environment

Given proposed expansion of developments in northern Australia and current tensions among different interest groups, there is a need to develop new planning approaches that support multiple uses of land and water, while maintaining environmental and cultural values. Our project aimed to demonstrate how to operationalise multi-objective catchment planning supported by scenario thinking, by which stakeholders collaboratively build and assess the outcomes of alternative development futures. The project used participatory scenario planning to guide stakeholders through a systematic and critical examination of possible development trajectories and their associated environmental and socioeconomic outcomes. A multi-stakeholder group worked through a series of workshops to explore alternative development pathways and their outcomes. On July 10-11, NESP researchers led the first project workshop, gathering 40 people from 26 organisations across all main interest groups, including the federal Department of the Environment and Energy, state agencies, local governments, mining, agriculture and tourism organisations, environmental NGOs, and Aboriginal organisations representing the views and interests of Traditional Owners. The workshop involved a series of activities for team members to get to know each other, strengthen relationships, and build trust – all critical elements of participatory scenario planning. During the workshop, we discussed the meaning of development, driving forces of land use change, and development initiatives proposed for the region. An important goal of the first workshop was to create shared understandings of what is happening in the region that could shape the future development of the catchment. Therefore, before exploring the future, we looked back into the past. We created a timeline for the Fitzroy, identifying the events and forces that have shaped how the catchment looks today and could drive land use change in the future. Such events included social movements, policy changes, resource exploration, early irrigation projects, road improvements, and the proclamation of the Native Title Act that recognizes the rights and interests of Aboriginal and Torres Strait Islander peoples in land and waters according to their traditional laws and customs, among many others. This report summarises the process underpinning the creation of a timeline of the Fitzroy River catchment. For this timeline, the group identified the things that have changed the region and shaped the way things are today. Building this timeline helped participants to understand and share ideas about driving forces of land-use change. This activity opened up thinking on how local and external events and processes have shaped and will continue to change the region. The Story Map referred to in this report (Looking back to look forward: A timeline of the Fitzroy River catchment) was created based on the timeline. The online application combines text, images, and maps to describe a series of key events that have shaped the Fitzroy catchment

Lattice Green's function approach to the solution of the spectrum of an array of quantum dots and its linear conductance

In this paper we derive general relations for the band-structure of an array of quantum dots and compute its transport properties when connected to two perfect leads. The exact lattice Green's functions for the perfect array and with an attached adatom are derived. The expressions for the linear conductance for the perfect array as well as for the array with a defect are presented. The calculations are illustrated for a dot made of three atoms. The results derived here are also the starting point to include the effect of electron-electron and electron-phonon interactions on the transport properties of quantum dot arrays. Different derivations of the exact lattice Green's functions are discussed

A pilot randomised controlled trial of the Peer Tree digital intervention targeting loneliness in young people: a study protocol

Background Young people are vulnerable to experiencing problematic levels of loneliness which can lead to poor mental health outcomes. Loneliness is a malleable treatment target and preliminary evidence has shown that it can be addressed with digital platforms. Peer Tree is a strength-based digital smartphone application aimed at reducing loneliness. The study aim is to reduce loneliness and assess the acceptability, usability, and feasibility of Peer Tree in young people enrolled at university. Methods This will be a pilot randomised controlled trial (RCT) comparing a strength-based digital smartphone application (Peer Tree) with a control condition. Forty-two young people enrolled at university will be recruited for this pilot RCT. Participants with suicidal ideation or behaviours, acute psychiatric symptoms in the past month, or a current diagnosis of a mood or social anxiety disorder will be excluded. Allocation will be made on a 1:1 ratio and will occur after the initial baseline assessment. Assessments are completed at baseline, at post-intervention, and at follow-up. Participants in the control condition complete the same three assessment sessions. The primary outcome of the study will be loneliness. Depression, social anxiety, quality of life, acceptability, usability, feasibility, and safety of Peer Tree will also be measured as secondary outcomes. Discussion This trial will report the findings of implementing Peer Tree, a smartphone application aimed at reducing loneliness in university students. Findings from this trial will highlight the initial efficacy, acceptability, and feasibility of using digital positive psychology interventions to reduce subthreshold mental health concerns. Findings from this trial will also describe the safety of Peer Tree as a digital tool. Results will contribute evidence for positive psychology interventions to address mental ill-health. Trial registration Australian New Zealand Clinical Trial Registry ACTRN12619000350123. Registered on 6 March 202

Lithium and aluminium carbamato derivatives of the utility amide 2, 2, 6, 6- tetramethylpiperidide

Insertion of CO2 into the metal-N bond of a series of synthetically-important alkali-metal TMP (2,2,6,6-tetramethylpiperidide) complexes has been studied. Determined by X-ray crystallography, the molecular structure of the TMEDA-solvated Li derivative shows a central 8-membered (LiOCO)2 ring lying in a chair conformation with distorted tetrahedral lithium centres. While trying to obtain crystals of a THF solvated derivative, a mixed carbonato/carbamato dodecanuclear lithium cluster was formed containing two central (CO3)2- fragments and eight O2CTMP ligands with four distinct bonding modes. A bisalkylaluminium carbamato complex has also been prepared via two different methods (CO2 insertion into a pre-formed Al-N bond and ligand transfer from the corresponding lithium reagent) which adopts a dimeric structure in the solid state

Novel and selective inactivators of Triosephosphate isomerase with anti-trematode activity

International audienceTrematode infections such as schistosomiasis and fascioliasis cause signifcant morbidity in an estimated 250 million people worldwide and the associated agricultural losses are estimated at more than US$ 6 billion per year. Current chemotherapy is limited. Triosephosphate isomerase (TIM), an enzyme of the glycolytic pathway, has emerged as a useful drug target in many parasites, including Fasciola hepatica TIM (FhTIM). We identifed 21 novel compounds that selectively inhibit this enzyme. Using microscale thermophoresis we explored the interaction between target and compounds and identifed a potent interaction between the sulfonyl-1,2,4-thiadiazole (compound 187) and FhTIM,which showed an IC50 of 5µM and a Kd of 66nM. In only 4hours, this compound killed the juvenile form of F. hepatica with an IC50 of 3µM, better than the reference drug triclabendazole (TCZ). Interestingly, we discovered in vitro inhibition of FhTIM by TCZ, with an IC50 of 7µM suggesting a previously uncharacterized role of FhTIM in the mechanism of action of this drug. Compound 187 was also active against various developmental stages of Schistosoma mansoni. The low toxicity in vitro in diferent cell types and lack of acute toxicity in mice was demonstrated for this compound, as was demonstrated the efcacy of 187 in vivo in F. hepatica infected mice. Finally, we obtained the frst crystal structure ofFhTIM at 1.9Å resolution which allows us using docking to suggest a mechanism of interaction between compound 187 and TIM. In conclusion, we describe a promising drug candidate to control neglected trematode infections in human and animal health