Transparent Orchestration of Task-based Parallel Applications in Containers Platforms

This paper presents a framework to easily build and execute parallel applications in container-based distributed computing platforms in a user-transparent way. The proposed framework is a combination of the COMP Superscalar (COMPSs) programming model and runtime, which provides a straightforward way to develop task-based parallel applications from sequential codes, and containers management platforms that ease the deployment of applications in computing environments (as Docker, Mesos or Singularity). This framework provides scientists and developers with an easy way to implement parallel distributed applications and deploy them in a one-click fashion. We have built a prototype which integrates COMPSs with different containers engines in different scenarios: i) a Docker cluster, ii) a Mesos cluster, and iii) Singularity in an HPC cluster. We have evaluated the overhead in the building phase, deployment and execution of two benchmark applications compared to a Cloud testbed based on KVM and OpenStack and to the usage of bare metal nodes. We have observed an important gain in comparison to cloud environments during the building and deployment phases. This enables better adaptation of resources with respect to the computational load. In contrast, we detected an extra overhead during the execution, which is mainly due to the multi-host Docker networking.This work is partly supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316 project, by the Generalitat de Catalunya under contracts 2014-SGR-1051 and 2014-SGR-1272, and by the European Union through the Horizon 2020 research and innovation program under grant 690116 (EUBra-BIGSEA Project). Results presented in this paper were obtained using the Chameleon testbed supported by the National Science Foundation.Peer ReviewedPostprint (author's final draft

Stadt- und Raumentwicklung Schweiz

In der Stadt- und Raumplanung der Schweiz fielen jüngst mehrere richtungsweisende Entscheide. So trat am 01.05.2014 das revidierte eidgenössische Raumplanungsgesetz in Kraft, welches die Innenentwicklung einfordert. Gefragt sind nun regional und städtebaulich angepasste Lösungen

Colony: Parallel functions as a service on the cloud-edge continuum

Although smart devices markets are increasing their sales figures, their computing capabilities are not sufficient to provide good-enough-quality services. This paper proposes a solution to organize the devices within the Cloud-Edge Continuum in such a way that each one, as an autonomous individual –Agent–, processes events/data on its embedded compute resources while offering its computing capacity to the rest of the infrastructure in a Function-as-a-Service manner. Unlike other FaaS solutions, the described approach proposes to transparently convert the logic of such functions into task-based workflows backing on task-based programming models; thus, agents hosting the execution of the method generate the corresponding workflow and offloading part of the workload onto other agents to improve the overall service performance. On our prototype, the function-to-workflow transformation is performed by COMPSs; thus, developers can efficiently code applications of any of the three envisaged computing scenarios – sense-process-actuate, streaming and batch processing – throughout the whole Cloud-Edge Continuum without struggling with different frameworks specifically designed for each of them.This work has been supported by the Spanish Government (PID2019-107255GB), by Generalitat de Catalunya (contract 2014-SGR-1051), and by the European Commission through the Horizon 2020 Research and Innovation program under Grant Agreement No. 101016577 (AI-SPRINT project).Peer ReviewedPostprint (author's final draft

Extension of a task-based model to functional programming

Recently, efforts have been made to bring together the areas of high-performance computing (HPC) and massive data processing (Big Data). Traditional HPC frameworks, like COMPSs, are mostly task-based, while popular big-data environments, like Spark, are based on functional programming principles. The earlier are know for their good performance for regular, matrix-based computations; on the other hand, for fine-grained, data-parallel workloads, the later has often been considered more successful. In this paper we present our experience with the integration of some dataflow techniques into COMPSs, a task-based framework, in an effort to bring together the best aspects of both worlds. We present our API, called DDF, which provides a new data abstraction that addresses the challenges of integrating Big Data application scenarios into COMPSs. DDF has a functional-based interface, similar to many Data Science tools, that allows us to use dynamic evaluation to adapt the task execution in runtime. Besides the performance optimization it provides, the API facilitates the development of applications by experts in the application domain. In this paper we evaluate DDF's effectiveness by comparing the resulting programs to their original versions in COMPSs and Spark. The results show that DDF can improve COMPSs execution time and even outperform Spark in many use cases.This work was partially supported by CAPES, CNPq, Fapemig and NIC.BR, and by projects Atmosphere (H2020-EU.2.1.1 777154) and INCT-Cyber.Peer ReviewedPostprint (author's final draft

An Architecture for Programming Distributed Applications on Fog to Cloud Systems

This paper presents a framework to develop and execute applications in distributed and highly dynamic computing systems composed of cloud resources and fog devices such as mobile phones, cloudlets, and micro-clouds. The work builds on the COMPSs programming framework, which includes a programming model and a runtime already validated in HPC and cloud environments for the transparent execution of parallel applications. As part of the proposed contribution, COMPSs has been enhanced to support the execution of applications on mobile platforms that offer GPUs and CPUs. The scheduling component of COMPSs is under design to be able to offload the computation to other fog devices in the same level of the hierarchy and to cloud resources when more computational power is required. The framework has been tested executing a sample application on a mobile phone offloading task to a laptop and a private cloud.This work is partly supported by the Spanish Ministry of Science and Technology through project TIN2015-65316-P and grant BES-2013-067167, by the Generalitat de Catalunya under contracts 2014-SGR-1051 and 2014-SGR-1272, and by the European Union through the Horizon 2020 research and innovation programme under grant 730929 (mF2C Project).Peer ReviewedPostprint (author's final draft

Two cases study of fouling colonization patterns in the Mediterranean Sea in the perspective of integrated aquaculture systems

Fouling assemblage colonizing fish-farms is considered mostly to produce negative impacts causing financial loss. By contrast, large evidences emerged on the bioremediation role by biofouling associated to aquaculture facilities, even if the fouling assemblages thriving in the water column was poorly investigated. The aim of the present work was to investigate the macrofouling assemblages over one year of immersion, in order to single out the fouling species, which play the most remarkable role for the bioremediation of the marine areas affected by aquaculture activities. With this in mind, we studied the fouling community dynamics in two Mediterranean maricultural facilities, respectively in the Mar Grande of Taranto (Ionian Sea) and in the Gulf of Gaeta (Tyrrhenian Sea), using the same experimental design and time frame. Two experiments were carried out using artificial panels anchored to two finfish cages. The one-year old fouling communities in the two sites were compared at four seasons of immersion, four submersion durations and three depths, both communities from structural and functional points of view. Notwithstanding the quite similar species composition of fouling of the two sites, the biofouling showed the highest biodiversity in the Mar Grande of Taranto. In the Gulf of Gaeta mussels, Mytilus galloprovincialis, dominated at all the times and depths, whilst in the Mar Grande of Taranto they were especially abundant at the surface with the deepest panels being largely colonized by polychaete sabellids. The co-occurrence of the filter-feeders Mytilus-sabellids recorded in the Gulf of Taranto also highlighted the highest filtration capability. Our results suggest two different fouling assemblages as candidates for bioremediation in integrated multitrophic aquaculture facilities: both a monospecific system dominated by mussels and a multi-specific system with sabellids and mussels as most abundant filter-feeders

Non-indigenous polychaetes along the coasts of Italy: a critical review

Non-indigenous species (NIS) represent one of the most relevant threats to biodiversity, ecosystem functioning and human activities, and their occurrence and spread have been the subject of numerous works and revisions. However, the information available is rather confused for several taxa, including polychaetes, which are characterised by having a high number of cryptogenic and questionable species. This work aims at providing a revised checklist of alien polychaetes occurring along the coasts of Italy, based on the examination of newly collected and deposited material and on the critical analysis of published and gray literature, and whenever possible on the re-examination of historical material. Of the 86 polychaete species reported as NIS in Italian waters, 25 are confirmed as alien species, while 3 are cryptogenic, and 40 should be considered questionable. Finally, 18 species were excluded from non-indigenous species checklists, either because they are native, or because they represent misidentifications of other species. The high number of cryptogenic and questionable species points at the need of molecular studies and taxonomic revisions for the majority of polychaete taxa reported as NIS, in order to clarify their taxonomy, origin, introduction pathways and spreading patterns

PyCOMPSs as an instrument for translational computer science

With the advent of distributed computing, the need for frameworks that facilitate its programming and management has also appeared. These tools have typically been used to support the research on application areas that require them. This poses good initial conditions for translational computer science (TCS), although this does not always occur. This article describes our experience with the PyCOMPSs project, a programming model for distributed computing. While it is a research instrument for our team, it has also been applied in multiple real use cases under the umbrella of European Funded projects, or as part of internal projects between various departments at the Barcelona Supercomputing Center. This article illustrates how the authors have engaged in TCS as an underlying research methodology, collecting experiences from three European projects.This work was supported in part by Spanish Government under Contract TIN2015-65316-P, in part by the Generalitat de Catalunya under Contract 2014-SGR-1051, and in part by the European Commission’s Horizon 2020 Framework program through BioExcel Center of Excellence under Contract 823830 and Contract 675728, in part by the ExaQUte Project under Contract 800898, in part by the European High-Performance Computing Joint Undertaking (JU) under Grant 955558, in part by the MCIN/AEI/10.13039/501100011033, and in part by the European Union NextGenerationEU/PRTR.Peer ReviewedPostprint (author's final draft

Effectiveness of nursing intervention in short-term hospitalization for patients suffered from borderline personality disorder and self-harm. A narrative literature review

Introduction: Personality disorder sufferers with severe self-harm and experience long psychiatric hospitalizations have complex mental health conditions and are at risk of suicide. When the symptoms of emotional instability are combined with self-harm, the resulting crisis often becomes difficult for patients and caregivers to manage. To improve care during these crises, the Dutch Multidisciplinary Guideline for Personality Disorders designates “brief admission” (BA) hospitalizations as an ameliorative intervention. Objective: To describe the effectiveness of short hospitalization nursing care for people with borderline personality disorder and who practice self-harm, compared to ordinary hospitalization. Methods: A narrative review was conducted through the Embase and CINAHL databases, the selected articles had to answer the following research questions: “what are the observable benefits of short-term hospitalization on patients with borderline personality disorder?”; and “what are the benefits compared to short hospitalization operators?”. Results: Seven studies were selected. The results show that BA was perceived as an effective nursing intervention, which promoted the patient’s self-determination and self-care. This helped increase confidence in daily life and allowed people to maintain their daily routines, work, and relationships by decreasing long hospitalizations and increasing patient compliance. There has also been benefit from the staff, who report an improvement in work quality. Conclusions: This type of hospitalization has developed in Northern European states. BA has never been tested in the Italian healthcare sector. It would be appropriate and desirable, given the results obtained, to experiment with this procedure also in Italy to obtain specific feedback regarding the relationship of short-term hospitalization with our National Health Service. It is hoped that this research can be a stimulus in this sense