Future computing platforms for biodiversity science

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1 Future computing platforms for biodiversity science Daniele Lezzi Rome, 5 September 2013

2 Motivation Lack of service integration and interoperability of research e- Infrastructure e-irg 2013 White Paper: e-infrastructure Commons Provide e-infrastructure services following the Cloud model Lack of standardization and concerns about security and vendor lock-in Importance of open e-infrastructures, sharing of raw data and results, and collaboration to enable more open science in Horizon 2020 Neelie Kroes, Vice President, European Commission Involvement from the user communities, ensuring alignment between user needs and the development of the e-infrastructures Re-use the results of successful projects Lack of a common understanding on how best to deploy e- infrastructures for biodiversity and ecosystem research A decadal view of biodiversity informatics: challenges and priorities White Paper Leverage existing projects and integrate existing tools and data

3 BSC Distributed Computing Activities BSC expertise in Distributed Infrastructures and Programming Models Helping user communities in the porting and optimized execution of scientific applications on several computing platforms Clusters Grids Clouds

4 BSC Distributed Computing Activities COMPSs: Platform unaware programming framework that simplifies the development and execution of applications in distributed infrastructures Same application runs on: Clusters, Grids, Clouds Interoperability through standards Cloud interoperability Commercial solutions: Azure, Amazon Open source: OpenNebula, EMOTIVE Cloud, OpenStack

5 Traditional on-premises Custom solution on an IaaS Cloud Custom solution on a PaaS Cloud VENUS-C (on an IaaS Cloud) VENUS-C (in a PaaS Cloud) VENUS-C: e-science as a service E-Science applications App App App App Platform Adaptation Hosting Glue Hosting Glue Hosting Glue VENUS-C Execution Environments Systems Administration Systems Provisioning Mgmt Cluster Mgmt IaaS PaaS Mgmt IaaS PaaS E-Science: What the researcher cares about Overhead: What the researcher has to do, but does not want to Infrastructure: What the researcher expects from someone else July 05, 2011

6 On Premises (not in the cloud) BSC Super Computer (not in the cloud) VENUS-C: e-science as a service Users Scenarios / Algorithm Type of workload Parameter Batch HTC Data flow Workflow sweep Map / Reduce CEP VENUS-C Execution Environments EMIC Generic Worker BSC COMPSs Infrastructure Operating System Cloud Technology Windows Windows Azure Windows OpenNebula Linux EMOTIVE Cloud Paradigm PaaS IaaS Cloud Provider Customer MSFT ENG KTH BSC

7 EU-Brazil OpenBio EU-Brazil Open Data and Cloud Computing e-infrastructure for Biodiversity Combining Biodiversity Science and the Open Access Movement to deploy a joint European and Brazilian e-infrastructure of open access resources supporting the needs of the biodiversity scientific community. Two biodiversity use cases Computing resources & SW platforms Further EU-Brazil collaboration in support of the biodiversity area & infrastructures Who benefit from EUBrazilOpenBio? EU & Brazilian biodiversity scientific communities Data and resource managers & Open Access community European & Brazilian policy and funding bodies

8 EU-Brazil OpenBio An Hybrid Infrastructure Integrating different technologies to make a large variety of services available for managing, manipulating and processing data and metadata within an autonomously-managed infrastructure: gcube system, openmodeller, COMPSs, EasyGrid AMS, VENUS-C, HTCondor, u.store Catalogue of Life Leveraging on existing European, Brazilian and global data sources ranging from species data - species names, synonyms, taxonomical classifications - to literature, occurrence maps and images: Catalogue of Life, List of Species of the Brazilian Flora, specieslink, Biodiversity Heritage Library, Bioline International, Global Biodiversity Information Facility (GBIF). Two use cases: Taxonomy Management and Ecological Niche Modelling

9 EU-Brazil OpenBio Use Case 2: Ecological Niche Modelling species (18 Sept. 2012) angiosperms (flowering plants) Assuming that 30% will have enough points to generate models (~9 000 species): 495k models, 540k tests, 90k projections 10 months to generate all models! But what if we want to generate models for All ~43 thousand plant species from Brazil? Using more than one spatial resolution? Projecting into different environmental climatic scenarios? With global coverage? Note: models may be regenerated every time new data is available for each species...

10 EU-Brazil OpenBio Use Case 2: Ecological Niche Modelling Multi-staging and multiparametric experiments implemented through COMPSs and the openmodeller software and managed through a Virtual Research Environment (VRE) portal COMPSs and the VENUS-C middleware middleware used to instantiate the workflows on cloud resources from different providers dynamically deployed by COMPSs More details of the application will be provided in the SESSION 8: TRAINING COURSES, HACKATONS AND WORKSHOPS of this Friday

11 EU-Brazil OpenBio Support to biodiversity communities ENM Service (OMWS2) VENUS-C Cloud Middleware COMPSs Workflow Orchestrator OCCI CDMI EGI Federated Cloud Integration of the EUBrazilOpenBio solution in the EGI Federated Cloud Shared requirements between EUBrazilOpenBio and BioVeL The EUBrazilOpenBio ENM service is exposed through an extended openmodeller Web Service interface (OMWS2 in the picture). The OMWS extensions are backwards compatible with the original specification, allowing existing clients, as the Taverna Workflow Management System in BioVeL, to be fully supported in the new implementation The EUBrazilOpenBio ENM Service is published in the BiodiversityCatalogue

12 EUBrazil Cloud Connect Objectives The main objective is the creation of a federated e-infrastructure for research using a user-centric approach. To achieve this, we need to pursue three objectives: Adaptation of existing applications to tackle new scenarios emerging from cooperation between Europe and Brazil relevant for both continents and with high social impact and innovation. Integration of frameworks and programming models for scientific gateways and complex workflows addressing not only the requirements of the selected use cases, but a potentially much larger user community. Federation of resources, to build up a general-purpose infrastructure comprising existing and heterogeneous resources Additionally, EUBrazilCC will perform an active and intense dissemination campaign, it will analyse innovation, and it will foster the involvement of Brazilian institutions in cloud standards definition. It will also be the first example of the internationalisation of the EU Cloudscape series.

13 EUBrazil Cloud Connect Use Case 1: Leishmania Virtual Laboratory Objective: Improve knowledge on the distribution and susceptibility of epidemiology outburst in Leishmaniasis Disease Technical Challenge: Easy access to computing and data federation for applications defined as workflows. Means: Integrate access to species/specimen distributed databases from parasites and vectors from Fiocruz (CLIOC and COLFLEB) and ISCIII and Species Occurrences (specieslink) databases in several processing pipelines (Bioinformatics and ENM) running on the cloud. Existing resources: Databases, openmodeller, EUBrazilOpenBio ENM service, NGS pipelines. Required developments: Integrate pipelines in the different workflow engines, integrate data access, develop an interface.

14 EUBrazil Cloud Connect Use Case 3: Biodiversity and Climate Change Objective: Understand the impact of climate change on terrestrial biodiversity through two workflows based on Earth observation and ground level data. Technical Challenge: Integrate parallel data analysis with other processing workflows in a geographically distributed environment. Means: Integration of models of plant species distribution with multilevel image data and processing in a scientific gateway. Existing resources: Parallel Data analysis service, satellite data, vegetation images, OpenModeller, EUBrazilOpenBio ENM service. Required developments: Adapting both simulators to cooperate by using the infrastructure of EUBrazilCC.

15 IaaS Business Model & Exploitation PaaS SaaS EUBrazil Cloud Connect UC1 Leishmania Virtual Lab UC2 Heart Simulation UC3 Climate Change Validation & Requirements COMPSs JiT Parallel Data Analysis OurGrid e-science Central CSGrid mc 2 ICFF Interoperability Dissemination Computing & Data Resources CloudScape

16 Conclusions: Future computing platforms User friendly approach for the uptake by the wider research community Built on previous experience Integration of services Interoperability Future Infrastructures Multidisciplinary science Technology transfer Virtual Research Environments for biodiversity Open Data Services Sharing and exploitation of results Platform Services Programming Environments Execution Services Innovative infrastructures Services Hybrid Clouds Federated Services Interoperability

17 Thank you! For further information please contact

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