newsletter
Issue #02
November 2016
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Message from the co-ordinator
End of the first project year is marked by the consolidation of a range of generic and discipline-specific e-Infrastructure services available through the VI-SEEM Virtual Research Environment. You are invited to browse and get to know our catalogue at https://services.vi-seem.eu and the related Virtual Research Environment at https://vre.vi-seem.eu/.
Year 1 marks also the opening up of this environment to the research communities in the fields of Climate, Digital Cultural Heritage and Life Sciences. First call for VRE access is now open to the communities from Southeast Europe and the Eastern Mediterranean with the deadline of 14th November.
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VI-SEEM service catalogue
The necessity for solid but flexible IT service management is one of the keystones for the service-oriented design. The specifics of the federated environment, such as the one found in VI-SEEM, impose requirements for service management tools that cannot be met using common off-the-shelf solutions. Hence, special care must be taken for the design and the implementation of easy to use, custom solution that is tailor made for scientific communities. VI-SEEM project has developed IT service catalogue and portfolio management that allows various ways of accessing and editing the information about the services offered by the project. For each service, relevant details are presented to the users, enabling them to discover and request access to the needed services.

VI-SEEM service catalogue lists 10 services, grouped in 5 categories:
- Compute: includes HPC, Grid and Cloud computing resources of the VI-SEEM infrastructure, available through the VRE to the user communities.
- Data Storage including: VI-SEEM Archival service provides safe data archiving, automatic replication according to predefined policies with high availability and performance, accessible through the VI-SEEM iRODS federation. VI-SEEM Simple storage allows users to keep and sync research data on various devices, as well as to share this data thus making it a useful tool in collaborative environment. VI-SEEM Repository represents the main storage service that allows users to deposit and share data, including regional datasets, publications and their associated data as well as software or references to software and workflows.
- Application specific: encompasses several services, ranging from discipline specific application environments, optimised and tailored for the needs of the VI-SEEM communities, workflow and code repositories designed to support the three target VI-SEEM communities, discipline specific dataset collections as well as two application level services. Clowder is a research data management system designed to support any data format and multiple research domains, with three major extension points: preprocessing, processing and previewing. Live Access Server is highly configurable server designed to provide flexible access to geo-referenced scientific data, usable by multiple user communities.
- Authentication and authorization infrastructure enables unified access to all VI-SEEM services.
- Service provisioning: contains the IT service management platform itself, as a tool for maintaining the service catalogue.
During the lifetime of the project, many new services will be added to this central service catalogue for the VI-SEEM project, enabling the users from the scientific communities to have a one-stop-shop for all the services available through the VI-SEEM Virtual Research Environment.
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VI-SEEM opens its 1st call for proposals for project access to services and supporting infrastructures
VI-SEEM opens its first Call for Proposals for projects accessing the VI-SEEM services and the supporting e-Infrastructure. The call is addressed to scientists and researchers that work in academic and research institutions in the region of Southeastern Europe and the Eastern Mediterranean, in particular Albania, Armenia, Azerbaijan, Bosnia and Herzegovina, Bulgaria, Cyprus, Egypt, FYR of Macedonia, Georgia, Greece, Hungary, Israel, Jordan, Lebanon, Moldova, Montenegro, Romania, Serbia and Turkey. The project proposals should address open research topics in specific fields of Life Sciences, Climate research, and Digital Cultural Heritage.
VI-SEEM offers a broad set of generic as well as application-specific services in the region of South-eastern Europe and the Eastern Mediterranean, with special focus on the scientific communities of Life Sciences, Climatology and Digital Cultural Heritage. Services are in the areas of: Compute resource (HPC, Grid and Cloud); Storage and Data services; Datasets; Software and Scientific Workflows; Application-specific services.
Access to underlying computational resources will be awarded for a maximum period of 12 months, while access to underlying storage resources may be provided for up to 2 years, beginning January 2017.
The list of services and resources offered by the VI-SEEM VRE can be found at: https://services.vi-seem.eu and in the VI-SEEM VRE at: https://vre.vi-seem.eu
These services create a unique Virtual Research Environment (VRE), thus improving research productivity and competitiveness on the pan-European level. Via this call VI-SEEM opens possibilities for regional scientists from the selected scientific fields to have access to the advanced resources and services that the VRE offers.
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VI-SEEM Login: seamless, secure access to the VI-SEEM VRE services
VI-SEEM Login enables individual researchers to seamlessly and securely access VI-SEEM services using federated authentication mechanisms. Through VI-SEEM Login, users are able to authenticate using the credentials provided by the Identity Provider (IdP) of their Home Organisation in eduGAIN, which has become the primary mechanism to interfederate for global research and education collaboration, bringing together more than 2000 Universities and Institutes around the world. Complementary to eduGAIN, VI-SEEM Login enables users that do not have an account on one of the federated IdPs, to still be able to access VI-SEEM services using social identity providers or other selected external identity providers. To achieve this, VI-SEEM Login has built-in support for SAML, OpenID Connect and OAuth2 providers and already enables user logins through Google, LinkedIn and Facebook.
VI-SEEM Login simplifies administrative processes for both community managers and service providers by serving as a central hub between federated Identity Providers and Service Providers. The main advantage of this approach is that it allows for all entities to establish and maintain technical and trust relation only to a single entity, the VI-SEEM Login service, which acts as a Service Provider towards the Identity Providers and as an Identity Provider towards the Service Providers. Common technical services, such as Identity Provider discovery and user account management are provided centrally by VI-SEEM Login, and do not have to be implemented by each individual service. VI-SEEM Login is also responsible for aggregating user attributes originating from various authoritative sources (IdPs and attribute authorities) and delivering them to the connected service providers in a harmonised and transparent way. Service Providers can then use the received attributes for controlling access to their resources.
What’s next: all the user communities of the VI-SEEM scientific disciplines are expected to be on board the VI-SEEM Login platform by the end of the year. Furthermore, the new OpenID Connect interface will be introduced, aiming for a faster and easier integration experience for new services.
https://services.vi-seem.eu/ui/catalogue/services/#VI-SEEM_Login
http://wiki.vi-seem.eu/index.php/Access_to_resources
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Climate Scientific Community paper: accelerated chemical kinetics in the EMAC chemistry-climate model

The global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC) is used to study climate change and air quality scenarios. The EMAC model is constituted by a nonlocal dynamical part with low scalability, and local physical/chemical processes with high scalability. The EMAC chemistry-climate model does not benefit from the support of accelerators which are nowadays installed in many HPC systems. We study strategies to offload the calculation of the atmospheric chemistry to accelerator technologies (GPU and Intel MIC), as in typical model configurations this is the most computational resource-demanding subtask. The proposed solutions extend the Kinetic Pre Processor (KPP) general purpose open-source software tool used in atmospheric chemistry. The changes proposed are expected to contribute to the eventual adoption of accelerated architectures in presently available implementations of Earth system models, towards exploiting the potential of a fully Exascale-capable platform.
This research paper has been supported by VI-SEEM and the detailed results can be found at: http://bit.ly/2ehSHUd
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Climate Scientific Community paper: WRF-ARW Model for the Prediction of High Temperatures in South and South East Regions of Armenia

The ultimate goal of the study is to develop an early warning system for the south and southeast regions of Armenia (11 in total) by defining specific thresholds for issuing alerts for adverse and severe weather phenomena. High temperature, wind and precipitation weather elements are discussed in the article, based on the experiments performed during the summer periods of 2011 and 2014. The system has been implemented based on the mesoscale Weather Research and Forecasting (WRF) model, which is adapted to the territory of Armenia and used for operational weather forecasting.
The verification methodology is to analyze the model results against observations received from four ground hydrometeorological stations located in the south and southeast regions of Armenia. The correlation coefficients, standard deviations of the differences and biases are calculated for the air temperature and wind speed and for precipitation amount and yes/no contingency tables are constructed.
The full paper, supported by VI-SEEM, is available at: http://bit.ly/2fORAwH
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