VI-SEEM newsletter

Issue #04

February 2018

Message from the co-ordinator

VI-SEEM project has entered its final phase where its Virtual Research Environment and related supporting infrastructure, services and data are in full exploitation mode. The services of the Virtual Research Environment are provided through a compact service catalogue available at https://services.vi-seem.eu/ui/catalogue/services/, while the VRE portal at https://vre.vi-seem.eu/ provides a comprehensive environment for collaborative research for the communities of Southeast Europe and the Eastern Mediterranean regions.

VI-SEEM third Call for Proposals for projects accessing the VI-SEEM services and associated infrastructure is now open, available at (https://vi-seem.eu/3rd-call/) The call is addressed to scientists and researchers that work in academic and research institutions in the region in the fields of Life Sciences, Climate research, and Digital Cultural Heritage, and we are excited to welcome new applications and user groups in joining our community.

We have also opened a continuous call for SMEs, to encourage collaboration between industry and the scientific communities and explore prospects for long-term sustainability of the VRE. The call is available at https://vi-seem.eu/2017/11/15/sme-call/.

This newsletter also showcases new applications and services provided by the project, as well as project key regional and national training and dissemination events.

Finally, we would like to invite all interested researchers, scientists, students, e-Infrastructure providers, industrial players, as well as policy makers, to join us in Sofia on 15-16 May, for the project-organized conference on “e-Infrastructures for excellent science in Southeast Europe and Eastern Mediterranean”.

International conference
“e-Infrastructures for excellent science
in Southeast Europe and Eastern Mediterranean”

15-16 May 2018, Sofia Bulgaria

“e-Infrastructures for excellent science in Southeast Europe and the Eastern Mediterranean” conference will be held in Sofia, Bulgaria, on 15-16 May 2018 in Grand Hotel Sofia. The conference will be a unique opportunity for regional scientists to showcase their work in selected research fields relevant for the region, as well as for presenting the latest achievements resulting from the collaboration of countries in the region of Southeast Europe and Eastern Mediterranean in the area of e-Infrastructures and their use. The conference will gather e-Infrastructure providers, scientists and researchers, and the policy makers from the region and beyond.

The conference program will be divided in two main parts: in the first part an overview of the history, present status and perspectives of the regional e-Infrastructure collaboration will be given, including the analysis of the developments, connection with European programmes and initiatives, regional contribution to the European goals, etc. In the second part, the scientific results in the areas of climatology, life sciences and digital cultural heritage, achieved using the integrated regional e-Infrastructure platform, will be presented.

For more information about the conference, please visit:
https://vi-seem.eu/regional-conference.

VI-SEEM 3rd call for proposals for project access to services and supporting infrastructures

Following two successful calls for project access to the VI-SEEM services and the associated infrastructure, VI-SEEM opens its 3rd call in February, addressing scientists and researchers that work in academic and research institutions in the region of Southeastern Europe and the Eastern Mediterranean in the fields of life sciences, digital cultural heritage and climate.

The applicants can use a simple form and rely on the peer-review process which will ensure high quality of accepted applications. For the applications that meet the selection criteria and are approved, previously established and well-tested procedures for deployment and support within the VI-SEEM Virtual Research Environment will be followed.

To date, VI-SEEM has supported 38 research projects, out of which 15 were related to climate research, 12 to life sciences, and 11 to cultural heritage. In total, 18 million CPU-hours, 5 million GPU-hours, 1 million Xeon Phi-hours, 80 Cloud virtual machines, and 100 TB of storage space has been offered to the communities.

The VI-SEEM is announced at: https://vi-seem.eu/3rd-call/. Join us and become a part of a unique Virtual Research Environment that improves research productivity and competitiveness on the pan-European level!

VI-SEEM continuous open call for SMEs: ecouraging collaboration between the Industry and Scientific Communities

VI-SEEM engagement with industry and external scientific communities is accelerating through its continuous SME Call (https://vi-seem.eu/2017/11/15/sme-call/). Launched in November 2017, the call supports partnerships involving SMEs and research institutions of South Eastern Europe and Eastern Mediterranean, through the development of projects using the VI-SEEM services. The access team is available to answer any questions from the prospective users while the call is open, at: service-access@lists.vi-seem.eu.

The application procedure for access to the services and underlying computational and storage resources through the SME call is simple: it starts with a submission of a proposal at any time, via an application form that takes no more than half an hour to fill in. After passing the completeness and eligibility review, which requires that at most 100,000 CPU core hours or 6,500 GPU or Phi node hours are requested, the application goes through a technical evaluation, based on which the final decision on resource allocation is made.

Access to the services and resources offered by the VI-SEEM VRE (https://services.vi-seem.eu) is awarded for a maximum period of 3 months, while access to the data repository service might be granted for up to 12 months.

Applications will be accepted until the end of May 2018.

CSAD: The Centre for the Study of Ancient Documents

The Centre for the Study of Ancient Documents was established in 1995 under the auspices of Oxford University’s Faculty of Literae Humaniores to provide a focus for the study of ancient documents. Over the last six years it has developed into a research centre of national and international importance.

The Centre provides a home for Oxford University’s epigraphical archive, which includes one of the largest collections of squeezes (paper impressions) of Greek inscriptions in the world, together with the Haverfield archive of Roman inscriptions from Britain, and a substantial photographic collection. The strengths of the epigraphical archive lie in its broad coverage of early Greek inscriptions, Attic epigraphy and the Hellenistic world. Individual sites well represented in the archive include Chios, Samos, Priene, Rhodes, and Samothrace. The material in the archive is currently being reorganised and catalogued.

The Center shares through VI-SEEM Clowder inscriptions of Ptolemaic and Roman Egypt namely inscribed monuments in Greek, Latin and Egyptian, from Roman Egypt as well as RTI inscriptions such as various examples of RTI imaging from museum objects.

Clowder is a research data management system deployed to support the VI-SEEM digital cultural heritage community by being able to handle any data format. Clowder provides three major extension points: pre-processing, processing and previewing. Users can upload, download, search, visualize and get various information about cultural heritage data in the region.

The south front of Kingston Lacy with the Philae obelisk on the lawn. Philae obelisk is an example of an ancient monument which has been inscripted through Reflectance Transformation Imaging.

DICOM: collecting, processing and visualizing medical images online

In the last decade medical institutions have been facing the challenge of storage and visualization of medical images collected by various medical equipment. At the same time, providing the scientific community and Institutions access to medical datasets and ensuring in parallel personal medical data protection requires a state-of-the-art technological solution. DICOM Network project is developed for tackling such issues for different actors in the system based on various customized roles.

DICOM is a service that aids the collection, process and visualization of medical images online. It consists of the DICOM Portal, a front-end user interface for patients, doctors and scientists, the DICOM Server, which collects and archives images to DICOM portal for online access, and the DICOM Viewer for visualization, 3D modelling and medical image editing.

The project is based on a number of self-installed components that are built using a number of modules. Assembling of components and modules provides a flexible architecture of the DICOM “Network” that is consolidated by DICOM DATA Interface into a radiology tests database.

Parallel wind simulation speedup using openFOAM

Wind simulation over mountainous regions is of great interest for planning of human activities, in particular for green energy production with wind farms. The Polytechnic University of Tirana (UPT) performs wind simulations over rugged terrain in regional scales, using the OpenFOAM software. The mountainous area that includes Albania was selected as the terrain model, obtained from NASA SRTM Digital Elevation Model.

The experiments were carried out in three parallel systems aiming at the evaluation of runtime requirements as a preparatory phase for running it in the VI-SEEM Virtual Research Environment: the first in the Faculty of Information Technology of UPT with dual Intel(R) Xeon(R) E5506 processors, 2GB RAM per node and 1 GB switch, the second – HPC Cluster with non-blocking DDR Infiniband with dual Intel(R) Xeon(R) X5560 and 24 GB RAM per node, and the third – the supercomputer system Avitohol with dual Intel(R) Xeon(R) E5-2650v2, non-blocking InfiniBand FDR and 64 GB RAM per node, both in the Institute of Information and Communication Technologies, Bulgarian Academy of Sciences.

The results of the experiment show the importance of such simulations for planning of wind energy farms, and for the air transport. The use of OpenFOAM for wind simulation models of medium resolution (spatial discretization steps 10km-1km) over rugged mountainous regional area of Albania and surroundings was possible in the HPC Avitohol shystem using reasonable resources. Besides the runtime, another limitation was the virtual memory in levels of 10-30 GB for medium sized models, requested by preparatory modules blockMesh, decomposePar, and reconstructPar. An optimistic extrapolation of the runtime for the model with resolution 100m of spatial discretization step using up to 640 parallel processes resulted up to 4 months, not considering limitations due to virtual memory and degeneration of parallelization efficiency.

North-South wind (bottom) in altitude 1,500m (left), East-West component (center), and vertical component (right)

Digital Cultural Heritage

Life Sciences

Climate

VI-SEEM services and integrated VRE were presented at the DI4R conference in Brussels

VI-SEEM services and Virtual Research Environment were presented in the second edition of Digital Infrastructures for Research conference that was held in Brussels, Belgium, from 30 November to 1 December 2017. The presentation titled “Federated digital services for Open Science in Southeast Europe and the Eastern Mediterranean” was accepted to be part of the session EOSC Building Blocks, among an overwhelming number of submissions – thus showcasing the VI-SEEEM services that are candidates for integration in a wider European Open Science Cloud ecosystem.

The presentation described the innovative approach developed by the VI-SEEM project focusing on the integrated state-of- the-art platform, built jointly by e-Infrastructure providers and end users, consisting of computational resources (HPC, cloud, Grid), data storage and management, visualization tools and discipline-specific services, provided via an integrated Virtual Research Environment, but also to the fact that the platform serves a large geographical area (South Eastern Europe and Eastern Mediterranean) of about 300 million inhabitants having a diversity of e-Infrastructures with the aim to enable high-caliber research in strategic areas for the region, namely the Life Sciences, Climatology and Meteorology, and Digital Cultural Heritage.

The service orientation of the VI-SEEM e-Infrastructure, especially its service catalogue, was acknowledged and highly valued by the eInfraCentral project during the conference, as one on the most innovative service catalogues among the EU e-Infrastructure providers.

The DI4R 2017 conference is jointly organized by the 5 biggest e-Infrastructures in Europe: EGI, EUDAT, GÉANT, OpenAIRE, PRACE and RDA Europe under the theme “Connecting the building blocks for Open Science”. With more than 400 attendees, DI4R proved to be the leading e-Infrastructures event in Europe.

VI-SEEM participation in
“Two years AVITOHOL: Advanced HPC applications” workshop

The most active users of Bulgaria’s AVITOHOL supercomputer gathered in Panagyurishte in October 2017 to present the recent results of their research, during the “Two years of AVITOHOL: Advanced HPC applications” workshop.

The workshop was organized by the Institute of Information and Communication Technologies – Bulgarian Academy of Sciences and had more than 40 participants, including distinguished scientists from VI-SEEM partnering countries Hungary, FYR of Macedonia, Armenia and Albania, all of them AVITOHOL users. The program included 27 presentations on HPC applications in bioinformatics, molecular dynamics, environmental protection, climatology, digital cultural heritage, etc., divided in two main tracks: HPC applications, and tools and services for HPC. Special attention was given to a presentation on the current status and future perspective of HPC in Bulgaria. VI-SEEM was presented by the Assoc. Prof. Todor Gurov. A book with selected papers has been published as a Special Issue of the open access journal CIT, seven papers of which contain VI-SEEM related scientific results.

AVITOHOL is the newest multifunctional HPC system in Bulgaria, purchased and installed at IICT in 2015, and it is part of the VI-SEEM infrastructure. It consists of 150 computational servers HP SL250s Gen8, equipped with two Intel Xeon E5-2650v2 CPUs and two Intel Xeon Phi 7120P coprocessors, 64GB RAM, two 500 GB hard drives, interconnected with non-blocking FDR InfiniBand running at 56 Gbps line speed. The total number of cores is 20700 and the total RAM is 9600 GB, respectively. The theoretical peak performance of the system is estimated at 412.3 TFlop/s in double precision while the RMAX Performance according the LINPACK benchmark is 264.2 TFlop/s. AVITOHOL was put into operation in 2015 and was ranked among the 500 most powerful supercomputers (Top500), taking the 332nd place.

15th SESAME Users’ Meeting

VI-SEEM project was presented at the 15th SESAME Users’ Meeting in Amman, on December 18th-19th, 2017. The meeting brought together scientists from the region and world experts in the various fields of synchrotron applications, and provided a platform for information exchange and discussions of ongoing collaborative efforts within the community. It included updates on the project and invited speakers on selected topics related to SESAME scientific plans.

Researchers from the Region presented their research results and/or their plans for SESAME by oral or poster contributions and they met together on-site for discussion, interaction and networking. A large number of researchers expressed great interest towards the services provided by VI-SEEM.

The VI-SEEM regional climate training event
11-13 October 2017, Belgrade, Serbia

A 3-day training event focusing primarily on the Climate community, but also addressing the opportunities and services that the VI-SEEM VRE offers to the cross-disciplinary research, was held in Belgrade in October 2017. The target audience were the researchers and developers from the Climate and other research communities, as well as current and potential users of the VI-SEEM e-Infrastructure and services.

The VI-SEEM Climate Scientific Community Leader Dr. Theodoros Christoudias (Cyprus Institute) presented topics related to Climate Modelling & Downscaling, Earth System Model Post-processing & Visualization. Prof Ljupčo Pejov of the Institute of Chemistry, Faculty of Natural Sciences and Mathematics, Skopje, gave a lecture on “Efficient exact computations for molecular species relevant to atmospheric chemistry, climate science and drug delivery”.

Participants received training on the WRF-Chem model and DREAMCLIMATE application usage for atmospheric chemistry and Aeolian dust transport modelling. Relevant computational themes, parallel programming with OpenMP, MPI and GPGPU co-processors, source code repositories and data services (discovery, staging, archiving, management, PID, metadata aggregation) were also covered.

The event gathered more than 40 participants, and more than a dozen trainers and presenters with topical expertise, covering all VI-SEEM partner countries and beyond.

National event on VI-SEEM services, training portal, VRE and applications
FYR of Macedonia, 18 October 2017

The VI-SEEM service catalogue, training portal, VRE and applications were presented in the national event that was held at the Faculty of Computer Science and Engineering, University Ss Cyril and Methodius in Skopje. The event was attended by more than 35 participants with quite diverse background and interests, mainly from the academia, including researchers and students from the Faculty of Computer Science and Engineering, Faculty of Natural Sciences, Medical Faculty and Pharmaceutical Faculty. During the event, several potential project applications were identified and discussed.

Representatives from the Industry expressed interest in the current VI-SEEM call for SMEs, while two institutions from the cultural heritage community, namely the National library and the Directorate for preservation of cultural heritage were inspired by the talk given by the cultural heritage virtual scientific community leader, Prof. Georgios Artopoulos from the Cyprus Institute. Participants coming from several public institutions, such as the M-Nav, state owned company responsible for management and control of civilian air traffic in the country, were specifically interested in the climate community developments.

VI-SEEM national training event in Thessaloniki

Climate Simulations for the European region, meteorological applications, Ab initio and Molecular Dynamics simulations in nanostructures, as well as applications on neutron stars and gravitational waves were just part of the research work that was presented during the VI-SEEM national training and dissemination event in Thessaloniki on 11-12 December 2017.

The event was attended by more than 35 students and researchers, current and potential users of the VI-SEEM e-Infrastructure and services, who had the opportunity to learn about successful applications that run on Greece’s HPC ARIS Infrastructure, followed by hands-on sessions. Furthermore, the training instructors presented in detail the access policy, tools and usage techniques of HPC ARIS, as well as the VI-SEEM project, Virtual Research Environment and services.

The event was held on 11-12 December 2017 at the Research Dissemination Center of the Aristotle University in Thessaloniki.

Commissioner Gabriel’s visit to IICT in Sofia, Bulgaria

European Commissioner for Digital Economy and Digital Society Maria Gabriel visited the Institute of Information and Communication Technologies at the Bulgarian Academy of Sciences in Sofia on 13 October 2017 to discuss the EuroHPC-related perspectives and challenges in Bulgaria. Earlier in the day the declaration that Bulgaria joins EuroHPC was signed in Sofia, by the Bulgarian Minister of Education and Science, Krasimir Valchev, in the presence of Commissioner Gabriel.

Commissioner Gabriel visited the IICT together with Dr. Thomas Skordas (Director of DG Connect), Dr. Thomas Lippert (Head of Jülich Supercomputing Centre), Dr. Ivan Dimov (Deputy-minister of Ministry of Education and Science) and other officials. They visited also the computing centre and were acquainted with the capabilities of the Bulgarian supercomputer AVITOHOL, which is the most powerful computing resource in the region of Southeast Europe. When AVITOHOL was put into operation in 2015, it took 332nd place in the ranking of world supercomputers (Top500). The supercomputer is used to solve major computational tasks in areas such as ecology, climatology, molecular dynamics, cultural and historical heritage, and more. Extensive calculations using its unique capabilities were performed for the forecasting of extreme snowfalls in Bulgaria during the past winter.

Upcoming events

VI-SEEM events and VI-SEEM related events:

VI-SEEM regional conference: “E-Infrastructures for excellent science”, 15-16 May 2018, Sofia, Bulgaria
EU conference: “Improving long-term sustainability and opening up research and innovation infrastructures to industry and society”, 22-23 March 2018, Sofia, Bulgaria
EU Digital Forum “High Performance Computing (HPC) – Sofia”, 19 April 2018
E-IRG workshop, 14-15 May, 2018, Sofia, Bulgaria
European HPC Summit Week 2018, 28 May – 1 June 2018, Ljubljana, Slovenia

VI-SEEM related conferences, organized or co-organized by the VI-SEEM partners:

About VI-SEEM

VI-SEEM is a three-year project that aims at creating a unique Virtual Research Environment in Southeast Europe and the Eastern Mediterranean, in order to facilitate regional interdisciplinary collaboration, with special focus on the scientific communities of Life Sciences, Climatology and Digital Cultural Heritage.
VI-SEEM unifies existing e-Infrastructures into an integrated platform to better utilize synergies, for an improved service provision that will leverage strengthen the research capacities of user communities, thus improving research productivity and competitiveness on the pan-European level.
The project kicked-off in October 2015 and the consortium consists of 16 partners: lead institutes from the SEEM region, specializing in provision of scientific computing and storage resources, and scientific user support.

VI-SEEM project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 675121.

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