D1.2 - Second progress report -...

www.chain-project.eu [email protected] Grant Agreement n. 306819

Project acronym : CHAIN-REDS

Project full title : Co-ordination & Harmonisation of Advanced and e-INfrastructures for Research Education Data Sharing

Grant agreement : 306819

Start date : December 1, 2012

Duration : 30 months

Programme : 7th Framework Programme (FP7)

Theme : Capacities specific program

Thematic area : Research Infrastructures

Funding scheme : Support action

Call identifier : FP7–INFRASTRUCTURES–2012-1

Project coordinator : Federico Ruggieri (INFN)

D1.2 - Second progress report

Deliverable Status : Draft File Name : D1.2 Second Progress Report V3.docx Due Date : November 2014 (M12) Submission Date : December 2014

Dissemination Level : Public Author : INFN ([email protected])

© Copyright 2012-2015 The CHAIN-REDS Consortium

INFN Istituto Nazionale di Fisica Nucleare – Italy

CIEMAT Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas - Spain

GRNET Greek Research and Technology Network S.A. – Greece

CESNET Zajmove Sdruzeni Pravnickych Osob - Czech Republic

UBUNTUNET The UbuntuNet Alliance for Research and Education Networking - Malawi

CLARA Cooperacion Latinoamericana de Redes Avanzadas - Uruguay

IHEP Institute of High Energy Physics, Chinese Academy of Sciences - China

ASREN Arab States Research and Education Network – Jordan

SIGMA Sigma Orionis – France

C-DAC Centre for Development of Advanced Computing – India

CHAIN-REDS Project - Deliverable D1.2 Page #2

2

Disclaimer

More details on the copyright holders can be found at www.chain-project.eu. CHAIN-REDS (“Co-ordination & Harmonisation of Advanced e-Infrastructures for Research and Education Data Sharing”) is a project co-funded by the European Union in the framework of the 7th FP for Research and Technological Development, as part of the “Capacities specific program - Research Infrastructures FP7–INFRASTRUCTURES–2012-1”. For more information on the project, its partners and contributors visit hwww.chain-project.eu. You are permitted to copy and distribute verbatim copies of this document containing this copyright notice, but modifying this document is not allowed. You are permitted to copy this document in whole or in part into other documents if you attach the following reference to the copied elements: "Copyright (C) 2013 - CHAIN-REDS Consortium - www.chain-project.eu". The information contained in this document represents the views of the CHAIN-REDS Consortium as of the date they are published. The CHAIN-REDS Consortium does not guarantee that any information contained herein is error-free, or up to date. THE CHAIN CONSORTIUM MAKES NO WARRANTIES, EXPRESS, IMPLIED, OR STATUTORY, BY PUBLISHING THIS DOCUMENT.

Revision Control

Issue Date Comment Author

V0 11/11/2013 TOC Federico Ruggieri (INFN)

V1 27/11/2013 First draft Francesca Maccioni, Federico Ruggieri

(INFN)

V2 20/12/2014 Review of the text and new

figures

Ognjen Prnjat (GRNET), Federico

Ruggieri (INFN)

V3 29/12/2014 Minor changes Rafael Mayo-Garcia (CIEMAT)


3

Abstract Deliverable 1.2 focuses on the achievements of the project in the second year. It is a

separate document from the Second Periodic Report that is due at the end of the first

period. It focuses more on the activities performed and the achievements and not on the

administrative part of the project (i.e. does not include a report on WP1).

It also includes an assessment of the work plan for the next 6 months with information

about the issues faced.


4

Table of contents ABSTRACT ________________________________________________________________________________________________ 3 TABLE OF CONTENTS ______________________________________________________________________________________ 4 INTRODUCTION ___________________________________________________________________________________________ 5 PURPOSE _________________________________________________________________________________________________ 5 GLOSSARY ________________________________________________________________________________________________ 5

1 STATUS OF THE ACTIVITIES ______________________________________________________________________ 7 1.1 OBJECTIVES _______________________________________________________________________________________ 7 1.2 ACTION LINES ____________________________________________________________________________________ 7

2 ACHIEVEMENTS ____________________________________________________________________________________ 9 2.1.1 Distributed Computing Infrastructure & Regional Operation Centres ____________________ 9 2.1.2 Clouds for Research and Education _________________________________________________________ 9 2.1.3 Data Infrastructures and Repositories _____________________________________________________ 11 2.1.4 DART ________________________________________________________________________________________ 11 2.1.5 Applications Matrix _________________________________________________________________________ 12 2.1.6 Science Gateways ___________________________________________________________________________ 13 2.1.7 Federations of Identity Providers __________________________________________________________ 13 2.1.8 Use Cases ____________________________________________________________________________________ 14 2.1.9 Dissemination _______________________________________________________________________________ 18

3 PLANNING FOR THE NEXT PERIOD ____________________________________________________________ 25 3.1.1 Distributed Computing Infrastructure & Regional Operation Centres ___________________ 25 3.1.2 Clouds for Research and Education ________________________________________________________ 25 3.1.3 Data Accessibility, Reproducibility and Trustworthiness _________________________________ 25 3.1.4 Success stories_______________________________________________________________________________ 25 3.1.5 Use Cases ____________________________________________________________________________________ 25 3.1.6 Science Gateways ___________________________________________________________________________ 27 3.1.7 Federations of Identity Providers __________________________________________________________ 27 3.1.8 Dissemination _______________________________________________________________________________ 27

4 CONCLUSIONS ____________________________________________________________________________________ 29


5

Introduction CHAIN-REDS is a FP7 project co-funded by the European Commission (DG CONNECT) which started on the 1st December 2012 and aiming at promoting and

supporting technological and scientific collaboration across different e-Infrastructures established and operated in various continents, in order to define

a path towards a global e-Infrastructure ecosystem that will allow Virtual Research Communities (VRCs), research groups and even single researchers to access and efficiently use worldwide distributed resources (i.e., computing,

storage, data, services, tools, applications).

Purpose The purpose of this deliverable is to present a status of the activities performed

during the second year by the CHAIN-REDS project (December 2013 – November 2014). It is also meant to describe the issues faced and the lessons learned

during this period.

Glossary

BoF Birds of a Feather

CAS Chinese Academy of Sciences

CHAIN Co-ordination and Harmonisation of Advanced e-INfrastructures

CNIC/CAS Computer Network Information Center of the Chinese Academy of Science

DCH Digital Cultural Heritage

DCI Distributed Computing Infrastructures

DoW Description of Work – Annex I to the Grant Agreement

eAGE Integrating Arab e-infrastructure in a Global Environment

EC European Commission

EGCT European Globus Community Forum

EGI European Grid Initiative

EGI CF EGI Community Forum

EGI TF13 EGI Technical Forum 2013

FP7 European Commission’s Framework Programme Seven

HP-SEE EU/FP7 project High-Performance Computing Infrastructure for South East

Europe’s Research Communities

HPC High Performance Computing

ISGC International Symposium on Grids and Clouds

M&E Monitoring and Evaluating

MoU Memorandum of Understanding

NKN National Knowledge Network

NREN National Research and Education Network

NSCC TJ National Supercomputer Center in Tianjin

NSII National Specimen Information Infrastructure


6

OADRs Open Access Document Repositories

OSDD Open Source Drug Discovery

ROC Regional Operation Center

SAGrid South African National Grid

SANREN South African National Research Network

SME Small Medium Enterprise

VRC Virtual Research Communities


7

1 Status of the activities The CHAIN-REDS project had a first periodic review in January 2014 in Madrid

where a number of recommendations were made by the EC reviewers. The consortium addressed these recommendations and proposed an Amendment to the Grant Agreement that was approved in July by the European Commission.

In the meantime 5 use cases were selected and the deployment started with task forces created by project’s partners and user representatives.

An intermediate review, held in Brussels in September 2014, has assessed the progress of the project towards its objectives. Since then the activities continued and have already concrete results that will be

described in the following chapters. As it was written in the DoW, the objectives and lines of action were clearly laid

out. In the following sub-chapters we recall the objectives of the project and then describe the activities performed so far.

1.1 Objectives O1. Extend and consolidate international cooperation of Europe with other

regions of the world in the domain of e-Infrastructures for Research and Education.

O2. Promote, coordinate and support the effort of a critical mass of non-

European e-Infrastructures for R&E to collaborate with Europe addressing interoperability and interoperation of Grids and other DCIs.

O3. Study the opportunities of data sharing across different e-Infrastructures and continents widening the scope of the existing CHAIN Knowledge Base to Data Infrastructures and Cloud implementations.

O4. Promote trust building towards open Scientific Data infrastructures across the world regions, including organisational, operational and technical

aspects. O5. Demonstrate the relevance of intercontinental cooperation in several

scientific data fields addressing existing and emerging VRCs and propose pragmatic approaches that could impact the everyday work of the single researcher, even if not structured in a VRC.

O6. Provide guidance and recommendations for roadmaps for long-term global collaboration in e-Infrastructures and harmonization of existing polices.

1.2 Action Lines The planned activities, notwithstanding their splitting in Work-Packages, are synthesised in the following main lines or topics.

Support for the Distributed Computing Infrastructures (DCIs) & Regional Operation Centres in the context of their intercontinental collaboration.

Support the coordination of Cloud developments for Research & Education

with other regions (e.g. China, India, Latin America and Arab Countries). Extend the CHAIN-REDS Knowledge Base with information on Data

Infrastructures: collecting issues, best practices and identifying data repositories of direct interest for VRCs.

Promote the usage of Science Gateways as a mean for attracting new

communities and enabling the use of e-Infrastructures for every


8

researcher. Encourage deployment of Identity Federations as well as continue support

for Certification Authorities and support integration of different AA approaches.

Development and demonstration of the Data Accessibility, Reproducibility

and Trustworthiness (DART) model. Identify and select, in the regions of interest, 5 Use Cases supporting their

deployment in order to demonstrate the importance of the CHAIN-REDS’s achievements.

The activities performed on these topics are described in the following chapter.


9

2 Achievements In this chapter we summarise the achievements of the project in the second

period of 12 months of activity. The synthetic description that follows makes reference to all the documents and information that could be consulted to have a wider view of the obtained results and their impact.

2.1.1 Distributed Computing Infrastructure & Regional Operation Centres

The activity makes reference to the WP3 in the CHAIN-REDS DoW and the most

important documents 1 in this respect were produced during the first year of activity. There was continuous communication and exchange with regional representatives

and ROC managers in the regions. The interoperation guidelines, customised per region, are maintained on the CHAIN-REDS Wiki. The project evaluates the

supported Regional Operation Centres (ROCs) in two main categories:

- Stable ROC that has implemented the functionalities required but still needs some improvement in terms of interoperations with EGI, or maturity

of technical staff and/or operational procedures; - Fully mature ROC which is not only stably operating, but has also reached

mature operation capabilities interoperating with EGI.

Specific targeted technical support has been provided for the Africa&Arabia Regional Operations Centre that is now considered, together with the South-East

Asia ROC, as fully mature in terms of operational capabilities. The China and Latin America ROCs are stable, and actions on improvements are ongoing.

India/Garuda ROC is also stable, while actions are ongoing regarding its interoperation with EGI as a peer infrastructure provider. On the policy level, regarding the long-term persistence of the EU-regional

collaboration, a set of Memoranda of Understanding (MoUs) has been prepared, defining the framework for long-term collaboration between EGI and the regional

Grids. The support was provided for the formulation and the signature of the 4 MoUs which have been signed: between EGI and Africa & Arabia ROC, China,

India and Latin America. This involves the effort from the regions. ROCs provide operational support for the deployment of 5 chosen use-cases.

2.1.2 Clouds for Research and Education

The main result of this activity in this period was the release of D3.3 – “Cloud Technical Survey”. This deliverable reports on the results of the survey regarding

the Research and Education (R&E) clouds in the CHAIN-REDS’ target regions as well as in Europe. The survey includes the technical aspects of R&E clouds, as well as issues related to interoperation, interoperability, compatibility,

orchestration and federation. The survey has been released in December 2013 and results collected until early February 2014. Taking into account the review

recommendation to decrease the surveying efforts, the finalisation of this state-of-the-art analysis was done through direct consultation with the regional representatives. Results obtained show a high interest in standards, thus pointing

to the fact that the solutions fostered/offered by CHAIN-REDS are indeed

1 D3.1 – Interoperation model and plan; D3.2 – Interoperability guidelines and design;

available in the project’s web site: www.chain-project.eu


10

relevant. Thus, the overall recommendation of this activity is to follow up with promotion of CHAIN-REDS-supported standards in these communities via

technical round tables, and specifically the promotion of cloud federations, as specified in the Project DoW.

The CHAIN-REDS Cloud Test-bed is active and soliciting contributions from the regions. It has been organised as a “virtual-cloud” made so far of resources

belonging to 10 sites, from 6 countries, of which one owned by an SME located in Egypt. 4 out of the 10 sites are also belonging to the EGI Federated Cloud and 3 different and well known cloud stacks are supported, namely Okeanos,

OpenNebula and OpenStack. The Cloud implementations were selected by soliciting resources from partners

and external contributors with the only limitation of having an OCCI compliant interface. The resulted list was the following:

Table 1 - List of resource providers with Cloud implementations, participating in CHAIN-REDS demo session

Country Cloud Middleware Resource Provider

Czech Republic

Greece

Spain

Spain

Italy

Italy

University of Messina

South Africa

Egypt

Furthermore, a round table on Clouds for R&E was facilitated under the EGI

umbrella, collocated with EGI User Forum in Helsinki, with a clear CHAIN-REDS contribution. Another cloud-related event was also organised by the project in

Rome, including a cloud tutorial and a CHAIN-REDS cloud workshop (June 24th to 26th). This latter event was attended by several representatives of EUMEDCONNECT3 and other EU co-funded projects.


11

2.1.3 Data Infrastructures and Repositories

The extension of the CHAIN-REDS Knowledge Base (KB) continued during this second year. The KB is one of the largest existing e-Infrastructure-related digital

information systems. It can be accessed from the project’s web site (www.chain-project.eu) and presents the information to visitors through geographic maps and tables.

Besides e-Infrastructure sites, services and applications, the CHAIN-REDS KB publishes information about Open Access Document Repositories (OADRs) and

Data Repositories (DRs). As of today, the KB contains about 2,500 OADRs and 600 DRs, out of which about 100 have been included thanks to the promotion and outreach activities carried out by the project and to the collaborations with

stakeholders such as DataCite and eIFL. The total number of resources that are indirectly included in the KB is well above 30 million.

It has been recently extended to Open Educational Repositories.

Figure 1 – Open Educational Repositories (OERs) available all over the world.

The CHAIN-REDS KB details are described in the project’s deliverable D4.3 - ”Use cases of the identified data infrastructures and data repositories”, available at the

project’s web site.

2.1.4 DART

The Data Accessibility, Reproducibility and Trustworthiness (DART) challenge has been developed in 2nd year period, linking together a number of project

developments in the area of Data Infrastructures, and based entirely on standard-based components and approaches.

The DART vision is that of a researcher of a given scientific domain finding publications she/he is interested in and be automatically redirected to the data used to produce those papers and to the applications used to produce those data.

Alternatively and simply, he/she can access raw data of interest that can be used, if required, as an input for an application. Then, it provides a solution to manage

data repositories and seamlessly integrate them in a typical scientist’s research

http://www.chain-project.eu/


12

according to the information that has been gathered on data infrastructure and data repositories through the first year of the project lifetime. DART is based

entirely on existing project technology and intercontinental service success stories. This means that the datasets can be found by means of either the CHAIN-REDS Knowledge Base or the Semantic Search Engine, the applications

can be run on the CHAIN-REDS Science Gateway (accessible through an Identity Federation) and the data can be both identified by and assigned with Persistent

Identifiers (PID). The user can then access the data and the corresponding application in order to either reproduce and extend the results of a given study or start a new one. The new data (and the new publication if any) are stored on the

Data Infrastructure and can be easily found by the people belonging to the same domain making possible to start the cycle again. The requirements that are

needed are related to intellectual properties issues and unique identifiers referring to papers, data and applications. DART has been proposed to the collaborative VRCs in order to adapt this

challenge to the characteristics of the (raw) data and applications that these VRCs are using. To do so, the related intellectual properties rights and the

adoption of standards have been analysed with them. This first DART example makes use of a cross section data repository and a chemical physics application (see the section on Use Cases for details).

DART has been included in the EUDAT Workflow Working Group document ‘SHIWA/SCI-BUS & CHAIN-REDS Assessment’. DART (and CHAIN-REDS) results

have been also promoted in the Research Data Alliance via RDA-Europe. Finally, DART has been presented as a proof-of-concept demo in the EGI TF 2014. Three promotional videos related to DART have been recorded by the project:

short introductory one (3 min), technical one (5 min), and tutorials (3*10 min).

2.1.5 Applications Matrix

CHAIN-REDS produced a Matrix that maps the different VRCs/user communities currently collaborating with the project. This Matrix also documents the

applications’ geographic coverage with respect to the CHAIN-REDS partner regions, and their importance/strength in that region. Provision of this matrix

within a document has been identified as a requirement after the first review, and is available in the already cited Deliverable D4.3.

In total, there are 144 applications related to the project work and coverage. In order to elaborate on the use of e-Infrastructure and the impact on the user

communities, the following indicators are documented: Large community in terms of users (international collaborations included)

and/or countries or regions involved (actual and/or potential): the matrix counts 47 applications falling under these criteria;

High scientific impact (publications, patents, or general impact): the matrix

counts 72 applications falling under this criterion; High social impact: the matrix counts 41 applications falling under this

criterion.

Some applications cover more than one criterion.

Applications were identified in collaboration with several other projects such as eI4Africa, EPIKH, EUMEDGRID-Support, GISELA, and/or via local dissemination


13

and training events.

2.1.6 Science Gateways

The CHAIN-REDS project has continued to promote the use of Science Gateways (SG) based on the implementation made by the INFN Catania Group.

CHAIN-REDS is committed to foster the adoption of the SG paradigm in all the regions addressed by the project since Science Gateways represent valuable

platforms to:

(i) seamlessly access various e-Infrastructures in a way that is transparent for end-users and

(ii) support the so-called “long tail of science”.

CHAIN-REDS has promoted and supported the creation of the EU-project-specific

SGs such as agINFRA’s, DCH-RP’s, EarthServer’s, eI4Africa’s and the country SGs in Algeria, Jordan, Italy, Mexico, Morocco, South Africa, Tanzania and Zambia. The total number of users registered in the SGs promoted and supported by

CHAIN-REDS is above 1,000 and the current number of applications integrated in Science Gateways is 25, both domain specific and general-purpose.

Figure 2 - Science Gateways implementations

2.1.7 Federations of Identity Providers

Promoting Federations of Identity Providers is a key action of the CHAIN-REDS project and other activities, such as Science Gateways, are based on users’ authentication by means of IdPs.


14

CHAIN-REDS supports the eduroam deployment as the best and easiest way to promote the benefits of Identity Federations (IdF). “Simple” identity management

is seen as the basic building step both for eduroam and IdF approaches. CHAIN-REDS focuses on both the technological components needed for the deployment as well as on the promotion and actual deployment of the services

(also in collaboration with other initiatives such as the ELCIRA project). With the CHAIN-REDS support, the promotion of eduroam started in Arab

countries (currently with on-going planning for actual deployment); in the sub-Saharan Africa CHAIN-REDS supported eduroam deployment or identity consolidation (identity management) in Kenya, Zambia and South Africa.

India is already connected to eduroam. In the Asia-Pacific region Macau, Singapore and Thailand are connected, while CHAIN-REDS supported the

deployment in Malaysia and is collaborating with Taiwan and Indonesia colleagues to support their eduroam-related activities. There is also a pilot eduroam setup in China, in particular at the Peking

University. In Latin America most of the technical work is done within the ELCIRA project, 8

countries have eduroam in production and 4 countries have pilot deployment, CHAIN-REDS works with individual institutions to support their connection to the eduroam infrastructure and currently it also helps Colombia to define its eduroam

infrastructure. The key document during this period has been the deliverable D5.3 – “eduroam &

Identity Federations - A World status report”.

2.1.8 Use Cases

During this second year of activity the project has identified a number of specific

use cases that were then analysed and considered by the project. Five of them have been selected to be supported by the project as candidates for success-stories on this level. All of the use

cases make use of the e-Infrastructure services promoted by

CHAIN-REDS in the different regions, but they cover different and

complementary aspects of users’ characteristics.

• Use case no. 1: LAGO The Latin America Giant Observatory

is a recent collaboration that counts on Water Cherenkov Detectors in 9 Latin American countries, more than

80 Latin American researchers and a close collaboration with European

teams such as IN2P3 in France and INFN in Italy. LAGO use-case success story is based on the DART challenge and currently the project is

analysing the best strategy for assigning PIDs to the current datasets and to the new simulation data produced. LAGO will address three different phenomena


15

thanks to the CHAIN-REDS DART workflow. CHAIN-REDS has collaborated with LAGO in the following activities:

incorporating the LAGO repository into the CHAIN-REDS Knowledge Base. This is done activating the OAI-PMH protocol at the LAGO repository allowing data search engine to discover LAGO curated data;

creating and adapting PIDs to each curated data set in the repository, the idea being to tag these datasets in a unique and timeless way;

operating a dedicated Virtual Organization, called lagoproject, and integrating it in EGI activities (GGUS, accounting system, etc.).

developing a Grid implementation of CORSIKA-GRID accessible via Science

Gateways environment; developing a cluster implementation of CORSIKA accessible via Science

Gateway; promoting the use of Identity Managers and Identity Federations in order

to granted the secure access to computational resources.

All the activities have been coordinated with the LAGO Working Groups (WG),

mainly with WG3 that deals with daata preservation and simulation infrastructure. • Use case no. 2: APHRC

The African Population and Health Research Centre (APHRC) undertakes

research in a wide range of topics related to societal health and well-being. This use-case supports data

management including assignment of Persistent IDentifiers (PIDs) to the wide plethora of datasets that APHRC

manages and curates. This is of utmost importance since these datasets are widely used by almost every country in Africa in order to improve societal health and well-being. The assignment of PIDs to the data sets constitutes a milestone

both for the APHRC as well as for the CHAIN-REDS project, since this now provides the ability to the APHRC to track the impact of its work, via data citation

networks.

• Use case no. 3: TreeThreader Threading is the leading method for protein structure prediction, and it is exceedingly time-

consuming. The code is already available to the desktop computing community, and is now made

available on a full-blown e-Infrastructure: Virtual Machines launched from physical servers belonging to the China ROC and managed with OpenStack.

They have consumed around 15,000 CPU hours in July 2014. All TreeThreader jobs can be submitted

both within China and Europe. CHAIN-REDS provided support for:

- porting the code to the different e-

Infrastructure; - implementation of specific monitoring tools for the CHAIN-REDS case

available at http://casathome.ihep.ac.cn/casstats/monitor.html and


16

http://casathome.ihep.ac.cn/casstats/monitor_cloud.html; - deploying a site in IHEP-Beijing with dedicated cloud nodes managed by

OpenStack. This site provides dedicated computing resources for TreeThreader application;

- creating a generic virtual machine image that includes the TreeThreader

application and the environments supporting its running. This image can be deployed on any other cloud computing infrastructure of the European sites

as well as to provide computing power to the TreeThreader application. This has been already done in the Catania (Italy) and in Okeanos (Greece) sites;

- setting up the CHINA ROC site, monitoring grid computing services of IHEP grid site;

The computing infrastructure for TreeThreader has thus been extended. The majority of its computing resources were non-dedicated volunteer computing

nodes, hence the computing tasks had high throughput but also high latencies. With the addition of CHAIN-REDS cloud computing resources, TreeThreader has

more dedicated resources and some of its tasks improved considerably in latency. • Use Case no. 4: GROMACS

GROMACS software package is used for molecular dynamics simulation. These kinds of studies present huge computational demand. 15 European, Arab, Indian

and Latin America Grid sites have already been enabled with GROMACS version with two flavours: both an installation package and a Science Gateway portlet.

Figure 3 – Sites running GROMACS in different regional e-Infrastructures

The actions carried out by CHAIN-REDS to support this application have been mainly:

GROMACS (v4.6.5) threaded version has been successfully installed, via

Software Manager, on the distributed computing resources of the European

http://casathome.ihep.ac.cn/casstats/monitor_cloud.html


17

the Mediterranean, the Latin American and the Indian infrastructures; A JSR 286 portlet has been developed and installed in the CHAIN-REDS

Science Gateway that is based on the Catania Science Gateway Framework (CSGF). Authenticated and Authorised researchers can now access the heterogeneous infrastructures to study molecular activity of various bio-

molecules. The gLibrary framework and in particular the gLibrary Data Management

APIs have been used to deal with the creation of big output files produced during each simulation and store results on a EMI-3 DPM Storage Element. This framework allows to create, access and manage digital assets on Grid

infrastructures; In this first implementation, thanks to the JSR-complaint portlet developed

in the context of the CHAIN-REDS project, the multi-threathed version of the GROMACS application can be executed on the production infrastructures of the EUMEDGrid-Support and SEEGRid projects.

Thanks to these activities the supported community can now count on more

dedicated computing resources to observe molecular activity using molecular dynamics simulation approach.

• Use Case no. 5: ABINIT Due the significant development of the ab-initio calculations especially the

Density Functional Theory in the fields of quantum chemistry and the physics of materials, the large-scale calculations in those areas become vital.

Figure 4 - Sites running ABINIT in different regional e-Infrastructures

Therefore introducing powerful code such as ABINIT within the Grid computing

environment facilitates this task for the researchers. A team of ABINIT users attended the CHAIN-REDS Science Gateway porting school held in Catania in June 2014 and ported to the Grid both sequential and MPI ABINIT versions. These

versions have been installed in several sites in Europe Latin America and Arab countries and the required portlet, for job submission through the Science

Gateway, has been implemented. Specifically CHAIN-REDS has contributed with


18

the following activities: The ABINIT package has been successfully compiled, installed and tested

on the distributed computing resources. A JSR286-compliant portlet has been developed. Researchers can now

access the CHAIN-REDS and the ARN Science Gateways and use the

heterogeneous infrastructures to find the total energy, charge density and electronic structure of systems made of electrons and nuclei using the

Density Functional Theory (DFT). From the Science Gateway researchers can run both sequential and MPI-based versions of ABINIT.

2.1.9 Dissemination

During the second year, the consortium kept using the communication materials

developed during the first year – with additional prints being provided for the main events – but also produced additional materials to disseminate specific project outputs:

A flyer describing the CHAIN-REDS Knowledge Base (KB); A flyer describing the CHAIN-REDS Semantic Search Engine;

A flyer presenting the Semantic Search Engine Application; A flyer presenting the CHAIN-REDS Data Accessibility, Reproducibility and

Trustworthiness (DART) solutions;

A flyer presenting the Africa and Arabia Regional Operation Centres (ROC); Two flyers describing how to deploy eduroam for Universities and National

Authorities, respectively. All that documentation was printed and distributed at each event the project

partners attended. Those paper tools were complemented by a series of videos showcasing important project outputs:

One video addressing the CHAIN-REDS Science Gateway Week; Three promotional videos related to DART have been recorded by the

project: short introductory one (3 min), technical one (5 min), and tutorials

(3*10 min). They are available both in English and in Spanish.

Additionally, this activity involved a complete redesign of the main project brochure and poster at M20 (Deliverable D2.1.1). This has given a new focus on

the project concrete outcomes that can be used and/or implemented by stakeholders in the regions. That new material, which started being used from M21, will contribute in ensuring a high level of sustainable exploitation of the

project outcomes.

The CHAIN-REDS project organised two workshops during the second year, in two different target regions:

A workshop entitled “e-Infrastructures for Education, Research and

Development”, organised in association with EUMEDCONNECT3 and in co-location with the e-AGE 2013 conference, held in Tunis, Tunisia on

December 12-13, 2013;


19

A workshop focusing on identity management jointly organised with the ELCIRA EU-funded project, held in Cancun, Mexico, on May 28-29, 2014, in co-location with the well acknowledged TICAL2014 Conference;

Figure 5 -Overview of the CHAIN-REDS project events

Additionally, the project partners have participated in 20 external events, with the CHAIN-REDS involvement ranging from distribution of project materials and

single presentations to demonstration booths and dedicated sessions. A few of


20

the most notable of those events are listed below: At ICRI2014 held in April 2014 in Athens, Greece, CHAIN-REDS displayed a

booth that allowed to demonstrate some of the project main solutions to a large audience of researchers and end-users. Second, a training workshop on data services was also organised by the project in partnership with

EUDAT during ICRI2014;

In May 2014, the CHAIN-REDS project was presented to the Minister of

Telecommunications of Lebanon in a focused meeting; In June 2014, the project participated in the European Commission

consultation meeting on e-Infrastructures – a key event launching the EC’s work on the 2016-17 H2020 Work Programme – where a lot of high-level

stakeholders were represented; In June 2014, a CHAIN-REDS session

was organised as part of the EUMEDCONNECT3-ASREN Meeting held

in Rome, Italy.

In order to give service providers (mostly NRENs) and Science Gateway developers the required knowledge to deploy, operate and connect their services

and applications, CHAIN-REDS has launched and run in the last reporting period a specific training programme organised around two important events: the CHAIN-REDS Science Gateway Week and the CHAIN-REDS School for Application Porting


21

to Science Gateways.

Table 2 - External events with CHAIN-REDS sessions

Date Place Main event Contribution

2 April 2014 Athens, Greece ICRI 2014 CHAIN-REDS / EUDAT Workshop +

Exhibition booth

3-5 April 2014 Athens, Greece CLOSER2014

(Workshop IoT)

Model/demo of Federated Clouds with a specific accent on the

international view, federated ids

16 May 2014 Pune, India GARUDA Technical Talk Demonstration of Science Gateway

19-23 May 2014 Helsinki, Finland EGI Community Forum

2014

Demonstration “The Catania Science Gateway Framework as cloud application

broker and infrastructure broker”

Demonstration “Data accessibility reproducibility and trustworthiness”

24-27 June 2014

Rome, Italy

Clouds for Research and Education Workshop +

EUMEDCONNECT / ASREN Meeting

90 minutes CHAIN-REDS session


22

Table 3 - External events with CHAIN-REDS presentation/participation

Date Place Main event Partner(s) Contribution Audience

12-13 December 2013

Tunis, Tunisia eAGE 2013 INFN, GRNET,

CIEMAT

3 presentations on “Science Gateways”; “Regional Development Approaches”; and “Data Access and

Metadata Management” and participation to roundtable discussions

Ministers present, and also people from councils and similar

10-11 March 2014

Nairobi, Kenya Promoting Discoverability of

African Scholarship UbuntuNet

Alliance Presentation and consultation

Research Institute directors, leading regional researchers,

librarians, communication officers

23-24 April 2014 Prague, Czech

Republic 3rd EUDAT User Forum GRNET Consultations and participation

Data users community, Data Infra operators

27 April – 02 May 2014

Vienna, Austria European Geosciences

Union General Assembly 2014

INFN CHAIN-REDS Poster Scientists, researchers, academia, policy makers, journalists

6-9 May 2014 Mauritius IST Africa 2014 CIEMAT, CESNET

Submitted paper "Perun - Modern Approach for User Identity and Service

Management"

Senior representatives of leading public, private, education and

research organisations

16 May 2014 Beirut, Lebanon Reunion with the Minister of

Telecommunications ASREN Meeting

Minister of Telecomunications of Lebanon with participants from

universities, Lebanon CNRS

19-23 May 2014 Helsinki, Finland EGI Community Forum 2014 CIEMAT

INFN, GRNET Presentation “A CHAIN-REDS solution

for data workflow”

Personnel representing policy, researchers on Grid and cloud,

final users, etc. attend. In addition, EC representatives

usually do.

26-28 May 2014 Cancun, Mexico TICAL 2014 CIEMAT, INFN Submitted paper "A CHAIN-REDS

solution for accessing computational services"

University stakeholders from Latin America, EU and USA

9-10 June 2014 Athens, Greece e-IRG workshop GRNET Attendance, distribution of material,

discussion with policy makers from EU but also South Africa

Policy makers


23


24-26 June 2014

Rome, Italy ASREN Clouds for Research

and Education Workshop

INFN, CESNET, CIEMAT,

ASREN, C-DAC

CHAIN-REDS vision presented in the closing session

Managers and professionals that need to understand the business

potential of Cloud Computing

19-20 September 2014

Bangalore, India GARUDA-NKN Partners Meet

2014 C-DAC

Distribution of brochures and discussions

Scientific community

1-2 October 2014 Almaty,

Kazakhstan 1st Central Asian R&E

Networking Conference GRNET

Keynote “Global computing infrastructures”: O. Prnjat, GRNET

e-Infrastructure operators, user community, policy makers

15-17 October 2014

Porto Alegre, Brazil

Acesso Aberto, Preservação Digital, Interoperabilidade,

Visibilidade e Dados Científicos 2014

RedCLARA Paper and oral presentation on the

"CHAIN-REDS DART Challenge"

Librarians, Open Access Repository administrators, scientists, vice-rectors, publishers of scientific

journals, students

22-23 October 2014

Chengdu, China CHOICE Event Fostering EU-

China Collaborative Innovation in ICT

IHEP Presentation “CHAIN-REDS Activities

on Cloud Computing”

Industrial companies, Consultancies specialised in service

design and deployment, Representatives of national,

regional and municipal government in China, Policy makers from

Europe and China, Researchers from academia

29 October 2014 Brussels, Belgium

e-Infrastructures for Africa : Gateways to the Future

Conference Sigma Orionis

CHAIN-REDS Poster and project outcomes flyer

Policy-makers, Government representatives, ICT project

managers, Heads of research labs, researchers, academia, industry

stakeholders

10-12 November 2014

Rome, Italy e-IRG workshop and

meeting INFN

Presentation “Coordination of intercontinental e-Infrastructures”

Policy Makers and Researchers

13-14 November 2014

Lusaka, Zambia UbuntuNet-Connect 2014 CIEMAT,

UbuntuNet Alliance

Paper submitted and accepted: “Jointly exploiting data and distributed computing e-Infrastructure”

Practitioners in the research and education networking community,

researchers, policy makers, academicians, connectivity

providers

16-21 November 2014

New Orleans, USA

SuperComputing 2014 INFN

CHAIN-REDS DART challenge presented as part of “INFN Open

Access Repository”

Scientists, engineers, researchers, educators, students, programmers,

system administrators, and developers


24


23-27 November 2014

Cape Town, South Africa

eResearch Africa conference UbuntuNet

Alliance Paper on APHRC accepted + SA-Grid-

2.0 (not CHAIN-REDS), A&A ROC Practitioners and researchers from

diverse disciplines


25

3 Planning for the next period

The project’s activities will continue along the lines that have been shown in the previous chapters and will follow the recommendations of the intermediate Review concerning “Success Stories” to be used to increase the project visibility

and impact.

3.1.1 Distributed Computing Infrastructure & Regional Operation Centres

The project will continue to implement the ROC action plan, as defined in D3.1, and will continue to support the ROCs in their operation. This will include

solutions for monitoring, accounting, helpdesks and user support, etc. These stable and interoperable Regional Operations Centres will support the project use-

cases.

3.1.2 Clouds for Research and Education

The adoption of Cloud technology appears to be increasing among the different regions addressed by the project. CHAIN-REDS, as a multi-regional e-

Infrastructure project, will thus continue to support the dialogue in order to bring these communities together and actively collaborate, suggesting interoperable, standards driven services. The project will work to widen the Federated Cloud

demo to other countries and regions, supporting also the use of such Clouds by the selected Use cases.

3.1.3 Data Accessibility, Reproducibility and Trustworthiness

The model of Data Accessibility, Reproducibility and Trustworthiness (DART) will

continue to be supported towards the communities that have already adopted it (e.g. LAGO). Moreover, such model will be proposed to other VRCs in order to

expand the DART functionalities to the datasets of interest to these communities.

3.1.4 Success stories

CHAIN-REDS is aiming at providing success stories, based also on the supported use Cases, that will demonstrate the importance of e-Infrastructures. This action

is related to the dissemination activity that is described in the following sub-section.

3.1.5 Use Cases

The use cases have already reached relevant results, as it has been described

previously, however the next months will be dedicated to consolidate these results and, possibly, add new significant achievements. In the following

paragraphs a synthesis of the main activities planned is described. A more extensive description is available in the Deliverable D4.4 on the project’s web site.

LAGO

CHAIN-REDS is working on:


26

Finalising the process of integration and fully operation of the lagoproject VO in EGI

Contact sites for supporting and enabling lagoproject jobs Providing LAGO with tools for a resilient execution of jobs on Distributed

Computing Infrastructures. This affects the use of Grid in first instance.

Supporting LAGO in the submission of jobs for adjusting the different input options and scripts.

As it has been stated previously, new LAGO detectors will soon start to operate. This will also help in incorporating new institutions that will make use of the LAGO

measurements. To the date, November 2014, LAGO is composed of 34 institutions.

APHRC The harvesting of metadata and automatic inclusion in the CHAIN-REDS

Knowledge Base has been considered. Currently the APHRC repository has been included “by hand” in the Knowledge Base, but no metadata is harvested due to

the fact that APHRC uses a DDI schema that is different from OAI-PMH. Since there is a harvester protocol, but the schema and other internals are not yet known to the CHAIN-REDS collaboration, this task carries a medium risk, but high

benefit: if harvesting of metadata can be done for NESSTAR repositories based on DDI, this immediately opens a vast new sector (the social sciences and household

statistics) for CHAIN-REDS data infrastructure support. As a minimum the technology landscape will be analysed and a comparison provided, with suggested potential solutions.

TreeThreader

A further enabling of cloud computing resources is considered. The project is working on setting up a OCCI/CDMI interface on local Chinese cloud nodes, so these can become part of the CHAIN-REDS cloud test-bed.

GROMACS

A few more Indian GROMACS users are expected to join, these will include potential users from Indian Institute of Technology-Guwahati and Anna

University-Chennai. A new version of the JSR-complaint portlet is under development to access the GARUDA infrastructure and enhance the available computing capacities for the

computation. Garuda operation team is planning to conduct regular technical talks in India and

provide support to the local community job submission to the Science Gateway. The CHAIN-REDS project, in collaboration with CDAC partners, is actively collaborating to support the developing of a JSAGA adaptor to access the

GARUDA resources and make them available through the Science Gateway.

ABINIT The CHAIN-REDS project will continue to support the deployment of the ABINIT code on DCIs to allow researchers from Quantum Chemistry and Physics of

materials to access bigger pool of resources. A dedicated workshop only for ABINIT users will be organized by ARN for

researchers of other Universities in Algeria during December 2014.


27

Moreover, one of the key users of ABINIT in Algeria has been invited to give a presentation at the e-AGE 2014 conference organised by ASREN in Muscat

(Oman). In order to accomplish the need of use of storage resources via the SG, further developments are on the way.

Integration of the ABINIT application to be run on Cloud resources is being

carried out as well. Firs tests have been executed.

3.1.6 Science Gateways

CHAIN-REDS will continue to promote the evolution of Science Gateways (SG) and suggest the deployment of new ones that address scientists, professors,

students and general users on the basis of geography (e.g. Algerian and Moroccan SGs), scientific domain (e.g. Agriculture, Cultural Heritage, etc.) and target users (e.g. Education, Citizen Scientists, etc.).

3.1.7 Federations of Identity Providers

CHAIN-REDS is committed to foster the deployment of IdFs in the regions addressed by the project. This is indeed what has actually happened in the reporting period and will continue to be the focus of the next period. Africa, Arab

Countries, Asia and Latin America are all taken into consideration in order to increase the awareness. The use of tools facilitating the deployment of IdPs and

IdF are expected to produce beneficial effects in terms of increased number of federated identities and services available to users.

Table 4 - Collaborating organisations and projects

Region Organisations Projects

Africa UbuntuNet, TERENA AfricaConnect, eI4Africa

Arab Countries ASREN EUMEDCONNECT3

Asia Pacific ASGC, APAN TEIN3

China

Chinese Academy of

Sciences, CSTNET, CERNET

ORIENT+

India C-DAC, PSA NKN

Latin America CLARA ELCIRA

Some of the projects listed in the table above ended during this period (i.e. eI4Africa, ELCIRA), but CHAIN-REDS will continue to co-operate with the stable organisations and with the new projects that will emerge.

3.1.8 Dissemination

The planning of future project events spans the last 6 months and is clearly defined as follows: A workshop on “Supporting collaborative applications for global research”

organised in co-location with the NKN (National Knowledge Network) Conference 2014 (17 December 2014 – Guwahati, India);


28

The project final conference to be held in Brussels, Belgium (March 2015).

A project final conference will be organised at the end of March 2015 in Brussels, Belgium, to present final outcomes of the project. Project partner SIGMA is the main organiser of this event.

The project will, however, keep contributing to other relevant events. In the

following table we summarise the foreseen opportunities during the next period.

Table 5 – Forthcoming events where the project can contribute

2 This event is beyond the end of the project (31 May 2015) but we expect many of the

partners to be present there and to disseminate the project’s achievements.

Date Place Main event

3-5 December 2014

Sydney, Australia IEEE International Conference on Big Data

Science and Engineering (BDSE 2013)

10-11 December 2014

Muscat, Oman eAGE 2014

15-17 December 2014

Guwahati, India Third NKN Annual workshop

20-22 January 2014

Abu Dhabi World Future Energy Summit

16-18 February 2015

Dubai, UAE Innovation Arabia 8

May 2015 Lilongwe, Malawi IST-Africa 2015

15-18 June 20152 Porto, Portugal TNC 15


29

4 Conclusions

The CHAIN-REDS project has completed the second year of activity which was mainly focused on the identification and support for the deployment of five Use Cases from the regions addressed by the project. Other achievements have also

been described within the various tasks performed. The work in Interoperation has led to agreements and MoUs between EGI and Regional Operation Centres

(ROCs) in Africa & Arabia, China, Latin America and with Garuda in India. The activity on Federated Clouds and DCIs continued with the presentation of a demonstration and the addition of new resources to support the demo and the

activity of Use Cases (e.g. TreeThreader). The coordinated activities of promoting eduroam and Federated Identities have

obtained concrete results in Africa, Asia and Latin America. The focus on data and document repositories has produced the extension of the CHAIN-REDS Knowledge Base to Open Educational Repositories and the

deployment of the DART model in concrete applications (e.g. LAGO Use Case). The project has successfully presented its results in several Workshops and in

other events in many regions addressed by CHAIN-REDS. The activities for the next period are defined and have been modified to include the dissemination of the project’s achievements and special materials on “Success

Stories” that are emerging from the five selected Use Cases during the next period of the project.

CHAIN-REDS is thus approaching the Final Conference in Brussels and the end of its activities in a very good shape and there are more than concrete indications that it will outperform the original objectives.

D1.2 - Second progress report -...

Documents

Transcript of D1.2 - Second progress report -...