=Paper= {{Paper |id=Vol-2363/paper9 |storemode=property |title=EGI Applications On Demand Service Catering for the Computational Needs of the Long Tail of Science |pdfUrl=https://ceur-ws.org/Vol-2363/paper9.pdf |volume=Vol-2363 |dblpUrl=https://dblp.org/rec/conf/iwsg/SiposRSS17 }} ==EGI Applications On Demand Service Catering for the Computational Needs of the Long Tail of Science== https://ceur-ws.org/Vol-2363/paper9.pdf
                          9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017



                    EGI Applications On Demand Service
                      Catering for the computational needs of the long tail of science

                        Gergely Sipos                                                        Giuseppe La Rocca
                      EGI Foundation                                                           EGI Foundation
                   Amsterdam, Netherlands                                                  Amsterdam, Netherlands
                    gergely.sipos@egi.eu                                                   giuseppe.larocca@egi.eu


                       Diego Scardaci                                                           Peter Solagna
                    INFN/EGI Foundation                                                        EGI Foundation
                        Catania, Italy                                                     Amsterdam, Netherlands
                    diego.scardaci@egi.eu                                                   peter.solagna@egi.eu



     Abstract—This paper describes the new EGI ‘Applications on        communities via ‘Virtual Organisations’ (VOs), according to
demand service’, that the EGI collaboration specifically designed      institutional or regional/national priorities. A VO is the online
for individual researchers, small research teams and early phase       representation of a scientific user group whose members are
research infrastructures that do not have dedicated                    usually work in similar or related research areas, or are part of
computational and storage resources, online applications and           the same scientific collaboration, for which reason they need
science gateways to perform scientific data analysis. The              the same applications, software and underlying hardware
described service is available at http://access.egi.eu and through a   capabilities. Some of the biggest VOs of EGI represent
lightweight registration and user identity vetting process allows      experiments of the Large Hadron Collider (ALICE, ATLAS,
user-friendly access to a growing number of scientific
                                                                       CMS, LHCb) [2], the VIRGO experiment [3], the Cerenkov
applications and application hosting frameworks (science
gateways, VREs) that are configured to use the dedicated pool of
                                                                       Telescope Array Observatory [4] or life science researchers
cloud computing and HTC clusters from EGI. The service                 from multiple countries and diverse background (biomed VO)
operates as an open and extensible ‘hub’ for providers and e-          [5].
infrastructure user support teams who wish to federated and                Since its start in 2010, EGI has well defined processes to
share applications and services with individual researchers, or        create and operate VOs for large, structured, international user
small, fragmented communities, typically referred to as ‘the long      communities. These communities have well established and
tail of science’.
                                                                       long-term presence, moreover they are resourced well enough
                                                                       to sustain skilled IT support teams who can instantiate and
  Keywords—long-tail;        SaaS;     e-infrastructures;    cloud;
HTC/HPC                                                                operate VO services for the researchers. The most advanced
                                                                       research infrastructures from the ESFRI Research
                                                                       Infrastructure Roadmap [6] are the typical operators of the
                       I. INTRODUCTION                                 largest VOs in EGI.
    EGI is an e-Infrastructure collaboration that provides
                                                                           At the same time individual researchers, small research
advanced computing and data services for research and
                                                                       teams and members of early phase research infrastructures
innovation. The collaboration operates a federated, publicly-
                                                                       often struggle to access applications, compute and data services
funded e-infrastructure that currently comprises more than 300
                                                                       in EGI. The tools and resource allocation policies that were
resource centers from Europe and beyond. Over the last decade
                                                                       designed for long-living, structured communities were
this infrastructure was the enabler of digital research conducted
                                                                       recognized as unsuitable for these type of users because they
by over 40,000 researchers through the whole spectrum of
                                                                       typically involve:
science from High-Energy Physics, to Earth Sciences, Life
Sciences, Chemistry, Astrophysics, and Humanities.                        •    Obtaining and using an X.509 personal digital
                                                                               certificate from Certification Authority (CA)
    EGI resource centers rely on the expertise of the ‘EGI
Foundation’, EGI’s coordinating institute located in                           recognized by EGI.
Amsterdam. EGI members – national compute/data centers (so                •    Joining an existing VO that matches the requester’s
called NGIs) and Intergovernmental Research Organizations,                     research subject/goals, or setting up a new VO.
such as CERN – operate the compute, storage, application and
software services that comprise the ‘EGI infrastructure’. These           •    Integrating relevant scientific applications with the VO
compute/storage providers allocate resources to scientific                     and fulfilling operational responsibilities, such as VO
                         9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017


        membership      management, resource  allocation               2. 100% coverage: anyone with Internet access can
        negotiations and community/application specific                   become a user, no need to ask for personal travel to
        service monitoring.                                               obtain special credentials (e.g. X.509 certificate).
    These individuals are often referred to as the ‘long tail of       3. Extendible and open: The service must be extendible
science’ [1] and they share the common characteristic of (1)              with additional application services to support
missing dedicated arrangement to computational and storage                specialized scientific disciplines and users. The
resources and online applications and services to manage and              extension should be possible via open interfaces and
analyze large amount of data, and (2) lacking the skills and              protocols.
experience with deploying and scaling applications to
distributed computer architectures. Despite some NGIs operate          4. User-centric: Support for users should be available in as
                                                                          many EGI member countries as possible.
national services for the long tail of science, such national
‘catch-all’ VOs are not available or not well maintained any
more in several cases [21].                                         B. Service providers’ constaints:
                                                                       1. Realistic: Define an architecture that’s implementable
    Recognizing the needs of this unique group, and trying to             under the available effort levels. Reuse existing EGI
compensate for the loss of NGI services in this domain we                 technological building blocks as much as possible.
designed and developed a new service within EGI: the
‘Applications on demand service’. The service was designed in          2. Secure: Provide as high quality user identity vetting,
late 2014, demonstrated in November 2015, reached Alpha                   and tracking of user activities as possible (close to the
release for early adopters in January 2017, and was opened for            existing solutions that are based on personal X.509
the general public in April 2017 as a Beta1 service. The service          certificates).
is available at http://access.egi.eu.
                                                                       3. Scalable: Be able to scale to 100s of
    This paper introduces this new service offering and details           compute/data/application providers. (The number and
the technologies and components that were developed and                   size of providers limits the users too).
integrated to realize the service. The rest of the paper is
                                                                       4. Recognized: Have sufficient policies and tools that
organized as follows: Section II introduces the user and
                                                                          enforce the users to acknowledge the use of the service
provider requirements that drove the system development.
                                                                          in scientific publications resulted from this use.
Section III describes the overall architecture and the main
design considerations. Section IV provides details about the
different system components that were developed/customized                              III. IMPLEMENTATION
from existing EGI tools to establish the service. Section V in a        The architecture of the Applications on Demand service is
table the already integrated applications and components of the     presented in Figure 1. In the heart of the service there is a 'User
service. In Section VI we describe the steps that an applications   Registration Portal' (URP). This is where new users enter to the
hosting framework provider has to follow to make his                service. The list of applications and underpinning services can
framework accessible within the EGI Applications on Demand          be publicly browsed on the URP. Usage requires login. Login
service. In Section VII we present our plans for the extensions     is possible with Google, Facebook and EGI Single-Sign-On
and improvement of the service, while in Section VIII we draw       accounts – All un-vetted accounts that are available for anyone
conclusions from the described work.                                with Internet access. Within the URP the user can setup a
                                                                    personal profile and can submit a resource access requests. The
                     II. REQUIREMENTS                               request includes an estimate of the compute and storage
                                                                    capacity that the user would like to use through the
The design process for the new service started with a
                                                                    application(s) he/she would like to use in the service. The
requirement collection and analysis that helped us to               request can use the default capacity allocation (at the time of
understand the needs/preferences of the long tail of science, as    writing this is 1000 CPUh and 10 TB storage) or can be a
well as the constraints from the EGI resource/service               customized request.
providers’ side that we have to consider as we are aiming at a
sustainable service. These needs and constraints are                    The access request is forwarded to the distributed service
summaries in this section:                                          support team. A team member – from the applicant’s country
                                                                    or from the EGI Foundation responds to the request and vets
A. Users’ needs:                                                    the user identity, checks the capacity request. The vetting is
   1. Zero-barrier access: any user who carries out non-for-        done by assessing the validity of the information provided by
      profit research should be able to get an account with a       the user in the profile, including links to departmental websites
      ‘start-up’ resource allocation on EGI to access scalable      and scientific publications and projects relating to the requested
      application services together with the underlying             e-infrastructure use. If needed, the support teams contacts the
      cloud/HTC/storage resources.                                  applicant in email or by phone. Routing the access requests to
                                                                    national EGI members not only allows us to conduct such
                                                                    conversation in local languages, but also to connect long tail
1
  EGI Beta service: Service being developed while available for     users to national EGI support teams, reaching recognition and
testing publicly.                                                   trust in national e-infrastructure initiatives. If the capacity
                          9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017


request exceeds the default allocation then the estimate is                          IV. ENABLING TECHNOLOGIES
double-checked and if needed negotiated resource providers of             The service was created by customizing various existing
the service.                                                          EGI components, and by developing a few new ones in order to
                                                                      glue together the required elements into a single service. The
                                                                      following customizations and developments were made:
                                                                         • The User Registration Portal (URP) was developed by
                                                                           CYFRONET as an extension of the e-GRANT EGI
                                                                           resource allocation tool [7]. The URP includes forms
                                                                           that guide users through the profile setup, resource
                                                                           request and application selection workflow. The tool
                                                                           was extended with web forms and an email notification
                                                                           subsystem to help the distributed user support team
                                                                           during the user identity vetting and user approval
                                                                           process. The URP provides an identity federation for the
                                                                           whole service, i.e. a user can authenticate to this portal
                                                                           and after his/her account is validated he/she will be able
                                                                           to login to any of the connected application hosting
                                                                           frameworks and respective hosted applications.
                                                                         • A resource pool was formed from EGI cloud and HTC
            Figure 1. Infrastructure architecture                          sites. The participating sites feel institutionally or
                                                                           nationally responsible for supporting the long tail of
    After the applicant’s resource access request is approved,             science, and therefore contribute with capacity into this
the user profile is set to ‘active’ in the URP. This information is        pool. The sites are joined together into an EGI Virtual
propagated to the connected application hosting environments               Organization called ‘vo.access.egi.eu’ [25]. The sites in
(science gateways, Virtual Research Environments or similar).              this pool accept special X.509 proxy certificates that are
These environments operate as applications hosting                         unique for the Applications on demand service and
frameworks, being equipped with a set of applications and user             which identify user workloads from the application
interfaces, manuals/guides best suited for those applications.             hosting frameworks (See details under next point). At
For example, some gateways can be suited for workflow type                 the time of writing the resource pool includes cloud
applications, others for parameter study jobs, yet others for              resources from Italy (INFN-Catania and INFN-Bari)
applications of a certain scientific discipline. The service is            and Spain (BIFI, CESGA) and HTC clusters from
open for any application hosting framework (See Section VI                 Belgium (VUB), Italy (INFN-Catania and INFN-Bari),
for more details). Science gateway and Virtual Research                    Poland (CYFRONET) and Spain (CESGA).
Environments supported by the European Commission FP7 and
H2020 work programmes are for example ideal candidates for               • Access to EGI resources requires short-living X.509
integration.                                                               proxy certificates from the client side. The traditional
                                                                           method is to generate such proxies either from a long-
    Approved users can login to any of the connected                       term personal certificate, or from a robot certificate [8]
application hosting frameworks and use the embedded                        that is used by an application hosting framework.
applications. These applications are already configured to scale           Unfortunately neither of these approaches were
to the distributed compute and storage systems that are                    sufficient for the Applications on Demand service,
contributed to the service by EGI members. The resources are               because (1) personal certificates are found difficult to
made accessible for the applications in the form of                        handle or impossible to obtain by certain long tail users,
Infrastructure as a Service clouds joint into the ‘EGI Federated           and (2) robot-proxies do not include any information
Cloud’ [22], or cluster resources federated with grid                      about the individual end-users, hiding all users
middleware into the EGI ‘HTC Service’ [23].                                workload under a single identity, making impossible for
                                                                           the identification of excessive or harmful use by certain
    The application use generates load on these resources and
                                                                           individuals. To overcome these limitations a new, so-
this is reported by the resources into the EGI accounting
                                                                           called ‘Per-User Sub-Proxy’ (PUSP) mechanism was
system. From this accounting system the user support teams
                                                                           developed. PSUPs are short-term proxies that are
can obtain statistics about individual users, as well as about
                                                                           generated from robot certificates in a special way: The
application hosting frameworks, cloud/HTC/HPC sites. When
                                                                           ‘distinguished name’ (DN) field of the proxy includes a
a user exceeds the amount of compute/storage/network
                                                                           unique string that is specific to the requester user. The
capacity that was allocated for him/her, the account can be
                                                                           DN is the same for a specific user for multiple user
suspended in the URP, blocking the user from further
                                                                           sessions, even if those sessions are initiated by different
consumption through this service. The continued use requires a
                                                                           application hosting frameworks. The compute and
new justification from the user and a corresponding evaluation
                                                                           storage resources report the proxy DN into the EGI
by the support team.
                                                                           accounting system, and based on the user-specific DNs
                     9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017


   we are able to trace back every e-infrastructure                 • 17 applications from different scientific areas and tools
   operation to the initiating user. The user-specific strings        have been already integrated into the existing
   are generated during the identity vetting and approval             applications hosting frameworks and are offered ‘as
   process, and they are propagated to every participating            services’ to users:
   application hosting framework. This tracing process is
   graphically presented in Figure 2.                                   o   Molecular Docking, Workflow and parameter
                                                                            study tool (WS-PGRADE portal).
• The connected application hosting frameworks must
  generate PSUPs from robot certificates. This is possible              o   Galaxy, Docker, Octave, Apache Tomcat,
                                                                            GnuPlot, NAMD, Hadoop, Marathon, Chronos,
  in two ways: (1) from a robot certificate that is deployed
  either locally on a USB smartcard on the server that                      Jupyter Notebook, Cloud orchestrator (in the
                                                                            EC3/IM portal).
  hosts the framework. (2) Because robot certificates are
  not available from EGI-recognised CAs in every                        o   Chipster, ClustalW2, Semantic Search, the
  country, we setup an ‘eToken server’ at INFN-Catania                      Statistical R for Computing (in the Catania
  that can serve any participating application hosting                      Science Gateway).
  frameworks with PSUPs. The application hosting
  frameworks can send a PSUP generation request to the                      Additional applications will be integrated into the
  server via its network API, including the userID as a                     frameworks following cost-value assessment
  parameter. The eToken server responds with the short-                     (more impactful, more broadly relevant
  term proxy certificate that can be used by the                            applications have priority).
  framework to interact with the VO resources (See step 5           • Two policies were developed: A security policy for
  and 6 in Figure 2.).                                                resource centers offering cloud/HTC/HPC/storage and
                                                                      an Acceptable Use Policy (AUP) for users.
                                                                        o   The first policy is compulsory to accept and
                                                                            implement by participating Resource Centers. The
                                                                            policy defines that offering resources in this
                                                                            service shall not negatively affect the security or
                                                                            change the security risk of any other VO. In
                                                                            particular, security incidents originating in the
                                                                            Applications on Demand service should not
                                                                            impact the IT Infrastructure in ways that are
                                                                            incompatible with the operational model of other
                                                                            VOs. This document also provides guidelines on
                                                                            the implementation of security procedures and
                                                                            controls to facilitate offering of the Service by
                                                                            Resource Centers and Science Gateways. The
                                                                            Guidelines contain normative information on how
                                                                            to implement the Policy.
                                                                        o   The user AUP defines the conditions of use, and
                                                                            responsibilities of the users – such as using the
                                                                            services only for activities that relate to the work
  Figure 2. Tracing user activity on VO resources                           that was described in the access request form; or
                                                                            what text to use in scientific publications to
                                                                            acknowledge the use of the infrastructure.
• Application hosting frameworks that can provide user-
  friendly interfaces to conduct scientific applications on                    V. ELEMENTS OF THE SERVICE
  VO platform resources in cloud or HTC/HPC clusters.
  The gateways use the identity federation of the URP to            The following Table 1 provides a summary of the
  allow access to approved users, and user the PUSP              components that are currently operated within the EGI
  mechanism to interact with cloud and HTC resources.            Applications on Demand service.
  The service currently includes three applications hosting
  frameworks: the WS-PGRADE [9], the EC3/IM [10]
  and the CSG [11]. The service is open for any additional
  framework that wish to make applications and
  application development/hosting services available at
  the European/worldwide scale. Technical instructions to
  integrate a new applications hosting framework to the
  service are provided in Section VI.
                            9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017


Table 1. Already connected services and resources.                   first requirement to integrate a new applications hosting
                                                                     framework into the service is to register the framework in
        Type of resource/service                   Providers         Unity to get a clientID and secretKey. These credentials will
                                             BIFI (Spain)            be used by Unity to identify the new provider and implement a
                                             CESGA (Spain)           secure connection with it.
IaaS clouds (compute and storage)                                        For applications hosting frameworks based on Liferay
                                             INFN-Bari (Italy)
                                                                     technology INFN-Catania has developed an OpenID Connect
                                             INFN-Catania (Italy)
                                                                     module [14] that enables Liferay-based gateways to
                                             CESGA (Spain)
                                                                     authenticate with OpenID Connect providers. This module is
                                             CYFRONET (Poland)
                                                                     adopted by the WS-PGRADE and CSG frameworks within
HTC clusters (compute and storage)           INFN-Bari (Italy)       this service.
                                             INFN-Catania (Italy)        A second step of integration is using the userID provided
                                             ULB-VUB (Belgium)       by Unity to generate Per-User Sub-Proxies (PUSP) to secure
                   Molecular Docking                                 user interaction with the EGI resources. For this, the provider
                                             WS-PGRADE
                   Workflow and                                      can rely on the eToken server that was already presented in the
                                             (SZTAKI, Hungary)
                   parameter study tool                              previous Section.
                   Galaxy                                                Lastly, the technical integration is complete when the
                   Docker                                            service support team together with the framework provider 1.)
                   Octave                                            registers the framework in the EGI service registry (GOCDB)
                   Apache Tomcat                                     to activate the availability and reliability monitoring for the
                   GnuPlot                                           framework with the EGI ARGO service [15], 2.) setup a
                   NAMD                                              framework-specific support unit in EGI Helpdesk [16] (this is
                                             EC3/IM (UPV, Spain)
Applications       Hadoop                                            for example tickets will be opened when the framework is
                   Marathon                                          noticed inaccessible by the monitor system and 3.) sign an
                   Chronos                                           Operation Level Agreement (OLA) defining for example
                   Jupyter Notebook                                  availability and reliability targets, helpdesk ticket response
                   Cloud orchestrator                                times.
                   tool
                                                                                         VII. FUTURE WORK
                   Chipster
                                             Catania Science
                   ClustalW2
                                             Gateway                      The ‘EGI Applications on Demand service’ was opened
                   Semantic Search
                                             (INFN-Catania, Italy)   for public use in April 2017. In the next few months we are
                   Statistical R
                                                                     working on promoting the system to potential users, mainly
        VI. HOW TO JOIN AS A GATEWAY/VRE PROVIDER                    through the user support teams of EGI member states.
                                                                     Promotion will be focused on countries where national support
    This section provides a short overview of the integration
                                                                     is lacking or insufficient for the long tail of science.
steps that gateway/VRE providers must complete to contribute
                                                                     In parallel with broadening the uptake of the new service we
to the service. Interested providers should consult with the
                                                                     are also planning to improve/expand the technical setup. This
online manual for details [12]. Compute and storage providers
                                                                     work will cover the following areas:
(cloud, HTC) can join the service by federating into the
‘vo.access.egi.eu’ Virtual Organisation [25], following the
                                                                      1. Replacing PUSPs with short-term proxies generated by
regular EGI guides for resource providers.
                                                                         the RC Auth service [17]. RC Auth was designed by the
    There are two fundamental prerequisites of integrating an
                                                                         AARC H2020 project [18] to have an open, European
application hosting framework: (1) the framework must be a
                                                                         proxy factory service that can be used by any e-
mature technology2 with demonstrated use within publicly
                                                                         infrastructure and Research Infrastructure that needs
funded science and (2) the framework must be already able to
                                                                         X.509 proxies for service access. The use of RC Auth in
use cloud, HTC or data services from EGI, or be ready to do
                                                                         the EGI Applications on Demand service would improve
so (to enable the scale-out of the hosted applications).
                                                                         the compatibility of our architecture with other European
    As reported in the previous Sections, the URP provides the
                                                                         initiatives, simplifying the integration of additional
identity federation that enables users to authenticate in any of
                                                                         applications and hosting environments. Besides, the
the connected application hosting frameworks with either
                                                                         change would improve the sustainability of our setup, by
social credentials or EGI SSO accounts. In the current
                                                                         eliminating components that EGI currently has to sustain
implementation, this identity federation is implemented with
                                                                         alone.
Unity [13], an authentication & authorization management
                                                                      2. In the current architecture every application framework
solution that uses OpenID Connect as standard interface. The
                                                                         and application should implement its own tools to
2                                                                        manage the users’ scientific data (for example importing
    For example at ‘Technology Readiness Level 8 or 9 [24]
                        9th International Workshop on Science Gateways (IWSG 2017), 19-21 June 2017


    data into the infrastructure from external storage systems,                                  REFERENCES
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                                                                  [24] Technology Readiness Levels by the European Commission:
                    ACKNOWLEDGMENT                                     https://ec.europa.eu/research/participants/data/ref/h2020/wp/2014_2015/
The work presented in this paper has been supported by the             annexes/h2020-wp1415-annex-g-trl_en.pdf, Accessed 9/May/2017.
EGI-Engage H2020 project (Grant number 654142). The               [25] vo.access.egi.eu Virtual Organisarion in the EGI Operations Portal:
                                                                       https://operations-portal.egi.eu/vo/view/voname/vo.access.egi.eu,
authors would like to thank the contribution to the                    Accessed 9/May/2017.
implementation of the described service to the following
institutes: BIFI, CESGA, CNRS, CYFRONET, INFN-Catania,
INFN-Bari, NIKHEF, SZTAKI, ULB-VUB, UPV.