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# An Enterprise Linux OS is used for both he front-node and the compute nodes of the cluster.
# An Enterprise Linux OS is used for both he front-node and the compute nodes of the cluster.
# The cluster provided with AoD is personal - users have root-access to the environment, and can setup and configure the system to their needs. It is meant to be shut down when no longer needed.  
# The cluster provided with AoD is personal - users have root-access to the environment, and can setup and configure the system to their needs. It is meant to be shut down when no longer needed.  
The EC3 platform requires that ports 8800 and 8989 have to be accessible from outside.


The EC3 platform integrated in the AoD is available [https://servproject.i3m.upv.es/ec3-ltos/index.php here]
The EC3 platform integrated in the AoD is available [https://servproject.i3m.upv.es/ec3-ltos/index.php here]

Revision as of 17:10, 28 February 2019


Applications on Demand (AoD) Service Information pages

Applications on Demand Service menu: Home Documentation for providers Documentation for developers Architecture




The EGI Applications on Demand service (AoD) is the EGI’s response to the requirements of researchers who are interested in using applications in a on-demand fashion together with the compute and storage environment needed to compute and store data.

The Service can be accessed through the EGI Marketplace

Description of service

The service allows user-friendly access to a portfolio of applications and application hosting frameworks (Science Gateways, VREs) that are configured to use the dedicated pool of cloud computing and HTC clusters from EGI. The service also allows users to run their own simulation/analysis models with custom input data.

The service operates as an open and extensible ‘hub’ for providers and e-infrastructure user support teams who wish to federated and share applications and services with individual researchers, or small, fragmented communities, typically referred to as ‘the long tail of science’.

The portfolio of applications is currently composed by a readily available set of applications relevant to different scientific and research areas. This portfolio is open to be extended thanks to the contributions of users of the service. If you are interested in this, please get in touch with us: support (at) egi.eu


Intended user groups

  • Researchers, scientists and engineers
  • Application developers who want to share their app available to the community through AoD
  • National e-Infrastructures who want to offer the EGI applications library to their national users by "plugging" compute and storage resources

Requirements and user registration

The service is open for any researchers, scientists and engineers who need a simple and user-friendly access to compute, storage and applications services in order to carry out data/compute intensive science and innovation. The user needs to be affiliated with, or at least have a partner (for example a referee), a research institution in Europe to qualify for access.

Access requires acceptance of Acceptable Use Policy (AUP) and Conditions of Use of the 'EGI Applications on Demand Service'.

Users of the service are asked to provide appropriate acknowledgement of the use in scientific publications. The following acknowledgement text can be used for this purpose:

This work used the EGI Applications on Demand service, which is co-funded by the EOSC-hub project (grant number 777536). The HNSciCloud project (grant number 687614) is also sponsoring the service, allowing users to access the HNSciCloud services pilot for limited scale usage using the voucher schemes provided by the two contractors: T-Systems and Exoscale.

When requesting access to AoD users are guided through a lightweight registration process. Through a lightweight vetting process, members of the EGI User Support team will perform the needed checks to validate the users' requests before to grant him/her the access to the large scale computing resources.

Service components

  • Scientific applications that are offered ‘as services’ through graphical environments.
  • Science gateways and Virtual Research Environments that offer integrated development environments to port custom applications with High throughput computing and cloud resources.
  • Cloud and High-throughput compute resources suited for both compute/data intensive applications and for the hosting of scientific services.
  • A network of Consultants and supporters who can provide guidance on the use of the service

Each authenticated and authorized user is offered a grant, providing a pre-defined quota of resources, which can be used to run an application of choice. The grant to run applications can be renewed upon request.


Benefits

Through this service:

  • Researchers can access applications underpinned by high-capacity compute and storage servers, to carry out compute and data-intensive simulations. Use of the service does not require advanced experience with distributed and/or cloud computing.
  • Developers can integrate custom applications into the service and offer them as 'scalable, online services' for researchers and scientists worldwide.
  • Providers of compute and storage services can share their clusters and clouds to serve 'the long tail of science'. For more information see AoD for infrastructure providers

Application library

The service operates as an open modular environment where any application developer can integrate and share applications, and providers can plug their own data centre share. The following components are already integrated into the service and are available for users to access:

Scientific Applications

AoDs_applications.jpg



Computer Science & Mathematics

  • The R Project for Statistical Computing (v3.2.2) is a language and environment for statistical computing and graphics.
    • The application is accessible through the Catania Science Gateway. The user manual is available here.
  • GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments.
    • The application is accessible through the EC3 portal.

Cultural Heritage

  • The Semantic Search Engine (SSE) is an application conceived to demonstrate the potential of information coupled with semantic web technologies to address the issues of data discovery and correlation.
    • The application is accessible through the Catania Science Gateway. The user manual is available here.

Life Sciences

  • Chispter is a user-friendly analysis software for high-throughput data. It contains over 300 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
    • The application is accessible through the Catania Science Gateway. The user manual is available here.
  • ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
    • The application is accessible through the Catania Science Gateway. The user manual is available here.
  • Galaxy is an open, web-based platform for data intensive biomedical research.
    • The application is accessible through the EC3 portal. Instructions on how to use Galaxy workflows with EC3 are available here.
  • AutoDock Vina is an open-source software for doing molecular docking.
    • The application is available through the WS-PGRADE/gUSE portal. The user guide to run the AutoDock Vina application is available here
  • NAMD is a parallel molecular dynamics code designed for high-performance simulation of large bio-molecular systems.
    • The application is available through the EC3 portal.

Others

  • Apache Tomcat is an open source implementation of the Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket technologies. The Java Servlet, JavaServer Pages, Java Expression Language and Java WebSocket specifications are developed under the Java Community Process.
    • The application is accessible through the EC3 portal.
  • Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
    • The application is accessible through the EC3 portal.
  • Docker is an open-source project that automates the deployment of Linux applications inside software containers.
    • The application is accessible through the EC3 portal.
  • Hadoop is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
    • The application is accessible through the EC3 portal.
  • Marathon a production-grade container orchestration platform for Mesosphere's Data Center/Operating System (DC/OS) and Apache Mesos.
    • The application is accessible through the EC3 portal.
  • Chronos is a distributed and fault-tolerant scheduler that runs on top of Apache Mesos that can be used for job orchestration.
    • The application is accessible through the EC3 portal.
  • Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text.
    • The application is accessible through the EC3 portal. Instructions on how to start Jupyter Notebook with EC3 are available here.

Science Gateways and Virtual Research Environments

  1. The CSG incorporates several applications and offers these "as services" for the user.
  2. The CSG provides users with an intuitive web interface to execute applications on the grid resources of the platform.
    • The CSG take cares of starting the job in one of the available resources of the platform, of transferring the needed files (e.g. executable, input files, etc.) and downloading the output(s) in behalf of the users. CSG is open source and released under the Apache 2.0 license.
  3. The CSG uses the Catania Grid & Cloud Engine to interconnect the SG presentation layer with the underlying e-Infrastructures using standard protocols.

The CSG integrated in the AoD is available here


  • The WS-PGRADE Portal (Web Services Parallel Grid Runtime and Developer Environment Portal) is the Liferay-based web portal (WS-PGRADE web application) of gUSE, wich also includes a graphical portal service.
  1. WS-PGRADE is a Web portal hosted in a standard portal framework, using the client APIs of gUSE services to turn user requests into sequences of gUSE specific Web service calls.
  2. WS-PGRADE is integrated with the cloud resources of the platform, and provides a 'job wizard' interface for the user.
  3. Through the wizard one can define with a few clicks a computational job that WS-PGRADE will execute on the cloud resources.
    • The environment takes care of instantiation of Virtual Machine image for the job, for sending input data for the job, and for the retrieval of job outputs.

The WS-PGRADE/gUSE integrated in the AoD is available here


  1. The cluster, which is defined with a 'job wizard' interface for the user, is composed by a front node, where a batch job scheduler is running, and a number of compute nodes.
    • These compute nodes will be dynamically deployed and provisioned to fit increasing load, and undeployed when they are in idle status.
  2. The list of application libraries/tools installed in the front-node can be exported via NFS in all the compute nodes.
  3. The installation and configuration of the cluster is performed by means of the execution of Ansible receipts.
  4. An Enterprise Linux OS is used for both he front-node and the compute nodes of the cluster.
  5. The cluster provided with AoD is personal - users have root-access to the environment, and can setup and configure the system to their needs. It is meant to be shut down when no longer needed.

The EC3 platform requires that ports 8800 and 8989 have to be accessible from outside.

The EC3 platform integrated in the AoD is available here


  • The EGI VMOps dashboard,a framework allows users to perform Virtual Machine (VM) management operations on the EGI Federated Cloud. The graphical interfaces of the dashboard allows the user to choose VMs from the AppDB Catalogue, to define an execution topology for them, and then to instantiate them on infrastructure as a service clouds.

The EGI VMOps dashboard is available here

How can you access the service ?

  1. Login to the EGI Marketplace with the EGI AAI Check-In service.
  2. Setup a profile, including details about your affiliation and role within a research institute/project/team.
  3. Navigate the marketplace top-menu and click on the category: "Applications".
  4. Click on the "Applications on Demand" service and submit an order to use one of the available applications.
  5. When the request is approved, run the requested application(s) hosted in one of the gateway/portal environment.

Please check the following guide for further details.

Help desk

For generic questions or inquiries, please contact the EGI Support team at applications-platform-support@mailman.egi.eu.

For gateway-specific support please contact:

  • Catania Science Gateway (CSG): sg-licence@ct.infn.it
  • WS-PGRAGE/gUSE portal: portalwide@lpds.sztaki.hu
  • EC3 portal: micafer1@upv.es

References

Scientific paper describing the service and its status at May 2017: https://documents.egi.eu/document/3132

Presentations about the service:

  • Overview of the EGI Infrastructure for serving the long tail (EGI Community Forum, November 2015): [1]
  • Poster and animated slides from Demo at EGI Community Forum, November 2015 (Winner of best demo prize): [2]
  • Slideset about the concept of the EGI long-tail of science platform (from Nov. 2014): [3]
  • Slideset about the authentication and authorization model adopted (from Nov. 2015): [4]
  • Slideset about the staus report of the platform at the EGI Conference 2016: [5]
  • Slideset about the staus report of the EGI platform at the DI4R Conference 2016: [6]
  • Webinar to introduce the Applicatios on Demand (AoD) service to NGIs/USTs representatives, RI architects, resource providers and researchers [7]
  • Slideset about the Applications on Demand (AoD) service introduced at IWSG 2017: [8]