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USP

User Support

How to become an IBERGRID VO user

Ibergrid Macro VOs

National and regional user activities are increasing with the establishment of formal e-science networks, connecting universities and research institutions, enabled by the National Grid Initiatives. Such e-science networks provide a valuable mechanism to cover the emerging necessities of researchers without resources of their own, and outside of big international collaborations. The Portuguese and Spanish NGIs offer support to a set of macro VOs with a traditional relation with e-Science domains, focused on specific scientific disciplines like Physics or Life Sciencies, and serving users from different areas:

Virtual Organisation

Scientific Discipline

phys.vo.ibergrid.eu

Physics and Space Sciences

life.vo.ibergrid.eu

Life Sciences

eng.vo.ibergrid.eu

Engineering

ict.vo.ibergrid.eu

Information and Communication Technologies

earth.vo.ibergrid.eu

Earth Sciences

social.vo.ibergrid.eu

Social Sciences

chem.vo.ibergrid.eu

Chemistry and Materials Science

Additional, 3 more VOs exist: ops.vo.ibergrid.eu, aimed for regional operations; iber.vo.ibergrid.eu, for general and transient activities; and tut.vo.ibergrid.eu, for tutorial sessions. Each regional VO was created with two different groups representing the two participating countries, and the user communities may be aggregated as VO subgroups according to their applications. The main advantage with this method is that it will limit the VO growth and minimize the effort involved in configuring VOs at the different Resource Centres. At the same time, this mechanism is general enough to encapsulate the user activity under a national scope, or alternatively, establish an Iberian context for international collaborations between the two countries.

Ibergrid User Applications

The following applications are the ones most representative of the work performed within the IBERGRID macro VOs. Other private code and Home Made Applications are also executed but are not taken into account in this summary:

Application Name

Institute

VO

Discipline

Legacy / Ownership

License

URL

Description

Esys-Particle

IAA-CSIC

phys.vo.ibergrid.eu

Space Sciences

Centre for Geoscience Computing, School of Earth Sciences at the University of Queensland, Brisbane, Australia

OpenSource

https://launchpad.net/esys-particle

ESyS-Particle is Open Source software for particle-based numerical modelling. The software implements the Discrete Element Method (DEM), a widely used technique for modelling processes involving large deformations, granular flow and/or fragmentation

Genetic Hybrid Hierarchical Fuzzy System

IAA-CSIC

eng.vo.ibergrid.eu

A. D. Benítez and J. Casillas

GIPSY

IAA-CSIC

phys.vo.ibergrid.eu

Astrophysics

Kapteyn Institute

OpenSource

http://www.astro.rug.nl/~gipsy/general/whatis.html

GIPSY is an acronym of Groningen Image Processing SYstem. It is a highly interactive software system for the reduction and display of astronomical data. It supports multi-tasking using a versatile user interface, it has an advanced data structure, a powerful script language and good display facilities based on the X Window system

GROMACS

IEM-CSIC

chem.vo.ibergrid.eu

Molecular Dynamics

Herman Berendsen'set al

OpenSource

http://www.gromacs.org/

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

GraCo

IAA-CSIC

phys.vo.ibergrid.eu

Astrophysics

Andrés Moya Bedón

Private

http://arxiv.org/abs/0711.2590

Granada oscillation code (GraCo) is a software constructed to compute adiabatic and non-adiabatic oscillation eigenfunctions and eigenvalues

MESA

IAA-CSIC

phys.vo.ibergrid.eu

Astrophysics

Bill Paxton et al.

OpenSource

http://mesa.sourceforge.net/

Modules for experiments in stellar astrophysics

MITgcm

Iniversity of Balearic Islands

earth.vo.ibergrid.eu

Weather and Clima

Marshall, J., C. Hill, L. Perelman, and A. Adcroft

OpenSource

http://mitgcm.org/

The MITgcm (MIT General Circulation Model) is a numerical model designed for study of the atmosphere, ocean, and climate.

OpenFoam

UPV

eng.vo.ibergrid.eu

Engineering

OpenFoam foundation

OpenSource

http://www.openfoam.com/

OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.

RPMDrate

UCM

chem.vo.ibergrid.eu

Chemical Reactions

MIT

OpenSource

http://web.mit.edu/greengp/RPMDrate/

Software package for using ring polymer molecular dynamics (RPMD) simulations to compute the bimolecular reaction rate coefficients for thermally activated processes in the gas phase.

StartLight

IAA-CSIC

phys.vo.ibergrid.eu

Astrophysics

UFSC

OpenSource

http://astro.ufsc.br/starlight/

Spectral synthesis code to decompose an observed spectrum in terms of a superposition of a base of simple stellar populations of various ages and metallicities, producing astrophysically interesting output such as the star-formation and chemical enrichment histories of a galaxy, its extinction and velocity dispersion

WRF4G

Universidad de Cantabria

earth.vo.ibergrid.ei

Weather and Clima

Santander Meteorology group

http://www.meteo.unican.es/software/wrf4g/

WRF for GRID (WRF4G) is a framework for the execution and monitoring of the WRF Modelling System in distributed computer resources

VO User Registration

User questionnaire

Start by filling the User questionnaire.

This will provide details about activities, applications and resource consumption. The questionnaire will try to capture the scientific problem under study, the application and software dependencies in use, operative details (hardware where the application is normally executed, parallel and latency requirements, operation system, ...) and execution details (storage needs, frequency of runs, requirements on privacy and confidentiality, ...). Through this process, the NGI user support teams will have a notion of how much resources will this community need, which software and hardware necessities are foreseen, redirect the request to the proper VO support, and find the experts to integrate the user community activities in the Iberian production infrastructure.

Request VO Membership

Afterwards, please perform the following steps:

  1. Obtain a certificate from your Certification Authority.
  2. Apply for VO membership (with your certificate loaded in the browser) through the following VO Enrolment URLs.

  3. Provide the necessary information in the web form and accept the VO AUP (see following section for further details)
  4. Confirm you VO membership request within 24h (an email should be sent by the VOMS server to your email).
  5. The VOMS administrators may accept or reject your request depending on the informations you provide in the questionnaire. VO administrators may contact you for further clarifications.
  6. Case you do not received any message withing a period of 5 working days, please contact the VO administrators.

Accept VO Acceptable User Policy

Users which apply to IBERGRID VOs should be aware of the VO Acceptable User Policy, and accept it at registration time. The VOMS VO AUP links are accessible in the following links

A copy of the VO AUPs in place follows:

  • By registering with the Virtual Organization (the "VO") as a GRID user you shall be deemed to accept these conditions of use:
    1. You shall only use the GRID to perform work, or transmit or store data consistent with the stated goals and policies of the VO of which you are a member and in compliance with these conditions of use.
    2. You shall not use the GRID for any unlawful purpose and not (attempt to) breach or circumvent any GRID administrative or security controls. You shall respect copyright and confidentiality agreements and protect your GRID credentials (e.g. private keys, passwords), sensitive data and files.
    3. You shall immediately report any known or suspected security breach or misuse of the GRID or GRID credentials to the incident reporting locations specified by the VO and to the relevant credential issuing authorities.
    4. Use of the GRID is at your own risk. There is no guarantee that the GRID will be available at any time or that it will suit any purpose.
    5. Logged information, including information provided by you for registration purposes, shall be used for administrative, operational, accounting, monitoring and security purposes only. This information may be disclosed to other organizations anywhere in the world for these purposes. Although efforts are made to maintain confidentiality, no guarantees are given.
    6. The Resource Providers, the VOs and the GRID operators are entitled to regulate and terminate access for administrative, operational and security purposes and you shall immediately comply with their instructions.
    7. You are liable for the consequences of any violation by you of these conditions of use.

Ibergrid Infrastructure for VOs

VO Resources

The support of IBERGRID VOs regarding CPU and Storage at the different sites depends on the available resources each site can offer the same level of service. The classification of sites according to their computing and storages capabilities was done according to the following table:

Site Classification

CPU

STORAGE

Type

Description

Sites

Type

Description

Sites

AAA

A minimum of 200 slots are available for the Ibergrid VOs (as a whole) at any time with HIGH PRIORITY. Jobs arriving to that site will enter in execution at the earliest possibility the cluster occupation permits

ARASGRID, BIFI, BIFI-IBERGRID, CETA-GRID, IAA-CSIC, IFCA, IFIC, IFISC, NCG-INGRID-PT

A

Persistent storage is available to the Ibergrid VOs (as a whole) up to a limit of "N TB" (with N > 1 TB).

ARASGRID, BIFI, BIFI-IBERGRID, CETA-GRID, CESGA, CIEMAT-LCG2, CIEMAT-TIC, ESA-ESAC, IAA-CSIC, IFCA, IFIC, IFISC, UPV-GRYCAP

AA

A minimum of 100 slots are available for the Ibergrid VOs (as a whole) at any time with HIGH PRIORITY. Jobs arriving to that site will enter in execution at the earliest possibility the cluster occupation permits

CESGA, UPV-GRYCAP,NCG-INGRID-PT

A

A minimum of 50 slots are available for the Ibergrid VOs (as a whole).

CIEMAT-TIC, ESA-ESAC, SGAI-CSIC

B

The VO is configured, but no resources are reserved. Only oportunistic runs are foreseen to happen.

CAPFE-GRANADA, CIEMAT-LCG2, CFP-IST, IFAE, LCG-USC2, LIP-COIMBRA, LIP-LISBON, PIC, UAM-LCG2, UB-LCG2

B

Non-persistent storage is available (as a whole), with a deadline of 30 days. Files will be deleted by the site administrator when older than 30 days. Each site willing to be in this category needs to configure at least 1TB on this status.

CAPFE-GRANADA, CFP-IST, LCG-USC2, LIP-COIMBRA, LIP-LISBON, SGAI-CSIC, UAM-LCG2, UB-LCG2

-

-

-

C

No support at the level of Storage Element is provided.

IFAE, PIC

Please note that in some cases, sites offering CPU resources in an oportunistic way, might offer a significant amount of resources during off-peak periods (when the owners of the resources are not using them). You can check the real usage of sites by the different VOs below:

  1. VO Activity - Site View

  2. VO activity - Summarized View

VO Activity

Summarized View

The following pictures provides a brief snapshoot of the VO activity during the last month.

gstat-jobs-phys.vo.ibergrid.eu.png

gstat-onlinestorage-phys.vo.ibergrid.eu.png

gstat-jobs-chem.vo.ibergrid.eu.png

gstat-onlinestorage-chem.vo.ibergrid.eu.png

gstat-jobs-eng.vo.ibergrid.eu.png

gstat-onlinestorage-eng.vo.ibergrid.eu.png

gstat-jobs-ict.vo.ibergrid.eu.png

gstat-onlinestorage-ict.vo.ibergrid.eu.png

gstat-jobs-earth.vo.ibergrid.eu.png

gstat-onlinestorage-earth.vo.ibergrid.eu.png

gstat-jobs-life.vo.ibergrid.eu.png

gstat-onlinestorage-life.vo.ibergrid.eu.png

gstat-jobs-social.vo.ibergrid.eu.png

gstat-onlinestorage-social.vo.ibergrid.eu.png

Site View

The following pictures provides a brief snapshoot of normalised CPU time to a reference value of 1000 SpecInt2000 spent by the different VOs at each site

phys.vo.ibergrid.eu.png

chem.vo.ibergrid.eu.png

eng.vo.ibergrid.eu.png

earth.vo.ibergrid.eu.png

ict.vo.ibergrid.eu.png

life.vo.ibergrid.eu.png

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VO Details

Check the ammount and the state of the offered resources (cpu and storage) to IBERGRID VOs through the '''VO Dashboard'''. Through the main VO Dashboard Web interface, visitors can select the appropriated VO (top left combobox) and access VO context information. The full list of applications available through the '''VO Dashboard''' is:

  • EGI Operations Portal: Consult VO ID Card, VO Resource Distribuition.
  • EGI Accounting portal Consult VO Number of Jobs, VO Norm. Sum CPU and VO Norm. Sum Elapsed
  • EGI Helpdesk portal (GGUS): Consult list of VO related tickets
  • GOCDB read and write portals: Consult site information
  • GSTAT portal: Consult number of running and waiting jobs (per site and total), ammount of available resources for the VO, etc...
  • EGI Application Database: Consult VO related applications
  • The central MyEGI instance
  • The VO VOMS-Admin interface: Consult the VO VOMS-Admin interface
  • EGI RT: Consult VO requirements

VO User Support

Users can open a ticket submitting an email to helpdesk-ibergrid@rediris.es . Tickets can also be opened via the RT web page, and in this case, equivalent to what is done in GGUS, additional information can be inserted such as priority, type of problem, site name (gathered from GOCDB), etc...

Contacts

VO Administrators

The following contacts can be used for security or operational issues concerning the IBERGRID VOs:

VO Users

The following contacts can be used to contact VO users. The user mailing lists are syncronized with the membership information available in the VOMS server so that, if a user is added or removed to a VO, the mailing list is properly syncronized.

Additional information

Site Support