Application porting and web services for the Molecular and Materials - - PowerPoint PPT Presentation

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Application porting and web services for the Molecular and Materials - - PowerPoint PPT Presentation

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Application porting and web services for the Molecular and Materials Sciences and Technologies community Alessandro COSTANTINI 1 , Daniele CESINI 1 , Diego MICHELOTTO 1 , Marco BENCIVENNI 1 , Vania BOCCIA 1 , Emidio GIORGIO 1 , and Antonio

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Application porting and web services for the Molecular and Materials Sciences and Technologies community ¡

Alessandro COSTANTINI1, Daniele CESINI1, Diego MICHELOTTO1, Marco BENCIVENNI1, Vania BOCCIA1, Emidio GIORGIO1, and Antonio LAGANA’2

1 INFN/IGI (IT) 2 Univ. of Perugia

¡

¡alessandro.costan:ni@pg.infn.it ¡

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Summary

  • The Italian NGI
  • The User Community: CMMST
  • The computational problem
  • Code Porting: 3 from the CC environment
  • A smart solution: IGI web portal
  • Conclusions
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Train users to use the new execution procedure Disseminate the work done to find new applications for long term sustainability Seek, identify, and closely support new communities to deploy their applications and create the computing model

Work-plan for application porting

The NGI_IT

User Support and Training (FUS in

Italian) team

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The CC domain in EGI

  • CC EGI Virtual Organizations (VO)s

– COMPCHEM , GAUSSIAN, CHEM.VO.IBERGRID.EU – Researchers out of the existing CC VOs

Normalised CPU time K.SI2K.Hours 1/2013 - 1/2014 COMPCHEM 18,311,531 GAUSSIAN 278,244 CHEM.VO.IBERGRI D.EU 2,137,536 TRGRIDB 222

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The training workshop

First Training Workshop on Grid porting of computational chemistry applications (Rome, 20-21 January 2014) Organizers

  • COMPCHEM Virtual Organisation
  • Italian NGI User Support and Training unit (IGI-FUS)

In collaboration with

  • GARR consortium, the Italian National Research and Education Networks

(NREN)

  • INSTM consortium, the National Institute of Materials Science and

Technology Active participation of 22 young researchers from 12 different departments of the various national institutes, including a remote participant from the Spanish National Research Council (CSIC) in Madrid.

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The training workshop

  • Main objectives

– give an overview, from a user perspective, of the Grid infrastructure in the European context. – give the needed know-how related to the application porting on distributed computing infrastructures.

  • Computational chemistry applications used to solve real-life

GRID use cases:

– VENUS (molecular dynamics) – CRYSTAL (electronic structures of solid materials) – QUANTUM ESPRESSO (electronic structures and modelling)

  • The event was preceded by two on-line meetings

– Aimed at how to cope with the most common issues when accessing distributed resources for the first time.

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Computational requirements

  • Strictly related to the application
  • VENUS (molecular dynamics)

– Parameter study approach – Monitoring of many jobs

  • CRYSTAL

– MPI calculations – Long simulation running

  • QE

– MPI calculations – Many modules, needs complex workflow

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Application porting

  • All the applications have been initially installed and

configured in some of the IGI domain

  • Some scripts have been developed to

– Interact with the middleware – Use MPI job – Checkpointing the job for runtime analysis and restart

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Grid Approach Problem

  • For new Users Grid is complex, they must:
  • have a recognized certificate
  • belong to a Virtual Organization (Certificate is necessary)
  • know JDL and commands syntax
  • know some basic Grid concepts

User Interface Certificate Command Line JDL SRM VO

New unsatisfied Grid Users

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Our solution

IGI WEB Portal

Federation users

CA Online My Proxy Storage User Interface Grid resources Cloud

Complexity hidden

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The IGI Portal facility

  • IGI Portal is a powerful and easy to use gateway to

access the grid:

– Job submission – Data management – Cloud – Application specific

  • Web GUIs has been provided through dedicated portlet

– To access the standard functionalities of the Grid – To minimize the skills needed by the user to use the Infrastructure ¡

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  • Built customizing the DIRAC portlet of the IGI portal
  • The user can set in an easy and intuitive way the needed

parameters, like:

– an identifier label for the submitted jobs, to distinguish each set of submission; – the input file, already stored in the grid Storage Elements (SEs), and selectable from the user with dropdown menu; – the output folder in the grid data management system directory, where the output will be stored; – the number of parameter sweep jobs to be run in a single submission.

VENUS graphical interface

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VENUS graphical interface

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VENUS graphical interface

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  • Built customizing the WS-PGRADE portlet of the IGI

portal

  • IGI Portal acts as a central component for workflow

instantiation

  • Special fields enable the user to define

– type of calculation – kind of resources to be used – number of required cores.

  • Handling the checkpointing of the calculation

– specialized bash functions developed for copying selected files from the Worker Node (WN) to Grid Storage Elements (SEs), – The same solution enables the user to access directly via the Web portal the outcomes, making them available at runtime

CRYSTAL graphical interface

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CRYSTAL graphical interface

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  • Built customizing the WS-PGRADE portlet of

the IGI portal

  • IGI Portal acts as a central component for

workflow instantiation

– Selection of parallel resources – Handling the checkpointing for restart

  • specialized bash functions developed for copying

selected files from the Worker Node (WN) to Grid Storage Elements (SE)s and vice versa

QE graphical interface

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QE graphical interface

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QE graphical interface

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Conclusion

  • CC applications successfully ported to Grid services in strong

partnership with the experienced users in order to address their requirements

  • The adoption of a “web based ad-hoc solution” allows also

inexperienced users to execute programs on the Grid

  • Training event workshop as a pilot activities for dissemination
  • Work in progress to build a solid platform, offered to users as a

service, for assembling accurate multi scale realistic simulations and workflows