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Petr Kulh á nek , 1,2 Jan Kmun íč ek, 1,3 and Martin Pet ř ek 1,2 1. CESNET, Czech Republic 2. National Centre for Biomolecular Research, Masaryk University in Brno, Czech Republic 3. Institute of Computer Science, Masaryk University in Brno, Czech Republic.

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Charon syst e m http egee cesnet cz en voce charon html

Petr Kulhánek,1,2 Jan Kmuníček,1,3 and Martin Petřek1,2

1. CESNET, Czech Republic

2. National Centre for Biomolecular Research, Masaryk University in Brno, Czech Republic

3. Institute of Computer Science, Masaryk University in Brno, Czech Republic

CHARON System


  • Contents

    • GRID Vocabulary

    • Summary of User Authentication/Authorization in GRID

    • Job Submission in Native LCG Middleware

    • Charon Extension Layer

      • Overview

      • Module System

      • Job Submission and Management

      • Configuration

    • Conclusions

  • Examples are in:<example>

    • input directory contains fresh input data

    • test directory contains results of test run

  • CHARON System

    • GRID Vocabulary

      • VOCE – Virtual Organization for Central Europe

      • UI – user interface

      • SE – storage element

      • CE – computing element

      • WN – worker node

    CHARON System

    • Summary of User Authentication/Authorization in GRID

      • grid-proxy-init orgrid-proxy-init-sc

        • grid-proxy-info

      • grid-proxy-destroy

      • myproxy-init or myproxy-init-sc

        • myproxy-info

        • myproxy-get-delegation

      • myproxy-destroy

        NOTE: grid-proxy-init-sc and myproxy-init-sc are not a regular part of LCG distribution. They serve for proxy certificate initialization using secure cards (HW Tokens).

    CHARON System

    • Job Submission in Native LCG Middleware

      Example #01:01_lcg_test



      edg-job-get-output–dir ./

    # LCG Test Job (lcg_job.jdl)

    Type = "Job";

    JobType = "Normal";

    Executable = "/bin/hostname";

    StdOutput = "lcg_job.stdout";

    StdError = "lcg_job.stdout";

    OutputSandbox = {"lcg_job.stdout"};

    Arguments = "";

    RetryCount = 2;

    Charon system
    CHARON System

    What is Charon?

    uniform and modular approach for (complex) computational jobs submission and management

    generic system for use of application programs in the Grid environment (LCG middleware, …)

    Why Charon?

    many various batch systems & scheduling components used in grid environment

    each batch system has unique tools and different philosophy of its utilization

    LCG provided tools are quite raw and simple

    many additional tasks to use computer resources properly

    Charon system1
    CHARON System

    Scheme of Charon (CEL - Charon Extension Layer)

    CHARON System

    • Activation of CEL on UI of VOCE

      1.login to

      2.type following command:


      3.logout from

      4.login to again

      NOTE: CEL installer modify .profile and .bashrc files.

    • Deactivation of CEL on UI of VOCE

      1.login to

      2.type following command:


    Charon system2
    CHARON System

    Module system

    manages application software

    each software package is described by a specific module

    configuration information is internally stored in XML format

    find the architecture and parallel mode that best fit available computational resources

    solve conflicts or dependencies between individual modules

    list available modules sorted into categories

    use pre-installed modules on WNs or install them on the fly

    if they are missing

    Charon system3
    CHARON System

    • Commands of Module System

      • module command: module [action] [module1 [module2] …]

        Most Important Actions:

        add (load)

        remove (unload)



        * list is default action

        NOTE: Type module -h for short summary info about module command.

      • modview command

        • menu driven configuration of visualization of modules

    Charon system4
    CHARON System

    • Module Name Completion


      amber  amber:8.0m:auto:auto  amber:8.0m:pn3:single

      user  default values  resolved final name

      pn3 – module is optimised for Pentium III architecture

      single – module is built for sequential execution

    CHARON System

    • Module Activation

      $ module add amber

      Module specification: amber (add action)


      Architecture : pn3

      Number of CPUs : 1

      Max CPUs per node : 1

      Exported module : amber:8.0m

      Complete module : amber:8.0m:pn3:single

      INFO: Module is taken from local software repository.

    Charon system5
    CHARON System

    • Charon System – Overview of Commands

      Job Submission and Management

      • psubmit

      • pinfo

      • psync

      • pgo (does not work in GRID environment)

        Charon Setup

      • pconfigure

      • palias (deprecated, it will be substituted with pconfigure)

      • pprofile (deprecated, it will be substituted with pconfigure)

      • psum

    CHARON System

    • Charon Job Restrictions

      • each job has to be in separate directory

      • job directories must not overlap

      • job is described by script

      • only relative paths to job directory contents have

        to be used in job script

      • software should be activated by Module System

    Charon system6
    CHARON System

    • Example of Charon Job (Example #02: 02_isomaltose)

    Charon system7
    CHARON System

    psubmit <VO/alias> <jobscript> [NCPU] [syncmode]

    Charon system10
    CHARON System

    • Results

    Charon system11
    CHARON System

    • Other Examples

      • Example #03: 03_complex_job

        psubmit skurut get_pdbs

      • Example #04: 04_parallel_sander

        psubmit skurut md_test 2

    CHARON System

    • Charon Configuration

      • Sync Mode – option for data transfer between UI and WN

        • gridcopy

          – all data within job directory as input

          – all data within job directory as result

        • stdout

          – all data within job directory as input

          – only standard output as result (other data are discarded)

      • Resources – identification of particular CE

      • Properties – fine grained selection of computational resources (throught Requirements item in JDL)

      • Alias - uniform combination of above setup in a single word

    CHARON System

    • palias

    $ palias

    Alias Queue/VO Syncmode Properties Resources


    stdout voce stdout - -

    tuke voce gridcopy -

    polgrid voce gridcopy -

    poznan voce gridcopy -

    skurut voce gridcopy -

    zeus voce gridcopy -

    • Next Release of Charon System (2006)

      • gLite support

      • more batch systems support within single Charon installation

      • simplification of configuration (e.g. only pconfigure will remain)

      • better handling of error states

      • documentation in WIKI

    • What Do We Need ?

      • What type of application software is required by users?

      • What data (type and size) does this software produce or operate with?

      • Do you require parallel execution of application software?

      • suggestions and criticism of Charon System

    CHARON System

    • Conclusions

      • Single job management

        • encapsulation of a single computational job

        • minimization of overhead resulting from direct middleware usage

          (JDL file preparation, etc.)

        • easy submission and navigation during job lifetime

      • Application programs management

        • powerful software management and administration

        • comfortable enlargement of available application portfolio

    • Acknowledgements

      • European Commission (contract number IST-2003-508833)

      • Ministry of Education, Youth, and Physical Training of the Czech

        Republic (contract number MSM0021622413)