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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http://egee.cesnet.cz/en/voce/Charon.html
slide2

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:

skurut4.cesnet.cz:/home/kulhanek/cesnet_seminar/<example>

        • input directory contains fresh input data
        • test directory contains results of test run
slide3

CHARON System

  • GRID Vocabulary
    • VOCE – Virtual Organization for Central Europe
    • UI – user interface
    • SE – storage element
    • CE – computing element
    • WN – worker node
slide4

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).

slide5

CHARON System

  • Job Submission in Native LCG Middleware

Example #01:01_lcg_test

edg-job-submitlcg_job.jdl

edg-job-statushttps://skurut3.cesnet.cz:9000/AXyE-vQ04qcFfM-kQFe6QQ

edg-job-get-output–dir ./ https://skurut3.cesnet.cz:9000/AXyE-vQ04qcFfM-kQFe6QQ

# 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)

slide8

CHARON System

  • Activation of CEL on UI of VOCE

1.login to skurut4.cesnet.cz

2.type following command:

/afs/ics.muni.cz/software/ncbr/voce/migrating/install_charon

3.logout from skurut4.cesnet.cz

4.login to skurut4.cesnet.cz again

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

  • Deactivation of CEL on UI of VOCE

1.login to skurut4.cesnet.cz

2.type following command:

/afs/ics.muni.cz/software/ncbr/voce/migrating/uninstall_charon

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)

avail

list*

* 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

Example:

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

slide12

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
slide14

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 system11
CHARON System
  • Other Examples
    • Example #03: 03_complex_job

psubmit skurut get_pdbs

    • Example #04: 04_parallel_sander

psubmit skurut md_test 2

slide21

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
slide22

CHARON System

  • palias

$ palias

Alias Queue/VO Syncmode Properties Resources

--------------------------------------------------------------------------------------

stdout voce stdout - -

tuke voce gridcopy - ce.grid.tuke.sk:2119/jobmanager-pbs-voce

polgrid voce gridcopy - ce.polgrid.pl:2119/jobmanager-lcgpbs-voce

poznan voce gridcopy - ce.egee.man.poznan.pl:2119/jobmanager-lcgpbs-voce

skurut voce gridcopy - skurut17.cesnet.cz:2119/jobmanager-lcgpbs-voce

zeus voce gridcopy - zeus02.cyf-kr.edu.pl:2119/jobmanager-lcgpbs-voce

slide23

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
slide24

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)

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