INFSO-RI-508833 Enabling Grids for E-sciencE CHARON System Petr Kulhánek, 1,2 Jan Kmuníček,

INFSO-RI-508833

Enabling Grids for E-sciencE

www.eu-egee.org

CHARON System 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

EGEE project is funded by European Commission (contract number IST-2003-508833) 2


INFSO-RI-508833

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



INFSO-RI-508833

• GRID Vocabulary

• VOCE – Virtual Organization for Central Europe

• UI – user interface• SE – storage element• CE – computing element• WN – worker node

CHARON System



INFSO-RI-508833

CHARON System

• Summary of User Authentication/Authorization in GRID

• grid-proxy-init or grid-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).



INFSO-RI-508833

• Job Submission in Native LCG Middleware

Example #01: 01_lcg_test

edg-job-submit lcg_job.jdl

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

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

CHARON System

# 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;



INFSO-RI-508833

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



INFSO-RI-508833

CHARON System

• Scheme of Charon (CEL - Charon Extension Layer)



INFSO-RI-508833

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



INFSO-RI-508833

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

nam e[: [: [: ]]]ve rsion a rch itectu re para lle lm ode



INFSO-RI-508833

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



INFSO-RI-508833

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



INFSO-RI-508833

• 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 System



INFSO-RI-508833

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



INFSO-RI-508833

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



INFSO-RI-508833

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

CHARON System

[jobdir]$ equi.rst isomaltose.top prep.in

lsmyjob

# sander calculation on VOCEmodule add ambersander -O -i prep.in \ -p isomaltose.top \ -c equi.rst -o prep.out \ -x prep.traj -r prep.rst

M olecu la r D ynam ics o f Isom a ltose



INFSO-RI-508833

CHARON System

Job name : myjobGrid job name : myjob (Job type: generic)Job directory : skurut4.cesnet.cz:/home/kulhanek/jobdirJob project : -none-========================================================Alias : -none-Organization : voceProfile : default----------------------------------------NCPU : 1Resources : -job match-Properties : -none-Sync mode : gridcopy----------------------------------------Start after : -not defined-========================================================Do you want to submit job to GRID environment (YES/NO) ? YES

Please wait packing data ...Submiting job ...

Job was successfully submitted to GRID environment.

[jobdir]$ voce myjobpsubmit

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



INFSO-RI-508833

CHARON System

[jobdir]$ pinfo

Job name : myjobJOb ID : https://skurut3.cesnet.cz:9000/bx06C-R9mB5uquZarwpCPQGrid job name : myjob (Job type: generic)Job directory : skurut4.cesnet.cz:/home/kulhanek/jobdirJob project : -none-========================================================Alias : -none-Organization : voceProfile : default----------------------------------------NCPU : 1Resources : -job match-Properties : -none-Sync mode : gridcopy----------------------------------------Start after : -not defined-========================================================Job was submited at : 2005-10-12 14:16:28 and was queued for : 0d 00:04:28Job was started at : 2005-10-12 14:20:56 and was running for : 0d 00:02:12Job was finished at : 2005-10-12 14:23:08

• pinfo



INFSO-RI-508833

CHARON System

[jobdir]$ psync

Starting synchronization procedure. downloading sandbox ... completing data ... dowloading data from SE ... unpacking result archive ... cleaning ...Synchronization was successfully finished !

• psync



INFSO-RI-508833

CHARON System

[jobdir]$

prep.in myjob.cesout mdinfoisomaltose.top myjob.jdl prep.trajmyjob myjob.info prep.rst

lsequi.rst myjob.ces myjob.stdout

prep.out

inpu t file s

resu lts

con tro l file s

M olecu la r D ynam ics o f Isom a ltose

• Results



INFSO-RI-508833

CHARON System

• Other Examples

• Example #03: 03_complex_job

psubmit skurut get_pdbs

• Example #04: 04_parallel_sander

psubmit skurut md_test 2



INFSO-RI-508833

• 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



INFSO-RI-508833

• palias

CHARON System

$ 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



INFSO-RI-508833

• 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



INFSO-RI-508833

• 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)

CHARON System

INFSO-RI-508833 Enabling Grids for E-sciencE CHARON System Petr Kulhánek, 1,2 Jan Kmuníček,

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Transcript of INFSO-RI-508833 Enabling Grids for E-sciencE CHARON System Petr Kulhánek, 1,2 Jan Kmuníček,