CHARON Syst e m egee.cesnet.cz/en/voce/Charon.html
description
Transcript of CHARON Syst e m egee.cesnet.cz/en/voce/Charon.html
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
Enabling Grids for E-sciencE
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
EGEE project is funded by European Commission (contract number IST-2003-508833) 3
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• GRID Vocabulary
• VOCE – Virtual Organization for Central Europe
• UI – user interface• SE – storage element• CE – computing element• WN – worker node
CHARON System
EGEE project is funded by European Commission (contract number IST-2003-508833) 4
Enabling Grids for E-sciencE
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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).
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Enabling Grids for E-sciencE
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• 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;
EGEE project is funded by European Commission (contract number IST-2003-508833) 6
Enabling Grids for E-sciencE
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
EGEE project is funded by European Commission (contract number IST-2003-508833) 7
Enabling Grids for E-sciencE
INFSO-RI-508833
CHARON System
• Scheme of Charon (CEL - Charon Extension Layer)
EGEE project is funded by European Commission (contract number IST-2003-508833) 8
Enabling Grids for E-sciencE
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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
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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
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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
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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
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• 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
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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
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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
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• 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
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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]
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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
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CHARON System
[jobdir]$ psync
Starting synchronization procedure. downloading sandbox ... completing data ... dowloading data from SE ... unpacking result archive ... cleaning ...Synchronization was successfully finished !
• psync
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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
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CHARON System
• Other Examples
• Example #03: 03_complex_job
psubmit skurut get_pdbs
• Example #04: 04_parallel_sander
psubmit skurut md_test 2
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• 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
EGEE project is funded by European Commission (contract number IST-2003-508833) 22
Enabling Grids for E-sciencE
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• 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
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• 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
EGEE project is funded by European Commission (contract number IST-2003-508833) 24
Enabling Grids for E-sciencE
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