1 Kihyeon Cho & Soonwook Hwang (KISTI) Super Belle with FKPPL VO & AMGA Data Handling.

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Kihyeon Cho &Kihyeon Cho &Soonwook Hwang Soonwook Hwang

(KISTI)(KISTI)

Super Belle with FKPPL VO Super Belle with FKPPL VO & AMGA Data Handling& AMGA Data Handling

ContentsContents

KISTI Super computing Center FKPPL VO Farm Super Belle Data Handling Summary

FKPPL VO Grid TestbedFKPPL VO Grid Testbed

GoalGoal

Background Collaborative work between KISTI and CC-IN2P3 in the area of

Grid computing under the framework of FKPPL Objective

(short-term) to provide a Grid testbed to the e-Science summer school participants in order to keep drawing their attention to Grid computing and e-Science by allowing them to submit jobs and access data on the Grid

(long-term) to support the other FKPPL projects by providing a production-level Grid testbed for the development and deployment of their applications on the Grid

Target Users FKPPL members 2008 Seoul e-Science summer school Participants

FKPPL TestbedFKPPL Testbed

Service Host Site

UI kenobi.kisti.re.kr KISTI

VOMS palpatine.kisti.re.kr KISTI

WMS/LB snow.kisti.re.kr KISTI

SE ccsrm02.in2p3.fr (0.5TB) CC-IN2P3

hansolo.kisti.re.kr (1.5TB) KISTI

CE cclcgceli03.in2p3.fr (5000 CPU cores) CC-IN2P3

darthvader.kisti.re.kr (100 CPU cores) KISTI

VOMS

WMSCE

SE

UI

CE

SE

FKPPL VO

KISTIIN2P3

LFC WIKI

VO Registration Detail Official VO Name

fkppl.kisti.re.kr

Description VO dedicated to joint research projects of the

FKPPL(France Korea Particle Physics Laboraroty), under a scientific research programme in the fields of high energy physics (notably LHC and ILC) and e-Science including Bioinformatics and related technologies

Information about the VO https://cic.gridops.org/index.php?section=vo

FKPPL VO Usage

Application porting support on FKPPL VO Geant4

Detector Simulation Toolkit Working with National Cancer Center

WISDOM MD part of the WISDOM drug discovery pipeline Working with the WISDOM Team

Support for FKPPL Member Projects

Grid Testbed for e-Science School Seoul e-Science summer school

How to access resources in FKPPL VO Testbed

Get your certificate issued by KISTI CA http://

ca.gridcenter.or.kr/request/certificte_request.php

Join a FKPPL VO membership https://palpatine.kisti.re.kr:8443/voms/fkppl.k

isti.re.kr

Get a user account on the UI node for FKPPL Vo Send an email to the system administrator at

[email protected]

User Support

FKPPL VO Wiki site http://anakin.kisti.re.kr/mediawiki/index.php/FKPPL_VO

User Accounts on UI machine 17 User accounts have been created

FKPPL VO Registration 4 users have been registered as of now

Contact Infomation Soonwook Hwang (KISTI), Dominique

Boutigny (CC-IN2P3) responsible person [email protected], [email protected]

Sunil Ahn (KISTI), Yonny Cardenas (CC-IN2P3) Technical contact person, [email protected], [email protected]

Namgyu Kim Site administrator [email protected]

Sehoon Lee User Support [email protected]

Monday, December 2, 2008Yonny CARDENAS

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KISTI site

VOMS, WMS, CE+WN*, UI, Wiki* Infrastructure installation in progress ( a cluster with 128 cores has

been purchased)

CC-IN2P3 site

CE+WN, SE, LFC

Configuration


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VO Registration procedure

– VO name: fkppl.kisti.re.kr

– VO manager: Sunil Ahn

– Status: Active

Configuration

Monday , December 2 , 2008Yonny CARDENAS

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Status (Operational Services)

KISTI site: VOMS OK WMS OK CE OK WIKI OK SE OK WN* in Progress

CC-IN2P3 site: SE OK dCache/SRM OK WN OK CE OK LFC OK

Monday, December 2 , 2008Yonny CARDENAS

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Available Services

Job Submission

Available since October 1, 2008

Resource allocation: 5 millions hours CPU SI2K

CC-IN2P3 Job monitoring

Quality of Service

Operation team

Monday , December 2 , 2008Yonny CARDENAS

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Available Services

Data storage

dCache SE/SRM

System for storing and retrieving data, distributed among a large number of heterogeneous server nodes.

Implements the SRM v2.2 interface required EGEE/LCG

Resource allocation: 0.5 Terabytes


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Available Services

Data storage

AFS (Andrew File System)

Network file system for personal and group files, experiment software, system tools (compilers, libraries , ... )

Indirect use (jobs)

Resource allocation: 2 Gigabytes

Monday, December 2 , 2008Yonny CARDENAS

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Available Services

Data storage

LFC - LCG File Catalog

Maintains mappings between logical file names (LFN) and SRM file identifiers.

Supports references to SRM files in several storage elements.


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Utilisation - Services

Jobs Submission

October

34 jobs for 150 hours CPU SI2K

November 1690 jobs for 48250 hours CPU SI2K


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Utilisation - Services

Data Storage

7193 files for 60 G bytes of used space

• 440 G bytes available.

User SupportUser Support

FKPPL VO Wiki site http://anakin.kisti.re.kr/mediawiki/index.php/FKPPL_VO

User Accounts on UI 20 User accounts has been created

FKPPL VO Membership Registration 7 Users have been registered at FKPPL VO membership

FKPPL VO UsageFKPPL VO Usage

Deployment of Geant4 applications on FKPPL VO Detector Simulation Toolkit Working with Jungwook Shin at National Cancer

Center

Grid Interoperability Testbed

Geant4 Application: GTR2_com Geant4 Application: GTR2_com Application name: GTR2_com (G4 app for proton therapy sim s/w by developed by NCC) -> GTR2 : Gantry Treatment Room #2, com: commissioning

(now GTR2 simulation code is under commissioning phase)

-> libraries: Geant4 , root (root.cern.ch) as simulation output library

/user/io/OpenFile root B6_1_1_0.root/GTR2/SNT/type 250/GTR2/SNT/aperture/rectangle open#Geant4 kernel initialize/run/initialize /GTR2/FS/lollipops 9 5/GTR2/SS/select 3/GTR2/RM/track 5/GTR2/RM/angle 80.26 /GTR2/VC/setVxVy cm 14.2 15.2/beam/particle proton/beam/energy E MeV 181.8 1.2 /beam/geometry mm 3 5/beam/emittance G mm 1.5/beam/current n 3000000#SOBP/beam/bcm TR2_B6_1 164 /beam/juseyo/user/io/CloseFile

user macro

output

GTR2_com

GTR2_com 의 input 은 nozzle 의 configuration 이며 , 이 configuration 이 명시된 macro 파일을 읽어서 최종 양성자 빔에 의한 선량분포를 3D-histogram 의 root 파일로 출력

Distribution of the completion time of 1000 Distribution of the completion time of 1000 GTR2_com jobs on FKPPL VO GTR2_com jobs on FKPPL VO

The submission of 1000 GTR2_com jobs was done around 18:05

BC408 M.C study

Purpose : the accurate simulation study will help to design and construct a dosimetry device

utilizing the BC408 scintilator

BC408 M.C on FKPPL resolution : 2mm in X,Y and 1mm

thicknes

From 1 file, ~3.5 hrs on WN of FKPPL

From 589 files, 589 files sucessfully generated among total 99*7 (693)

jobsTrial # Total job Completed Err

1 99 65 34

2 99 66 33

3 99 99 0

4 99 98 1

5 99 84 15

6 99 80 19

7 99 97 2

693 589 104

I immediately submit parametric job after initializing the proxy

Super Belle Data HandlingSuper Belle Data Handling

Super Belle ComputingSuper Belle Computing

Conveners: T. Hara, T. Kuhr

Distributed Computing (Martin Seviour) Data Handling (Kihyeon Cho) Data Base (Vacant)

Super Belle Data HandlingSuper Belle Data Handling

Data Handling depends on distribution computing. Cloud Computing? Grid farm?

Data Handling Suggestions (2/17) SAM (Sequential Access through Metadata)

CDF by Thomas Kuhr

AMGA KISTI by Soonwook Hwang

EGEE (Enabling Grids for E-SciencE)EGEE (Enabling Grids for E-SciencE)

• the largest multi-disciplinary grid infrastructure in the world

Objectives• Build large-scale, production-quality

grid infrastructure for e-Science

• Available to scientists 24/7

EGEE grid Infrastructure• 300 sites in 50 countries• 80,000 CPU cores• 20 PBytes• 10,000 User

Overview of AMGA (1/2) Overview of AMGA (1/2) Metadata is data about data AMGA provides:

Access to Metadata for files stored on the Grid A simplified general access to relational data stored in database systems.

2004 – the ARDA project evaluated existing Metadata Services from HEP experiments AMI (ATLAS), RefDB (CMS), Alien Metadata Catalogue (ALICE) Similar goals, similar concepts Each designed for a particular application domain

Reuse outside intended domain difficult Several technical limitations: large answers, scalability, speed, lack of flexibility

ARDA proposed an interface for Metadata access on the GRID Based on requirements of LHC experiments But generic - not bound to a particular application domain Designed jointly with the gLite/EGEE team

Overview of AMGA (2/2) Overview of AMGA (2/2)

What is AMGA ? (ARDA Metadata Grid Application) Began as prototype to evaluate the Metadata Interface

Evaluated by community since the beginning: Matured quickly thanks to users feedback

Now part of gLite middleware : EGEE’s gLite 3.1 MW

Requirements from HEP community Millions of files, 6000+ users, 200+ computing centres Mainly (real-only) file metadata Main concerns : scalability, performance, fault-tolerance, Support

for Hierarchical Collection

Requirements from Biomed community Smaller scale than HEP Main concerns : Security

ARDA Project (A Realisation of Distributed Analysis for LHC)ARDA Project (A Realisation of Distributed Analysis for LHC)

Metadata user requirementsMetadata user requirements

I want to store some information about files

In a structured way query a system about those information keep information about jobs

I want my jobs to have read/write access to those information

have easy access to structured data using the grid proxy certificate

NOT use a database

Metadata ConceptsMetadata Concepts Schema (table, think directory)

Has hierarchical name and list of attributes /prod/events

Attributes (columns) Have name and storage type Interface handles all types as strings

Entry (row) Live in a schema, assign values to attributes

Collections A set of entries associated with schema

Query SELECT ... WHERE ... clause in SQL-like or SQL query language

AMGA data organizationAMGA data organization

Relational schema AMGA(hierarchy)

/HOSPITAL//HOSPITAL/

PATIENTS/PATIENTS/ DOCTORS/DOCTORS/

johnjohn george

george

#name sickness age

john malaria 68

george otitis 84sickness otitis

age 84

Attributes

Entries

Schema/Directory

Schema/Directory

TABLE: PATIENTS

#name

PATIENTS

DOCTORS

TABLE: HOSPITAL

Collection

#type

people_group

people_group

Importing existing dataImporting existing data

Suppose that you have the data A reasonable question would be:

Can I use my existing database data?? The answer is YES

Importing data to AMGA Pretty simple Connect a database to AMGA

Execute the import command import table directory

Ready to go!

AMGA Use CasesAMGA Use Cases

AMGA Features in One SlideAMGA Features in One Slide Official gLite middleware component for metadata catalogue Metadata is relationally structured

Schema (aka table, think directory)Has hierarchical name and list of attributes /prod/events

Attributes (aka columns)Have name and storage type, Interface handles types as strings

Entry (aka row)Live in a schema, assign values to attributes

Query: SELECT ... WHERE ... clause in SQL Fine grained access control (ACL) support

Table level and entry level Tight integration into the Virtual Organization Management System (VOMS)

X509 Grid certificate Native SQL support in AMGA 1.9

Direct DB access to existing databases on the Grid via SQL OGF WS-DAIR compatible interface support in AMGA 2.0 Uniform interface to Heterogeneous Database backend

Oracle, Postgres SQL, MySQL, etc. Support for Many Programming APIs

Diverse user community requested/provided e.g., C/C++, Java, Python, Perl, PHP

Replication Support Full replication, Partial replication, Federation

Support for “Import of pre-existing databases”

AMGA WebsiteAMGA Website

http://amga.web.cern.ch/amga

To doTo do

Prototype of AMGA Using Belle flat form, we will use AMGA

(Namkyu Kim and Dr. Junghyun Kim) Belle flat form => flag

Using Super Belle flat form (Grid or Cloud computing), we will use AMGA.

1 Kihyeon Cho & Soonwook Hwang (KISTI) Super Belle with FKPPL VO & AMGA Data Handling.

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