Top Banner
EuroGrid EuroGrid - Seamless Access to Seamless Access to Computer Resources with Computer Resources with Unicore Unicore Piotr Bala ICM Warsaw University – Warsaw (PL) N. Copernicus University – Toru (PL) Funding by European Commission Grant No. IST-1999-20247 (EUROGRID) and IST-2001-32257 (GRIP) EUROGRID Vision Build a European Grid infrastructure that gives users a seamless, secure access to High Performance Computing resources and that advances computational science in Europe
17

EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

Mar 19, 2018

Download

Documents

ngokhanh
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Page 1: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

EuroGridEuroGrid -- Seamless Access to Seamless Access to Computer Resources with Computer Resources with

UnicoreUnicore

Piotr Bała

ICM Warsaw University – Warsaw (PL)

N. Copernicus University – Toru� (PL)

Funding by European Commission Grant No. IST-1999-20247 (EUROGRID) and IST-2001-32257 (GRIP)

�������������� ������������������������������������������������ �

EUROGRID Vision

Build a European Grid infrastructure

that gives users

a seamless, secure access to

High Performance Computing resources

and that advances computational science

in Europe

Page 2: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ �

UNICORE architecture

UNICORE Client

UNICORE Gateway A

UNICORE Server

(NJS)

TSI

NQE (Cray T3E)

UNICORE Gateway B

UNICORE Server

(NJS)

TSI

PBS (Linux cluster)

Insecure Internet

�������������� ������������������������������������������������ �

UNICORE Security

� Based on the PKA� Industrial standard X509

� Secure communication• Gateway, NJS cetificates

• Gateway, NJS check user certificate

• Multiuple CA accepted

� User certificates• User certificate stored in client• Public key stored in UUDB database at each site

• PKA mapped to user account (XLOGIN)

– more than one certificate can map to xlogin

– multiple CA allowed

• Multiple certificates allowed

Page 3: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ �

EUROGRID resources

� European HPC GRID testbed� Agreement on security standards, certification, access policies

etc.

CRAY SV1 (16PE)NEC SX4B/2ALinux Cluster (4 PE)Linux Cluster (16PE)

SGI O2000 (64 PE)SGI Onyx 2000 (64PE)IBM SP4

CRAY T3E - 1200 (816 PE)FUJITSU VPP300 (8 PE)SGI O2000 (128 PE)SGI O3000 (256 PE)Sony Playstation2

IBM SP3 (8 PE)NEC SX5 cluster (40 PE)IBM Power4 (256 PE, 1.3 TFLOPS)COMPAQ Linux Cluster (24 PE)

Linux Intel Cluster (36 PE)IBM (1PE)CRAY T3E - 600 (512 PE)CRAY T3E - 1200 (512 PE)

FZJ

�������������� ������������������������������������������������ �

UNICORE Client

� Single application � Job preparation� Job monitoring

Page 4: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������

UNICORE Client

�������������� ������������������������������������������������ !

UNICORE Client – Gaussian98 job preparation

Page 5: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ ��

UNICORE Client – edit resources for job

�������������� ������������������������������������������������ ��

UNICORE Applications

� Job files for user applications• script tasks• command tasks• file transfer tasks (client-vsite, vsite-vsite)

� Plug-in for job and input preparation

� User can run the same script at all VSITEs • Introduction of IDB entries for site dependent installation

�"#�#$!�%���&�&��'� !�(�)*������"#�#$!�

�+�$$,-.-/�"%���&�&�0 �1�&! (�)*������+�$$,-.-/�"

+��-"2#�-%���&��'3)��(�)*�����+��-"2#�-

�2+"��%���&�����''����3��)*)���4)�����''(�)*������2+"��

Page 6: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ ��

Gaussian98 in EUROGRID

�������������� ������������������������������������������������ �4

BioGRID

� UNICORE Client (ver 3.6.7) unix and Windows• Easy installation (www.unicore.org)

� Example jobs: • Gaussian98

• Amber• Gromos

� Plugins• Gaussian98

• AMBER

• CPMD (Unicore Plus project)

• PDB Search• List Jobs

•Local Model (DWD, SCSC)

•Crash code (T-Systems)

•Electromagnetic code (EADS)

•Fluent (Unicore Plus project)

•Nastran (Unicore Plus project)

Page 7: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ ��

Gaussian98 plugin

Input preparationreads existing input, recognizes keywords

Molecule coordinate editorformats: •XYZ•Z-matrix•text

�������������� ������������������������������������������������ ��

Gaussian98 plugin

CPU time estimatebased on known algorithm scaling O(N4)

Checks program avaliability

Page 8: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ ��

Gaussian98 plugin

Prepares and transfers files for visualization

�������������� ������������������������������������������������ ��

Gaussian98 plugin

Output

Page 9: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ �!

Amber 6.0 plugin

Input preparation

�������������� ������������������������������������������������ ��

Amber 6.0 plugin

Input can be edited by user

Errors are marked in red

Page 10: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

�������������� ������������������������������������������������ ��

Amber 6.0 plugin

Panel for each group of options

Default options

Help window

�������������� ������������������������������������������������ ��

Amber 6.0 plugin

Find parameter button

Page 11: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ �4

CPMD plugin

CPMD input

�������������� ������������������������������������������������ ��

PDB search plugin

Litesearch

Page 12: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ ��

PDB search plugin

User can use different mirrors

The best one is selected(fastest answer)

�������������� ������������������������������������������������ �

PDB search plugin

Visualization with external packages

Page 13: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ �!

PDB search plugin

Search results

�������������� ������������������������������������������������ 4�

PDB search plugin

Rasmol

JMV

Jmol

User-defined

Page 14: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ 4�

List All Jobs Plugin

�������������� ������������������������������������������������ 4�

File filter plugin

Pick up job from JMC

Define file to process

Submit job

Page 15: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ 4�

File filter plugin

Tail of the Amberstatus file

�������������� ������������������������������������������������ 4�

BioGRID

� Operate a GRID for biomolecular simulations

� Develop interfaces to existing biological andchemical codes

� Web site: biogrid.icm.edu.pl

Page 16: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ 4!

UNICORE 4.0

� UNICORE 4.0• Loops, conditional execution

� Plugins available for 4.0• List All Jobs Plugin

• PDB Search Plugin• Gaussian98 Plugin

• CPMD Plugin (V. Huber)

� Work in progress:• Amber plugins should be available soon

• Text and graphical postprocessing

• Resource Broker (UoM)• Interactive Access (Parallab)

�������������� ������������������������������������������������ ��

GRIP Project

Extend EUROGRID to cooperativity with

globus middleware.

Provide UNICORE users with access to

resources avaliable trough globus.

Page 17: EuroGrid -Seamless Access to Computer Resources … and GRIP... · EuroGrid -Seamless Access to Computer Resources with Unicore ... NQE (Cray T3E) UNICORE ... An Uniform Platform

��

�������������� ������������������������������������������������ ��

Dissemination - papers

� A. Nowinski, K. Nowinski, P. BałaWeb based system for wavepacket dynamicsLecture Notes in Computer Science 2329, pp. 552-561

� J. Pytli � ski, Ł. Skorwider, P. Bała, M. Nazaruk, K. WawruchBioGRID - uniform platform for biomolecular applicationsLecture Notes in Computer Science 2400, pp 881-884

� J. Pytli � ski, Ł. Skorwider, K. Bednarczyk, V. Huber, P. BałaUNICORE - An Uniform Platform for Chemistry on the GridJournal of Computational Methods in Science and Engineering 2 (3s-4s) p.

369-376

� P. Bała, B. Lesyng, D. ErwinEUROGRID – European Computational Grid TestbedJournal of Parallel and Distributed Computing (in press)

� J. Pytli � skiMaster degree in computer science thesis, UMK 2002

� Ł. SkorwiderMaster degree in computer science thesis, UMK 2002

Funding by European Commission Grant No. IST-1999-20247 (EUROGRID) and IST-2001-32257 (GRIP)

biogrid.icm.edu.pl

www.eurogrid.org

Piotr Bała

J. Pytli�ski, Ł. Skorwider, M. Wro

�ski, K.

Benedyczak, J. Wypychowski, A. Nowi�ski,

M. Nazaruk, K. Wawruch

ICM Warsaw University (PL) N. Copernicus University – Toru

� (PL)