Polish InfrastructurePolish Infrastructurefor Supporting Computational Sciencefor Supporting Computational Science

in the European Research Spacein the European Research Space

Recent Advancements of National Grid Recent Advancements of National Grid Infrastructure in PolandInfrastructure in Poland

( (PL-GridPL-Grid))

ACC Cyfronet AGH, Krakow, Poland

Cracow Grid Workshop – CGW’1011-13.10.2010, Krakow, Poland

www.plgrid.pl/enwww.plgrid.pl/en

Jacek Kitowski

2

Acknowledgements

ACC Cyfronet AGH Kazimierz Wiatr Marian Bubak Łukasz Dutka Karol Krawentek Andrzej Oziębło Maciej Malawski Zofia Mosurska Robert Pająk Marcin Radecki Renata Słota Mariusz Sterzel Tomasz Szepieniec Agnieszka Szymańska Teresa Ozga

ICM Piotr Bała Maciej Filocha

PCSS Norbert Meyer Bartek Palak Krzysztof Kurowski Tomasz Piontek Dawid Szejnfeld Paweł Wolniewicz

WCSS Jerzy Janyszek Bartłomiej Balcerek

TASK Rafał Tylman Mścislaw Nakonieczny

3

Outline

General Introduction to PL-Grid Project Motivation, consortium and objectives PL-Grid and EGI Organization of the project

Current Status and Advancements Status of hardware infrastructure Operational Centre – tasks and services e-Infrastructure software, software packages and user’s tools Training and user support Security aspects

Conclusions – Future work

4

PL-Grid Consortium Consortium Creation – agreement signed January 2007

a response to requirements of Polish scientists and due to ongoing Grid activities in Europe within the framework of EGI_DS.

Consortium members – make up of 5 Polish supercomputing and networking centres: Academic Computer Centre CYFRONET AGH, Krakow (coordinator) Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University Poznan Supercomputing and Networking Centre Academic Computer Centre, Gdansk Wroclaw Centre for Networking and Supercomputing

PL-Grid Project proposal got funded by the European Regional Development Fund as part of the Innovative Economy Program on March 2, 2009.

Result: First working NGI in Europe in the framework of EGI.eu

The Consortium consists of five High Performance Computing Polish Centres representing Communities, coordinated by ACC Cyfronet Participation in international and national projects

35+ international projects FP5, FP6, FP7 on Grids (~50% common)(~45 currently, including EDA)

15+ Polish projects (~50% common)

Polish scientific communities ~75% highly rated Polish publications in 5 Communities

Computational resources Top500 list

European/Worldwide integration Activities EGEE I-III, EGI_DS, EGI, e-IRG, PRACE, DEISA, OMII, EU Unit F3 „Research Infrastructure” Experts,

Representatives in EGI Council, Members of EGI Executive Board

National Network Infrastructure available Pionier National Project

5

Rationales behind PL-Grid Consortium

Rank Site System Cores Rmax (TFlops) Rpeak (TFlops)

161 Cyfronet AGH Krakow Cluster Platform 3000 BL2x220, L54xx 2.5 Ghz, Infiniband / 2010 Hewlett-Packard 6144 39.93 55.54

181Gdansk University of Technology, CI Task ACTION Cluster Xeon E5345 Infiniband /

2008, Action 5336 38.17 49.73

444 PCSS Poznan Cluster Platform 3000 BL 2x220, E5530 2.4 GHz, Infiniband GDR / 2010, Hewlett-Packard 3456 26.22 31.24

TOP500 – June 2010

6

PL-Grid Project - Basic Data

The Project is co-funded by the European Regional Development Fund as part of the Innovative Economy Program.

Total budget: 83 M PLN (~ 21 M EUR)• Personel cost 27 M PLN (~7 M EUR)• Equipment cost 33 M PLN (~8 M EUR)• Other cost 23 M PLN (~6 M EUR)

Funding from the EC: 68 M PLN (~ 17 M EUR) Project duration: 01 January 2009 – 31 December 2011 Beneficiary: Academic Computer Centre Cyfronet AGH, Krakow, Poland Contract number: POIG.02.03.00-00-007/08

Project website: www.plgrid.pl/en

7

Grid infrastructure (Grid services) PL-Grid

App

licat

ion

App

licat

ion

App

licat

ion

App

licat

ion

Clusters High Performance Computers Data repositories

National Computer Network PIONIER

DomainGrid

Advanced Service Platforms

DomainGrid

DomainGrid

DomainGrid

Main Objectives of PL-Grid

Polish Grid is developing a common base infrastructure – compatible and interoperable with European and Worldwide Grids

Capacity to construct specialized, domain Grid systems – including services and tools focused on specific types of applications

This approach should enable efficient use of available financial resources Plans for HPC and Scalability Computing enabled with more focus on domain specific Grids

Offer for the Users Computing Power 215 Tflops Storage 2500 TBytes Support from PL-Grid staff

on using advanced Grid tools Support on porting legacy codes

to Grid environment Support on designing applications

for PL-Grid environment

8

PL-Grid Building Blocks

PL-Grid software comprises: user tools (portals, systems for

applications management and monitoring, result visualization and other purposes, compatible with the lower-layer software used in PL-Grid)

software libraries virtual organization systems:

certificates, accounting, security, dynamic

data management systems: metadata catalogues, replica management, file transfer

resource management systems: job management, applications, grid services and infrastructure monitoring, license management, local resource management, monitoring

Users

Nationalcomputernetwork

Grid Application

Programming Interface

Virtual organizations andsecurity systems

Basic Grid services

Gridservices

LCG/gLite(EGEE)

UNICORE(DEISA)

OtherGrids

systems

Gridresources

Distributedcomputational

resources

Grid portals, development tools

Distributed data

repositories

Three Grid structures are maintained: production research development / testing

9

EGI.eu – European organization being developed to coordinate the European Grid Infrastructure, based on the federation of individual National Grid Initiatives (NGI), to support a multi-disciplinary user community.

PL-Grid tasks in EGI (planned/fixed) Grid operation and oversight of the

e-Infrastructure Coordination of resource allocation

and of brokering support for VOs from NGIs

Computational Chemistry – organization and management of Computational Chemistry and Material Science and Technology Specialized Support Centre and EGI liaisons

Development of unified middleware via European Middleware Initiative

PL-Grid – first operational NGI in Europe

Integration Activity in the framework of European Grid Infrastructure

Scientific application porting, especially concerning UNICORE architecture, within Application Porting SSC

PL-Grid

On 30 March 2010, Poland - as the first country in Europe - has initiated functioning of the National

Grid Initiative (NGI)

10

Organization of the PL-Grid project

PLANNING AND DEVELOPMENT

OF INFRASTRUCTURE

P2

Coordination Strategic Planning Dissemination

PROJECT MANAGEMENTP1

SECURITY CENTER

P6

Training

SUPPORT FOR VARIOUSDOMAIN GRIDS

P5P4 GRID SOFTWAREAND USERS

TOOLS DEVELOPMENTEGEE DEISA … .

OPERATIONS CENTERP3

Current Status and AdvancementsCurrent Status and Advancements

12

13

Status of Hardware Infrastructure

Computational power CYFRONET: 29,3 Tflops ICM: 13,1 Tflops PCSS: 23,2 Tflops

Disk storage CYFRONET: 313 TBytes ICM: 433 TBytes PCSS: 300 TBytes

Total: 65,6 Tflops Total: 1046 TBytes

Plans until the end of 2010:

Plans until the end of the Project (end of 2011):

185 Tflops

215 Tflops

1900 TBytes

2500 TBytes

Current status (October 2010):

14

Operational Center – just in operation

Tasks Coordination of operations Management and accounting Collaboration with EGI and

PRACE/DEISA Users’ requirements analysis for

operational issues Running infrastructure for:

Production Developers Research

Future consideration: Computational Cloud Data Cloud Internal and External

Clouds Virtualization aspects

15

Services of the Operational Center for Users Operational Center aims at facilitating access to the infrastructure by simplifying the

procedures and deployment of useful tools: System of registration of account management of the PL-Grid user

• available at https://konto.plgrid.pl/• required entry in the Polish database of „People of Science” or confirmation

of the scientific tutor• grid access to PL-Grid resources

5 centers – gLite 1 center – UNICORE

• local access to the queue system „zeus” cluster in ACC CYFRONET AGH

• ability of application for a grid certificate on-line• application for access to computational services in other centers

Helpdesk system in PL-Grid• enables reporting and tracking issues• available at https://helpdesk.plgrid.pl (for registered users)• access also by e-mail: helpdesk@plgrid.pl• manual: https://wiki.plgrid.pl/doku.php?id=pakiet5:publiczne:podrecznik_uzytkownika_pl-grid → System

Pomocy Helpdesk

16

Services of the Operational Center for Users (cont’d) Operational Center cares for a proper functioning of the infrastructure for PL-Grid

users by pro-active monitoring of the following infrastructure elements: availability of the infrastructure services software packages supported by PL-Grid

Provision of the conformity of the PL-Grid and European (EGI) infrastructures software operational procedures security procedures

Advanced work on the „PL-Grid grants” idea Integration of the data presentation concerning resources usage for a user Work on provision of the integrated user portal

17

Development of the e-Infrastructure Software and the User’s Tools

Close cooperation of 8 programming and testing groups, about 20 people Installation and provision for testing purposes gLite, Unicore and QosCosGrid About 30 various configurations of virtual machines with installed software used for

development and testing of the tools for users – the choice of the technology made Functional, conformity and efficiency tests of selected packages of the research

software made in order to perform the deployment and support of the new tools and services on the production level

18

Development of the e-Infrastructure Software and the User’s Tools (cont’d)

Direct contact with new users on the basis of a survey, available at: www.plgrid.pl/ankieta

Requirements of the Polish users (results ~190 surveys) considered in the new applications, tools and services developed and tested in the framework of the Package 4

Large group of users cooperating with the software and tools team Department of Chemistry of the Jagiellonian University Department of Bioinformatics and Telemedicine of the Collegium Medicum of

the Jagiellonian University University of Adam Mickiewicz Poznan Technical University Wrocław Technical University Administrators of the computing centers …

19

Development of the e-Infrastructure Software and the User’s Tools (cont’d)

Test versions of tools for users and systems administrators: Grid Resource Bazaar, mobile access to the infrastructure, new security modules

Extending of the GridSpace2 platform with a set of new functions, support for new scripting languages and integration with new grid services

Integration of the Migrating Desktop and gEclipse tools with various PL-Grid middleware services

Extension and deployment of FiVO – a new tool for VO management and monitoring

Performance and functional tests of middleware service QosCosGrid and integration with gLite and Unicore infrastructure at the queue systems level

Implementation and provision of the advanced graphical interfaces, visualization and tasks and data management for selected user applications via the Vine Toolkit

Integration of the selected tools and web applications with Liferay portal framework and Nagios monitoring system

20

Grid Resource Bazaar Providing resources to users with required

qualities of services Required = specified in Service Level Agreement

RU – Resource UsersRP – Resource Providers

21

Grid Resource Bazaar (cont’d)

Resource Allocation-related Operation Model

22

http://grid.cyfronet.pl/bazaar

Grid Resource Bazaar (cont’d)

23

GridSpace2 Experiment Workbench in the PL-Grid Virtual Laboratory

Use of distributed computational resources and data repositories High-level tools offered for the user for in-silico experiments

24

GridSpace2 - working with the Experiment Workbench

The PL-Grid Virtual Laboratory provides an Experiment Workbench – a Web 2.0 interface supporting the development and execution of in silico experiments.

Working with the Experiment Workbench: Open the workbench in your browser

(https://wl.plgrid.pl) Log into one of the available servers with your PL-

Grid account Start your usual work. Your files are already there.

Your code snippets may play the role of scripts (in Python, Perl, Ruby etc.), bash commands or input to external applications (such as Gaussian or Gnuplot);

All the files you generate may be viewed with visualization tools (such as Jmol)

Save your work – the experiment is now visible among your other files

Share the experiment with other members of your research team

25

GridSpace2 - sample experiment in ViroLab environment

Patient’s data Medical examination HIV genetic sequence put into

database Experiment in-silico

Collect HIV genetic sequences from database

Perform sequence matching Calculate virus resistance

http://gs2.cyfronet.pl/ http://www.virolab.org

26

Migrating Desktop Platform – the Framework for Grid Applications

Main product features: Simple integration with grid applications Easy job defining, submission, monitoring and visualization of results Support for batch and interactive jobs Handling of sequential and parallel applications Intuitive management of grid data Easy extendable framework

Migrating Desktop main window

Description: The Migrating Desktop Platform is a powerful

and flexible user interface to Grid resources that gives a transparent user work environment and easy access to resources and network file systems independently of the system version and hardware

It allows the user to run applications and tools, manage data files, and store personal settings independently of the location or the terminal

27

Migrating Desktop Platform – the Framework for Grid Applications (cont’d)

Application support: The key feature: the possibility of easy

adding various tools, applications and supporting different visualization formats

The Migrating Desktop offers a framework that can be easily extended on the basis of a set of well‑defined plug-ins used for: accessing data, defining job parameters, pre-processing job parameters, and visualization of job results

Open architecture of the Migrating Desktop speeds up the application integration process and makes that product significantly more flexible than specialized tools (e.g. portals) designed only for a specific application

Job defining and visualization of results (examples of Migrating Desktop plug-ins)

28

g-Eclipse – to Access the Power of the Grid

Benefits from using g-Eclipse: Grid application users will benefit from the

desktop-like access to Grid resources Grid operators and resource providers will be able

to reduce the time-to-service by using the Grid management and Grid site configuration tools

Grid application developers will reduce the time-to-market for new Grid applications by accelerating the development and deployment cycle

Features: The g-Eclipse framework provides tools to

customize Grid users’ applications, to manage remote resources and to support the development cycle of new Grid applications

The framework consists of general Grid workbench tools that can be extended for many different Grid and Cloud middleware’s (such as gLite, UNICORE, Globus Toolkit, Amazon Cloud)

29

g-Eclipse – to Access the Power of the Grid (cont’d)g-Eclipse elements (functionalities): Grid Virtual Organisation management allows the

dynamic creation and management of Virtual Organisations and their resources

Grid job management supports Grid users and developers in creating and managing Grid jobs independent of the middleware

Grid file management provides access and management of local and foreign resources which are seamlessly integrated into the Eclipse Workbench

Grid application deployment supports Grid application developers and Grid application users with the deployment of their applications on the Grid

g-Eclipse provides API and User Interface modules for all above functionalities.

Grid visualisation tools offer functionalities that allow the visualisation of scientific and numerical calculations

Grid workflow builder supports the creation and management of middleware independent workflows by use of a provided graphical editor

Grid command console is a command line interface to access the Grid

30

FiVO/QStorMan toolkit – the goals

Provisioning PL-Grid users an appropriate quality of access to storage systems with the following means: Definition of the non-functional requirements for the storage systems, e.g.

expected transfer rate of the read/write operations or parameters related to expected availability level of the resource or security.

Monitoring of the storage systems parameters, e.g. a distributed file system. Data localization management based on the provided requirements and the

current state of an environment.

QStorMan is a part of the Framework for Inteligent Virtual Organization (FiVO)

31

FiVO/QStorMan toolkit - architecture and components

Components of the toolkit: Portal – a graphical user interface for

defining requirements for storage systems

GOM (Grid Organizational Memory) – a knowledge base for storing semantic

description of the storage systems along with defined requirements

SMED – a knowledge-supported monitoring system

SES (Storage Element Selection) library – a programming library for selecting storage resource based on provided requirements and current state of the environment

SE – Storage Element

32

QCG – QosCosGrid MiddlewareDescription: The QosCosGrid (QCG) middleware is an integrated e-infrastructure

offering advanced job and resource management capabilities to deliver to end-users supercomputer-like performance and structure

By connecting many computing clusters together, QosCosGrid offers easy-to-use mapping, execution and monitoring capabilities for variety of applications, such as parameter sweep, workflows, MPI or hybrid MPI-OpenMP

QCG architecture

33

QCG – QosCosGrid Middleware (cont’d)

Benefits: for End Users – efficient and secure access to

dynamically discovered computational resources located in the PL-Grid environment

for Cluster and Grid Administrators – a great opportunity to share and use their clusters more efficiently by scheduling local and Grid end users’ applications according to defined policies and constraints

Several portal based and mobile applications have been developed and integrated with QCG

infrastructure to give the users intuitive - experiment and domain oriented - access to resources.

QCG mobile client

34

Vine Toolkit – Distributed Resources at Your Fingertips for Developers and End Users

Main features: Single Sign-On – users log in once and use all resources Support for different grid infrastructures Advanced web applications (integration with Adobe Flex / BazeDS technology) Extensible, module based open architecture based on plugins Many applications included „out-of-the-box” such as: Job Manager, File Manager,

Resource Manager, Credential Manager, Certificate Manager, GSI-SSHTerm applet Support for scientific applications: ABINIT, Quantum Espresso (and others…) Integration with portal environments Liferay and GridSphere installed on Tomcat server

General description: Vine Toolkit was designed as an environment to facilitate the development

and integration of web-based applications with HPC resources, Grid services and various existing large-scale computing infrastructures managed by Grid middleware, such as gLite, Unicore, Globus, QosCosGrid and GRIA.

It is possible to create a computational web-based Science Gateway using a modular structure and existing Vine components.

35

Vine Toolkit – Distributed Resources at Your Fingertips for Developers and End Users (cont’d)

For whom: web applications developers – a base for building advanced

computational scientific portal gateways and applications with many ready to use components, integration layer for portal frameworks and advanced installation engine

administrators of grid infrastructures – possibility of deployment of a web portal “out-of-the-box” to access existing grid infrastructure

end users – many ready to use web applications for grid computations and data management in grid infrastructure

scientists – dedicated web applications for scientific applications for different scientific domains

Example of the advanced web interface in the Nano-Science Gateway based on Vine Toolkit

36

Scientific software packages

Access to software packages is provided to users through: gLite UNICORE

Examples of available packages in various fields: biology: AutoDock, BLAST, ClustalW2, CPMD, Gromacs, NAMD quantum chemistry: ADF, CFOUR, Dalton, GAMESS, Gaussian, Molcas, Molpro,

MOPAC, NWChem, OpenBabel, Siesta, TURBOMOLE physics: ANSYS FLUENT, Meep numerical computations and simulation: Mathematica, MATLAB other: Blender, POV-Ray

Users may report us their expectations through a survey available at:http://www.plgrid.pl/ankieta

The system of testing the software packages in the grid environment has been prepared and deployed

The correctness of functioning of the packages is monitored automatically in each of the centers

37

Training and Users’ Support

Basic training on access to the PL-Grid infrastructure through gLite and UNICORE conducted in all centers participating in the project – in Gdańsk / Kraków / Poznań / Warszawa / Wrocław

More advanced training started Similar (free) training may be conducted in other centers, if necessary eLearning courses offered through the Blackboard system ( available for

registered users of the PL-Grid infrastructure) Helpdesk system implemented

it’s a novel support system for people using the Project resources it involves the technical support and organization of the current users’

support by the experts (maintenance of trouble tickets) tickets in Helpdesk may be created by sending an email to:

helpdesk@plgrid.pl or through the online system, available at: https://helpdesk.plgrid.pl

38

Security in PL-Grid

Provision of two CAs – PKI certification centers – for grid users Project and implementation of the SimpleCA system, facilitating the

users obtaining PKI certificates and their usage Project and implementation of the secure configuration of the

infrastructure, in conformity with the most actual security standards Project of the system monitoring the conformance of the

configuration deployed in the centers with the security policy Creation of the group of experts from the field of security, in order to

continuously monitor the environment, immediate react on incidents and support users and administrators

Prototype version of the system of correlation of information about the attacks on the infrastructure (ACARM-ng)

Audits of applications crucial for grid security

ConclusionsConclusions

Good and promising partial results of the PL-Grid Project Justified expectations to Project completion according to its goals and

requirements Generic services and generic applications in development

Futher developement needed, as identified currently, mainly on Domain Specific Grids

Request from the users’ communities Capacity for organization of future development according to

Expertise and experience Strong scientific potential of the users’ communities being represented by PL-

Grid Partners Wide international cooperation concerning the Consortium and individual

Partners, good recognition worldwide Good managerial capacity

39

40

http://www.plgrid.pl/en