Facilitating access to the scientific data service with the use of the Data

Management System

Cezary Mazurekmazurek@man.poznan.pl

Agenda

• Introduction• Data management issues• Data Management System –

functionality and architecture• Accessing SRS resources• Conclusions

R&D Center

• PSNC was established in 1993 and is an R&D Center in:– New Generation Networks

• POZMAN and PIONIER networks• 6-NET, ATRIUM, Muppet,

– HPC and Grids• GRIDLAB, CROSSGRID, VLAB,

PROGRESS projects, Clusterix, HPCEuropa

– Portals and Content Management Tools• Polish Educational Portal "Interkl@sa",

Multimedia City Guide, Digital Library Framework,Interactive TV

PROGRESS (1)

• Project Partners– SUN Microsystems Poland– PSNC IBCh Poznań– Cyfronet AMM, Kraków– Technical University Łódź

• Co-funded by The State Committee for Scientific Research (KBN) and SUN Microsystems Poland

PROGRESS (2)

• Deployment phase (2004)– Grid constructors– Computational applications developers– Computing portals operators

• Enabling access to global grid through deployment of PROGRESS open source packages

PROGRESS (3)

• Cluster of 80 processors

• Networked Storage of 1,3 TB

• Software: ORACLE, HPC Cluster Tools, Sun ONE, Sun Grid Engine, Globus

Wrocław

Gdańsk

Polish Optical Internet PIONIER

Data Management Issues

• Hiding the data management complexity from the end user

• Ability to use new standards defined by grid organizations

• Cooperation with the different kinds of applications

• Providing seamless access to data and information for grid computing

• Enabling intuitive and efficient method for resource exploration

• Facilitating interface to data management for administrators and scientists

PROGRESS

PROGRESS Communication

HPC PortalGrid

Service Provider

DataManagement System

GridResource Broker

saveJob()getApplications()getTemplates()saveTaskOfJob()saveStdOfTask()submitJob()getUserJobs()getJobStatus()

listUserDirectory()addUserFile()

getUserFileLocation()

submitJob() changeTaskStatus()

Web Services and Progress

PORTLETSPORTLETS GRID SERVICEGRID SERVICEPROVIDERPROVIDER

DATADATAMANAGEMENTMANAGEMENT

GRID GRID RESOURCERESOURCE

BROKERBROKER

WSWS

Data Management System

• A distributed system enabling the management of grid data files

• Storing files in distributed storage modules of various types: generic filesystems, archivers, relational databases

• Uses metadata to describe files• Allows access to data banks like a mirror of

Sequence Retrieval System• Exposes its functionality within the Data

Broker Service

DMS Functionality

• Virtual file system keeping the data organized in a tree structure.– Metadirectories - hierarchize other objects– Metafiles - represent a logical view of computational

data regardless of their physical storage’s location.

• DMS provides its services in a form of Web Services API to the front-end applications.

• DMS is a middleware system, belonging to the collective layer as well as the resource layer (Data Container), according to the grid services view.

DMS Functionality

• Web Services interface with storing, access, describing and delivery of data.– directory mgmt.: e.g. add, remove and rename

directories, retrieve root and current path, change path,– file mgmt.: e.g. add, remove and rename files, add,

remove and retrieve physical file location,– metadata mgmt.: e.g. retrieve list of schemes and

attributes, assign schemes to files and edit values– external datasource mgmt.: e.g. databanks content

retrieving, entry resolving, databanks exploring

DMS Architecture

Data Broker

• Serves as an interface (Web Services) for external clients, such as the HPC Portal and the grid resource broker

• Mediates in the flow of all requests directed to the DMS.

• Authorizes the client that submitted the request

• Data Broker is distributed in the data management environment

Metadata Repository

• Central and single point of metadata management• Responsible for all metadata operations and their

storage and maintenance.• It stores the following sorts of information:

– metadata about resources: data files, its physical localization and possible way to access them,

– metadata about rights: all information related to the rights – users, their groups, access rights.

– metadata describing the standards of file description, e.g. Dublin Core (DC)

– metadata about services: data brokers, data containers

Data Container

• Enables access to physical data

• Data is arranged in Data Containers and can be stored on various media types

• Data can be organized as files on generic filesystems, BLOBs in databases or files on data tapes

• Each Container possesses a uniform interface regardles of media types which they manage

• Container do not perform file transfers but it uses the external services and demons, like FTP, HTTPS, GASS, GRIDftp

Proxy (SRS Container)

• Enables access to external scientific databases• Includes both Repository (listing entries,

retrieving attached metadata, building queries) and Data Container (downloading files) functionality

• DMS treats the Proxy as a separate, independent module, that manages read-only data

• Within the PROGRESS grid-portal environment the Proxy (named SRS Container) enables access to SRS resources

Administrative Portal

• Web application letting user handle DMS through the web browser

• An intuitive interface allowing to execute superset of DMS services

• Basic and extended interface (regarding user privileges)

• An effective way to explore huge SRS resources • Online, sensitive help

SRS

• Sequence Retrieval System• Platform for biological databases

integration• Delivers uniform data querying interface

for resources retrieval• Integration of application performing

computational tasks on data stored in SRS resources

SRS Resources in PSNC

• Genbank Release (about 32 mln of entries)Updates (about 2 mlns of entries)

• EMBL - European Molecular Biology Laboratory Release (about 42 mln of entries)Updates (about 2 mln of entries)

• PDB – Protein Data Bank• Swissprot

Swissprot Releas, Swissprot New, SPTREMBL, REMTREMBL

SRS Installation

• Installation uses different storage recources• Data access interface delivered via common portal

(srs.man.poznan.pl)• Administrative tasks (retrieval and data

preparation) splited onto different machines• Parallel data retrieving from remote resources• Offline data indexing and packing on

computational machine (0.5Tb storage)• Compressed online data (2*250Gb storage)

SRS Installation - Schema

storage 02

SRSsrs.man.poznan.pl

offlineonline

indexing offindex flatfiles

storage 01

flatfilesindex

viola.man.poznan.pl

bellis-e.man.poznan.pl

SRS Container• Using shell-based access to the SRS

– Operations commited to execute using SRS mechanisms are send via shell command

• Access interface based on Web Services– Internal functionality delivered using SOAP communication

• Data access - ftp, gsiftp, gass protocols– Data are accessed with using external file servers integrated

with SRS module

• Advanced caching system– Databanks and entries are cached and reused in next user

requests

Portal Interface – databanks list

Portal Interface – databank content

Portal Interface - searching

Portal Interface – search results

Portal Interface – copying entries

Portal Interface – file properties

DMS Installation Requirements

• Java virtual machine, recommended Java(TM) 2 Runtime Environment, Standard Edition 1.4.1 or higher.

• Database server. DMS is ready to cooperate with Oracle and PostgreSQL engine:– Oracle - Oracle8i or higher recommended– PostgreSQL - version 7.3 or higher is required with the

additional extends:• chkpass and tablefunc

from contrib package• plpqsql support

Conclusions

• SRS resources have been integrated with the distributed file structure of DMS

• A web interface enhances the efficiency of the SRS resources exploration:– fast copying an interesting entries directly to the users’ home

directory– merging files– saving files in the different format (e.g. Fasta)

• The universal access layer to the to the scientific databases may by successfully used to connect other data sources to the Data Management System (e.g. digital libraries).

In Closing

• Check http://dms.progress.psnc.pl for more information about DMS

• Download it now: http://progress.psnc.pl/English/opensource.html

• Mail DMS team: szd@man.poznan.pl