InSilicoLab : from Generic Solutions to Application-Specific - - PowerPoint PPT Presentation

Joanna Kocot, Mariusz Sterzel, Tomasz Szepieniec, Maciej Golik, Tomasz Grabarczyk, Tomasz Twaróg, Piotr Wójcik

ACC CYFRONET AGH,

• ul. Nawojki 11, 30-059 Kraków, Poland

InSilicoLab:

from Generic Solutions to Application-Specific Science Gateway

The Idea of InSilicoLab

• Workspace gathering all that a

researcher needs for their in silico experiments

› Enabling performing large-scale, long- lasting data- and computation-intensive experiments › Facilitating categorisation and description of data

• Enabling searches and browsing

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For Whom?

• Reaserchers from different domains
• f science

› Whose experiments are composed of different activities – creating non-trivial workflows › Who need control over the flow of their data and organizing it › Who want to collaborate within a group

• r with other groups

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For Whom?

• Computational Chemistry

› Simulation of the solute-solvent system at the Molecular Dynamics level › Reduction of the system

• Selection of the solute with its solvation shell
• Selection of relevant frames

› Performing quantum-chemical calculations for large sets of data › Analysis and comparison of results › Visualisation at every stage

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How to create a useful system?

• Analysing the researchers work:

› Specific group › Ways of working › Common problems

• We intend to aid in solving SPECIFIC

problems

• We cannot support solving ANY scientific

problem

› We assume it cannot be done in a universal and comprehensive way

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For Computational Chemistry

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For Whom?

• Cherenkov Telescope Array

› Simulation of the behaviour of a telescope with different configurations, including, e.g.:

• Camera configuration
• Trigger – filtering

› Analysis and comparison of results

• Integration of results from many experiments

› Reconstruction of the original event › Dedicated software that has to be installed on machines + hand-made scripts › Large input and output files

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How to reuse the existing solution and stay useful?

• Using the same model
• Reusing common parts
• Creating a specific tool, but:

› Having the general model in mind, › Thinking how the new solutions could be used to improve others

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For Cherenkov Telescope Array

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InSilicolab Features

• Environment for running experiments on

computer infrastructure

› Parallelization of tasks › Application- and domain-specific interface

• Data management

› Automatic attachment of metadata › Possibility to tag and annotate data objects › Results of one experiment can directly serve as input to another › Tracking of the data objects origin

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InSilicoLab Architecture

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Data Management Experiment Management Result Management Specification Execution Browsing Analysis Reuse Sharing Classification Preparation Storing Viewing Provenance Provenance Tracking Data Structure Annotations Tagging Metadata Model Automatic Parallelization Execution Engine Experiment Logic Computational Resources Storage Resources Metadata Repository

Domain Layer

Managed by the user

Mediation Layer

translation from domain- to resource-specific language

Resource Access Layer

access to e-infrastructures

How to start in a new domain?

• Discover a pattern in the researchers work

› A joint effort of the developers and the researchers teams

• Put it down as experiment logic

› Implement input and results management › Specify metadata descriptions

• Adjust interface

› Input specification › Result display › If neccessary: new data types management

This can be done also by people who are not InSilicoLab developers

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Validation

• MHD code created at Centre for Astronomy,

Nicolaus Copernicus University in Toruń, Poland

› http://piernik.astri.umk.pl/

• Integration with the InSilicoLab framework was

performed by the Piernik application developer

› Only aided by the InSilicoLab team

• First prototype created in less than one month
• Production deployment planned for September

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Validation

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Summary

• InSilicoLab is an abstract model of creating

specific portals/science gateways

• Available to researchers performing in silico

experiments in many domains of science

• Operational in three different instances:

› Computational Chemistry › Cherenkov Telescope Array › Piernik for AstroGrid-PL (Beta)

• Open for new collaborations

› Planned: Biochemistry portal

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http://insilicolab.cyfronet.pl insilicolab@cyfronet.pl Thank you!