Polish Infrastructure for Supporting Computational Science in the European Research Space

The Capabilities of the GridSpace2 Experiment Workbench

M. Bubak, E. Ciepiela, J. Kocot, J. Meizner, and P. Nowakowski

Distributed Computing Environments Team Academic Computer Centre CYFRONET Cracow Grid Workshop 11.10.2010

EUROPEAN UNION

Motivation

      Complex scientific applications on modern computing infrastructures  Clusters, Grids, Clouds Diverse software packages  Applications (Gaussian, NAMD,…)  Web Services  Scripts: Perl, Python, Ruby Different users   Chemists, biologists Programmers  End users Various data types  Files, databases, URLs Exploratory programming  Unstructured, dynamic, prototyping Collaboration  Teams, communities

GridSpace2 Objectives

 Facilitate dealing with application throughout its entire lifecycle (development, deployment, sharing, operation, maintenance) from single “workbench” where all available software is integrated  Reflect and support a natural daily style of work with a suite of software – workflows, (not formalized) procedures, task paths etc.

 Addresses a specific type of application called

experiments

GridSpace2 Experiment

 Experiment - a process that combines a sequence of activities (usage of programs, services) that act on input data in order to produce experiment results   Experiment plan – a specification of the sequence of activites Experiment run – an enactment of the experiment plan on particular input data, producing particular results   Complex workflow going beyond manual simple and repeatable execution of single programs Exploratory programming  Unstructured, dynamic, prototyping, further activities not known a priori

GridSpace2 Features

 Platform – as opposed to concrete application  General-purpose  Exploits Web 2.0 opportunities in facilitating application development, operation, provisioning

GridSpace2 Experiment Plan

 Combines steps realized on a range of software environments, platforms, tools, languages etc  Developed, shared and reused collaboratively amongst ad-hoc researching teams  Composed of collaboratively owned libraries and services used (called

gems

) and experiment parts (called

snippets

)

Exploratory Programming

     Involves experimentation and exploring – step by step programming where steps are likely not known in advance but rather provided ad-hoc basing on the results of previous ones Experiment needs to be re-enacted many times with some ad-hoc customization made dynamically while the workflow enactment has already started Cannot be fully automated and needs continuous supervision, validation or even intrusion Dynamic nature of experiment plan – certain decisions taken at runtime (e.g. code provided from input data)

But

: Despite its indirect development process experiment still needs to be traceable, verifiable, easily re-runnable and its outcome – straightforwardly reproducible,

Working with GridSpace2

 Easy access using Web browser 

Experiment Workbench

 Constructing experiment plans from code snippets  Interactively run experiments 

Experiment Execution Environment

  Access to libraries, programs and services (gems)  Access to

computing infrastructure

 Multiple interpreters Cluster, grid, cloud 8

Application: Analysis of water solutions of aminoacids

 Involving multiple steps realized with many tools, langauges and libraries used for      Packmol – molecular dynamics simulations of packing molecules in a defined regions of space Jmol – visualization of solution Gaussian – computing a spectrum of the solution Python/CCLIB – extracting spectrum info jqPlot – displaying plot Collaboration with computational chemists of ACC Cyfronet AGH and Departament of Chemistry, Jagiellonian University, Dr. Mariusz Sterzel, Klemens Noga

Conclusions

 Complex scientific applications need dedicated tools and approaches.

 In-silico experiments are supported by Virtual Laboratory powered by GridSpace2 technology.

 Applications:  Bioinformatics  Computational chemistry  More are welcome!

 Virtual laboratory is open for PL-Grid users.

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References

 http://wl.plgrid.pl

– open the Virtual Laboratory in your browser  http://dice.cyfronet.pl/gridspace – learn more about GridSpace technology  http:/dice.cyfronet.pl/ – Distributed Computing Environemnts Team (DICE) website 11