Transcript Slajd 1 - Projekt PL-Grid
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