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The Capabilities of the GridSpace2 Experiment Workbench

The Capabilities of the GridSpace2 Experiment Workbench. J an Meizner and Distributed Computing Environments (DICE) Team Academic Computer Centre CYFRONET. i3: I nternet - I nfrastruktury - I nnowacje 1-3.12.2010. Motivation.

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The Capabilities of the GridSpace2 Experiment Workbench

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  1. The Capabilities of the GridSpace2 Experiment Workbench JanMeiznerand Distributed Computing Environments (DICE) Team Academic Computer Centre CYFRONET i3: Internet - Infrastruktury - Innowacje 1-3.12.2010

  2. 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

  3. GridSpace2 Objectives Facilitate dealing with application throughout its entire lifecycle (development, deployment, sharing, operation, maintenance)from single “workbench” where all available software is integrated Reflectand 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

  4. GridSpace2 Features • Platform – as opposed to concrete application • General-purpose • Exploits Web 2.0 opportunities in facilitating application development, operation, provisioning

  5. GridSpace2 Experiment Experiment - a process that combines a sequence ofactivities (usage of programs, services) that act on input data in order to produce experiment results Experiment plan – a specification of the sequence of activities 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

  6. GridSpace2 Experiment Plan Combines steps realized on a range of softwareenvironments, 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)

  7. Involves experimentation andexploring – step by step programmingwhere steps are likely not known inadvance but rather provided ad-hocbasing on the results of previous ones Experiment needs to be re-enactedmany times with some ad-hoccustomization made dynamicallywhile the workflow enactment hasalready started Cannot be fully automated and needscontinuous supervision, validation or even intrusion Dynamic nature of experiment plan – certain decisions taken at runtime (e.g. codeprovided from input data) But:Despite its indirect development process experiment still needs to be traceable, verifiable, easily re-runnable and its outcome – straightforwardly reproducible, ExploratoryProgramming

  8. Connectivity via: HTTPS (browser <-> Experiment Workbench) SSH/SCP/SFTP (ExperimentWorkbench <-> Experiment Host) User account context on Experiment Host OS-level accessibility rights to files Snippet code can contain a „secret” literal introduced by meta-markup <SECRET:MY_SECRET_NAME> During the execution this meta-markup is replaced with secret value taken from personal secret database called Wallet Available Wallet implementations: Simple file database located on the Experiment Host Remote Central Wallet (ReCeW) ReCeW (Remote Central Wallet) – key features: Security – HTTPS protected REST API and AES-256 encryption of stored credentials Highly efficient implementation as native (C++) application Extendable through plug-in mechanism (4 types of plug-ins) Security in GridSpace2

  9. Workingwith GridSpace2 Easy access using Web browser Experiment Workbench Constructing experiment plans from code snippets Interactively run experiments Experiment Execution Environment Multiple interpreters Access to libraries, programs and services (gems) Access to computing infrastructure Cluster, grid, cloud

  10. Application:Analysis of watersolutions 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 thesolution 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

  11. 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.

  12. 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

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