RCAC Research Computing Presents: DiaGird Overview

1. INFORMATION TECHNOLOGY AT PURDUE RCAC Research Computing Presents:DiaGird Overview

2. Agenda • What is DiaGrid? • What can DiaGrid do for me today? • How can I make DiaGrid work for me? • User Experience (Prof. Wen Jiang, Biological Sciences) • Q&A • Posters • Meet the team

3. What is DiaGrid? Carol Song Scientific Solutions RCAC

4. What is DiaGrid? http://diagrid.org

5. What is DiaGrid? • Science-as-a-Service • Online applications and tools, no software download or installation • Interactive, graphics user interface • Access to large computing resources, workflow engine • 50,000 HT Condor pool for high throughput computing • Nodes in the community clusters for parallel computation • Instant access: no forms, no wait • Supported infrastructure, 24x7 availability • Feedback for tools, datasets, and other publications • Collaboration and dissemination platform • Group, Project, Forum, Wiki, Sharing, Publishing, etc.

6. What can DiaGrid do for me today? Brian Raub Scientific Solutions RCAC

7. Tools available today What tools can I use today? • BLASTer • SubmitR • CryoEM • GROMACSIMUM • CESM

8. BLASTer • BLAST - popular tool to scan genomes for target sequencing • Searches can contain thousands of sequences • Split input file because all sequences are independent • Greatly improves search speed with the help of HTCondor

9. BLASTer

10. SubmitR • Allows users to submit their R scripts for execution on the community clusters • Supports different execution modes • Single – one process • Parallel – multiple processes communicating with each other • Sweep – many isolated processes with different parameters, inputs or both

11. SubmitR • Users upload and run scripts without having to know technical details of where and how R is executing • Supports a wide range of R libraries: • snow/snowfall • Rmpi • rgdal • Biobase • RSQLite • Request more libraries! • Submit a ticket on DiaGrid to request libraries currently unavailable

12. CryoEM • Analyzes images taken at cryogenic temperatures within an electron microscope to reveal much about microscopic structure of samples • First user-developed tool for DiaGrid • Image processing is a good candidate for parallelization

13. CryoEM • DiaGrid staff helped adapt CryoEM to the HUB environment • Split tasks for image breakdown analysis (HTCondor) • Reassembled the images for 3D visualization using MPI

14. GROMACSIMUM • GROMACS – designed to perform molecular dynamics • First DiaGrid tool to modify and improve an existing open source project • Extends the features of GROMACS GUI and jSimMacs to include new features for high performance computing

15. GROMACSIMUM • A unified interface for all GROMACS simulation tools. • Advanced project management system. • A powerful molecular design and 3D protein visualization tool. • Access your models and data from anywhere in the world.

16. CESM • Global climate model coupling many aspects of Earth sciences research • First DiaGrid tool to provide access to existing Purdue gateway • Purdue developed CESM web gateway and designed it to support multiple interfaces • Provides an alternate interface to the CESM gateway service from within the HUB environment

17. How can I make DiaGrid work for me? Rob Campbell Scientific Solutions RCAC

18. How can I make DiaGrid work for me? • What are my options? • Run an existing tool • Use your existing code • Create a new tool • Let us create - or adapt - a tool for you

19. How can I make DiaGrid work for me? How can I use code I already have? Command line? Use Rappture…  (“Rapid APPlication infrastrucTURE”)  Graphical User Interface (GUI)? Enable it to run on DiaGrid…

20. How can I make DiaGrid work for me? What is Rappture? • Toolkit- makes it easy to develop a GUI for scientific modeling code • Describe your code’s input & output, Rappture automatically builds GUI • Rappture API: get input values, save results –bindings for many programming languages • Embed Rappture in your code - or create a wrapper script around your code • Users see standard graphical controls plus line graphs, contour plots, 3D isosurfaces, …

21. How can I make DiaGrid work for me? • How will my code run on DiaGrid? • Needs cluster resources or parallel execution? •  Tap into HPC resources via “submit” • Inputs and outputs files? •  Upload to remote server via sftp, WebDAV, “importfile” • Pulls data from external sites or databases? •  We can open a connection • Relies on a graphics card for acceleration? •  Will function with performance difference • Requires Windows or Mac? •  Tools run in a Linux/X11 environment •  GUI toolkits and Wine are available

22. How can I make DiaGrid work for me? • What can “submit” do? • Complex job scheduling made easy • Long runners, parallel processing, parameter sweeps • Splits out sweep runs (derives param. combos) • Gathers files • Transports to HPC resource • Schedules & watches job(s) • Returns results submit

23. How can I make DiaGrid work for me? • How can I create something new? • Use Rappture - or a familiar development environment… C/C++ • C/C++ • Fortran • Java • MATLAB • Octave • Perl • Python • Ruby • TCL • More…

24. How can I make DiaGrid work for me? • Can you make a tool for me? • Yes! We can… •  Adapt your existing code •  Or, start with your choice of open source packages •  Or, build a tool from scratch based on your specifications

25. User Experience Professor Wen Jiang Biological Sciences