1. RCAC Research Computing Presents: DiaGird Overview Tuesday, September 24, 2013

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 2

3. What is DiaGrid? Carol Song Scientific Solutions RCAC

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

5. What is DiaGrid? 5 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 7

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 8

9. BLASTer 9

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 10

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 11

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 12

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 13

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 14

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. 15

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 16

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

18. How can I make DiaGrid work for me? 18 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? 19 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? 20 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? 21 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? 22 What can “submit” do? Complex job scheduling made easy Long runners, parallel processing, parameter sweeps Splits out sweep runs (derives param. combos) 1.Gathers files 2.Transports to HPC resource 3.Schedules & watches job(s) 4.Returns results submit

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

24. How can I make DiaGrid work for me? 24 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