Rcac research computing presents diagird overview
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INFORMATION TECHNOLOGY AT PURDUE. RCAC Research Computing Presents: DiaGird Overview. 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.

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RCAC Research Computing Presents: DiaGird Overview

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Rcac research computing presents diagird overview

INFORMATION TECHNOLOGY AT PURDUE

RCAC Research Computing Presents:DiaGird Overview


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

What is DiaGrid?

Carol Song

Scientific Solutions

RCAC


Rcac research computing presents diagird overview

What is DiaGrid?

http://diagrid.org


Rcac research computing presents diagird overview

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.


Rcac research computing presents diagird overview

What can DiaGrid do for me today?

Brian Raub

Scientific Solutions

RCAC


Rcac research computing presents diagird overview

Tools available today

What tools can I use today?

  • BLASTer

  • SubmitR

  • CryoEM

  • GROMACSIMUM

  • CESM


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

BLASTer


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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.


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

How can I make DiaGrid work for me?

Rob Campbell

Scientific Solutions

RCAC


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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…


Rcac research computing presents diagird overview

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, …


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

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…


Rcac research computing presents diagird overview

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


Rcac research computing presents diagird overview

User Experience

Professor Wen Jiang

Biological Sciences


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