Integrating Scientific Tools and Web Portals Kevin Chen

Integrating Scientific Tools and Web Portals Kevin Chen chenk@tacc. utexas. edu

Overview • What is Dia. Grid? • Supporting Science • Tools • Gromacsimum • Interactive Parallelization Tool (IPT)

What Is Dia. Grid ? • To the users Dia. Grid is… • A HUBzero portal for collaboration and community building. • Scientific Software-as-a-Service with easy access to a vast set of computing resources. • A remotely accessible home for research. • To the developers Dia. Grid is… • • A federation of a vast set of computing resources. A pipeline for the whole development process. Managed deployment straight to users. A support platform for communicating directly with end users. Java R Pyth on C++ Data Res ults

The Hardware • Large high-throughput and distributed network, available through HT Condor. • Utilizes spare cycles from: • Campus lab workstations • Departmental desktop computers • XSEDE Resources • Community clusters at Purdue • Coates, Rossmann, Hansen, & Carter • Nearly 100 million jobs run to date!

Building Communities • Users have access to a full inbox-style messaging system.

Supporting Science • The true power of the HUBzero platform lies in transparently bridging the gap between the grid and the web.

Supporting Science • Dia. Grid applications execute within a VM. • Imbedded Java applet/Html 5 interfaces give users access from any web browser. • No local installation of anything is required at user’s location.

Supporting Science • From creation to release, tool development has a full lifecycle managed by the Dia. Grid site. • Published version continues to live on site for users while next version is still in testing. Create Tool Upload/Edit Sources Stage & Test Viewable to Devs Publicly Available Approve? Published!

Supporting Science Dia. Grid. org • The HUBzero team has created the “submit” shell command to abstract grid access for tool developers. • Tools run a subprocess through “submit” to handle all their grid computation needs. • Utilizes Pegasus engine for HT Condor on resources. Tool Session Tool Submit Pegasus HT Condor CPU CPU CPU

What is GROMACSIMUM ? • GROMACSIMUM is a graphical user interface for popular molecular dynamics package, GROMACSIMUM’s combined accuracy and speed make possible long time molecular dynamics simulations. • Seamlessly integrated with newly developed GUI interfaces, GROMACSIMUM provides comprehensive setup, simulation, analysis and job submission tools. • With its highly visual, easy-to-use interface, GROMACSIMUM guides you through each stage of the MD simulation process; in guiding your project workflow, its user friendly environment directs you to a successful outcome. • Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting.

Easy-to-use, instantly interactive • Newly incorporated workflow management system. • A significant relief from tedium of typing and scripting • Easy job submission mechanism. • Dedicated HPC resources.

Easy-to-use, instantly interactive

Data analysis and decision making • Plotting, editing, visual data mining and filtering to identify key interactions. • Trajectory viewing and analysis. • Free energy surfaces, Principal component, Clustering and Secondary structure analysis, . • Seamless support for Xmgrace, VMD, Py. MOL and other 3 rd party software packages.

Usage: Overview

Interactive Parallelization Tool (IPT)

Interactive Parallelization Tool • Interactive Parallelization Tool (IPT) is a semi-automatic tool that can be used by domain experts and students for transforming certain classes of existing applications into multiple parallel variants. • The parallel programming paradigms that are currently supported by IPT are MPI, Open. MP, and CUDA. • The supported base languages are C and C++.