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

Overview What is DiaGrid? Supporting Science Tools Gromacsimum Interactive Parallelization Tool (IPT)

What Is DiaGrid ? R Java Data Science C++ To the users DiaGrid 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 DiaGrid 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. Python Java Data Results R Science C++

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 DiaGrid applications execute within a VM. Imbedded Java applet/Html5 interfaces give users access from any web browser. No local installation of anything is required at user’s location.

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

Supporting Science DiaGrid.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 CPU CPU

What is GROMACSIMUM ? GROMACSIMUM is a graphical user interface for popular molecular dynamics package, GROMACS. 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

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, PyMOL and other 3rd party software packages.

Usage: Overview

Interactive Parallelization Tool (IPT) 16

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,OpenMP, and CUDA. The supported base languages are C and C++. 

Interactive Parallelization Tool GUI to IPT Workspace on DiaGrid Hub showing the parallelization of the program named “circuit_serial.cpp”

Interactive Parallelization Tool

Looking to the Future… Any other future projects?

Questions? 21