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Monday, July 18 • 8:00am - 12:00pm
Tutorial: XSEDE New User Tutorial: Using Science Gateways

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Overview: This tutorial will build upon the well-attended, well-reviewed XSEDE15 tutorial (http://sched.co/3YdG). The purpose of this tutorial is to supplement the standard XSEDE new user tutorial with overviews of how to use science gateways so that the new users can start using XSEDE for scientific research right away, at the conference, and continue at their home institution, without getting bogged down in the allocation process at the beginning. The tutorial is also appropriate for XSEDE Campus and Domain Champions who are interested in using science gateways to support their outreach and support work on their local campuses. The target audience members are scientists in particular domains (chemistry, neuroscience, atmospheric science) who are new to XSEDE and who optionally are familiar with common software packages in their field, but who do not have deep experience with using supercomputers and clusters. Campus Champions who work closely with new users are also encouraged to attend. The tutorial will provide a brief overview of XSEDE and the science gateway program, including a list of other available gateways not covered by the tutorial. The bulk of the tutorial will be a sequence of hands-on activities that introduce attendees to domain specific gateways. The tutorial organizers will work with XSEDE conference organizers and the outreach team to recruit new user attendees from the selected domains.

Attendees will not need to be researchers in a specific science domain to participate in a specific gateway exercise. The organizers will provide all required input files and data for the exercises. Attendees will be encouraged to work with gateway providers on their specific research problems. Each hands on session will demonstrate how to create an account on the science gateway; how to create, submit, and monitor a submission of a specific application code; and how to retrieve final results. Each session will also include a feedback opportunity to help new users understand the additional capabilities of each gateway and optionally try out attendee-provided input data. The following are participating gateways.

CIPRES (http://www.phylo.org/sub_sections/portal/) is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to large computational resources of XSEDE through a simple browser interface. The CIPRES Science Gateway provides access to a number of important parallel phylogenetics codes to insure the fastest possible run times for submitted jobs. Users configure job runs by completing a web form; on submission the user-entered information is used to configure the runs efficiently on XSEDE resources. CIPRES has supported 17,000+ users and 2,000+ publications in all areas of biology since 2009. Example tutorial material: http://www.phylo.org/tools/flash/cipresportal2_data_management.htm and http://www.phylo.org/tools/flash/cipresportal2_task_management.htm

SEAGrid (http://seagrid.org) enables researchers to run commonly used computational chemistry codes such as Gaussian, Lammps, Tinker and other applications on XSEDE resources. GridChem has been used by about 600 users since 2005, supporting more than 100 research papers, and more than 10 Graduate theses. The science gateway registered with XSEDE SEAGrid provides a Java desktop client called GridChem and manages user registration and jobs and related data through a virtual organization and transparently provided through the client. Example tutorial information: https://scigap.atlassian.net/wiki/display/SEAGrid/SEAGrid+Documentation

The Neuroscience Gateway (NSG - http://www.nsgportal.org) facilitates access and use of NSF’s High Performance Computing (HPC) resources by neuroscientists. NSG offers to computational neuroscientists free supercomputer time acquired using an NSG-managed allocation. Through a simple web-based portal, the NSG provides an administratively and technologically streamlined environment for uploading models, specifying HPC job parameters, querying running job status, receiving job completion notices, and storing and retrieving output data. Neuronal simulation tools provided by NSG includes NEURON, GENESIS, Brian, PyNN, NEST, and Freesurfer. More tools are added based on users’ requests. Example tutorial information: http://www.nsgportal.org/tutorial.html

The Apache Airavata Test Drive Gateway is a general purpose gateway that can be used to execute a wide range of codes, including computational chemistry, bioinformatics, computational fluid dynamics, and weather modeling applications. The Test Drive gateway can also be used to quickly enable new XSEDE applications to be available through a Web interface. This module of the tutorial will allow users to configure an advanced, non-hydrostatic numerical weather prediction model (WRF-ARW) through a graphical user interface, specifying physics and numerical techniques options, selecting analyses for initial/boundary conditions. The generated model outputs will be displayed as plots generated by the NCAR graphics library. Example tutorial information:(Walk through users to perform a generic WRF tutorial but utilizing XSEDE resources http://www2.mmm.ucar.edu/wrf/OnLineTutorial/)

avatar for Suresh Marru

Suresh Marru

Member, Indiana University
Suresh Marru is a Member of the Apache Software Foundation and is the current PMC chair of the Apache Airavata project. He is the deputy director of Science Gateways Research Center at Indiana University. Suresh focuses on research topics at the intersection of application domain... Read More →

Monday July 18, 2016 8:00am - 12:00pm EDT
Bayfront B