April 21, 2023

Science Gateways and the XSEDE Advanced User Support Services (AUSS) program

Nancy Wilkins-Diehr

Science GatewaysWhat are they?

• A novel concept for accessing supercomputers• Web-based portal or client software front

ends, supercomputers on the back end• Individuals have an account on the portal, but

not the supercomputer• “Community accounts” or service accounts

used to do all the processing for the portal‒ Portal developer keeps track of per user CPU use

How did the Gateway program develop?A natural result of the impact of the internet on worldwide communication and information retrieval

• Implications on the conduct of science are still evolving‒ 1980’s, Early gateways, National Center for Biotechnology Information BLAST

server, search results sent by email, still a working portal today‒ 1989 World Wide Web developed at CERN‒ 1992 Mosaic web browser developed‒ 1995 “International Protein Data Bank Enhanced by Computer Browser”‒ 2004 TeraGrid project director Rick Stevens recognized growth in scientific

portal development and proposed the Science Gateway Program‒ Today, Web 3.0 and programmatic exchange of data between web pages

• Simultaneous explosion of digital information‒ Growing analysis needs in many, many scientific areas‒ Sensors, telescopes, satellites, digital images and video,‒ #1 machine on Top500 today is 10000x more powerful than all combined

entries on the first list in 1993

Less than 20 years since the release of Mosaic!

vt100 in the 1980s and alogin window on Ranger today

Why are gateways worth the effort?

• Increasing range of expertise needed to tackle the most challenging scientific problems• How many details do you

want each individual scientist to need to know?

• PBS, RSL, Condor• Coupling multi-scale codes• Assembling data from

multiple sources• Collaboration frameworks

#! /bin/sh#PBS -q dque#PBS -l nodes=1:ppn=2 #PBS -l walltime=00:02:00#PBS -o pbs.out#PBS -e pbs.err#PBS -Vcd /users/wilkinsn/tutorial/exercise_3../bin/mcell nmj_recon.main.mdl

+( &(resourceManagerContact="tg-login1.sdsc.teragrid.org/jobmanager-pbs") (executable="/users/birnbaum/tutorial/bin/mcell") (arguments=nmj_recon.main.mdl) (count=128) (hostCount=10) (maxtime=2) (directory="/users/birnbaum/tutorial/exercise_3") (stdout="/users/birnbaum/tutorial/exercise_3/globus.out") (stderr="/users/birnbaum/tutorial/exercise_3/globus.err"))

=======# Full path to executableexecutable=/users/wilkinsn/tutorial/bin/mcell

# Working directory, where Condor-G will write # its output and error files on the local machine.initialdir=/users/wilkinsn/tutorial/exercise_3

# To set the working directory of the remote job, we# specify it in this globus RSL, which will be appended# to the RSL that Condor-G generatesglobusrsl=(directory='/users/wilkinsn/tutorial/exercise_3')

# Arguments to pass to executable.arguments=nmj_recon.main.mdl

# Condor-G can stage the executabletransfer_executable=false

# Specify the globus resource to execute the jobglobusscheduler=tg-login1.sdsc.teragrid.org/jobmanager-pbs

# Condor has multiple universes, but Condor-G always uses globusuniverse=globus

# Files to receive sdout and stderr.output=condor.outerror=condor.err

# Specify the number of copies of the job to submit to the condor queue.queue 1

Gateways democratize access to high end resources• Almost anyone can investigate scientific questions using

high end resources‒ Not just those in the research groups of those who request

allocations‒ Gateways allow anyone with a web browser to explore

◦ Opportunities can be uncovered via google» My then 11-year-old son discovered nanoHUB.org himself while his class was

studying Bucky Balls

• Foster new ideas, cross-disciplinary approaches‒ Encourage students to experiment

• But used in production too‒ Significant number of papers resulting from gateways including

GridChem, nanoHUB‒ Scientists can focus on challenging science problems rather than

challenging infrastructure problems

3 steps to connect a gateway to XSEDE• Request an allocation

• Only a 1 paragraph abstract required for up to 200k CPU hours

• Register your gateway• Visibility on xsede.org

• Request a community account• Run jobs for others via

your portal• Staff support is

available!• www.xsede.org/

gateways

Today, there are approximately 35 gateways using the XSEDE

Gateways in the marketplaceKids control telescopes and share images

• “In seconds my computer screen was transformed into a live telescopic view”• “Slooh's users include newbies

and professional astronomers in 70 countries”

• Observatories in the Canary Islands and Chile, Australia coming soon

• 5000 images/month since 2003

• Increases public support for investment in these facilities

CyberGISSoftware Integration for Sustained Geospatial Innovation

• Application of high-end cyberinfrastructure to GIS

• Influence on multiple domains

• Improved decision support• Spatial joins, layers of

multiple datasets at different resolutions

• Goal is core set of composable, interoperable, manageable, and reusable software elements

• Collaborative geospatial problem solving environment

Linked Environments for Atmospheric DiscoveryLEAD

•Providing tools that are needed to make accurate predictions of tornados and hurricanes•Data exploration and Grid workflow

Social Informatics Data GridCollaborative access to large, complex datasets• SIDGrid is unique among social

science data archive projects• Streaming data which change

over time• Voice, video, images (e.g. fMRI),

text, numerical (e.g. heart rate, eye movement)

• Investigate multiple datasets, collected at different time scales, simultaneously

• Large data requirements• Sophisticated analysis tools

• Especially valuable for multi-disciplinary course• Computer science, linguistics,

psychology http://www.ci.uchicago.edu/research/files/sidgrid.mov

Viewing multimodal data like a symphony conductor

• “Music-score” display and synchronized playback of video and audio files• Pitch tracks• Text• Head nods, pause, gesture

references• Central archive of multi-modal data,

annotations, and analyses• Distributed annotation efforts by

multiple researchers working on a common data set

• History of updates• Computational tools

• Distributed acoustic analysis using Praat

• Statistical analysis using R• Matrix computations using Matlab

and OctaveSource: Studying Discourse and Dialog with SIDGrid, Levow, 2008

Now back to Advanced User Support Services

• Really EUSS, not AUSS – extended support‒ But that sounds like something a first grader would

say• Mission is to provide extended support to users in

many areas of cyberinfrastructure‒ Not just for advanced users!‒ Support can last from 1-12 months‒ Requested through allocations process

• Significant area of focus in XSEDE‒ Over one third of total XSEDE funding‒ Extensive and varied expertise

◦ 70 staffers (35 FTEs) at 8 sites

Backdrop against which AUSS exists

Science requires diverse digital capabilities

• XSEDE will be a comprehensive, expertly managed set of advanced heterogeneous high-end digital services, integrated into a general-purpose infrastructure.

• XSEDE is about increased user productivity‒ increased productivity leads to more science. ‒ increased productivity is sometimes the difference

between a feasible project and an impractical one.

Source: John Towns

XSEDE will support a breadth of research

• Earthquake Science and Civil Engineering

• Molecular Dynamics • Nanotechnology • Plant Science • Storm modeling• Epidemiology • Particle Physics• Economic analysis of phone

network patterns

• Brain science • Analysis of large cosmological

simulations • DNA sequencing • Computational Molecular

Sciences• Neutron Science • International Collaboration in

Cosmology and Plasma Physics

Sampling of much larger set. Many examples are new to TeraGrid/HPC. Range from petascale to disjoint HTC to large shared memory, many are data driven. XSEDE will support thousands of projects.

From direct contact with user community as part of requirements collections

Source: John Towns

AUSS Focus Areas

• Advanced Support for Research Teams• Novel and Innovative Projects

• Advanced Support for Community Codes• Science Gateways• Advanced Support for Training, Education and

Outreach

Ralph Roskies

Nancy Wilkins- Diehr

Support available through XSEDE allocations process

• Peer-reviewed• Request CPU time, data

storage and dedicated support from XSEDE staff• https://www.xsede.org/

allocations• AUSS team has expertise

in many areas of cyberinfrastructure, many domains

• Support can last up to a year

Required questions as part of a request

• What do you want to accomplish with the help of advanced support? Have you already done any work on this aspect of your software?

• How would the success of this advanced support benefit your project?

• Which member(s) of your team would collaborate with XSEDE advanced support staff?

• Have you had significant interaction on previous projects related to your current proposal or discussed your advanced support needs with any XSEDE staff? If so, please indicate with whom.

• Have you received TeraGrid/XSEDE advanced support in the past? If so, please indicate the time period, and how the support you received then relates to the support you request now.

Advanced Support for Research TeamsMark Fahey, NICS

• Examples:‒ optimization and scaling of application codes to >100,000 way

parallelism; ‒ aggregating petabyte databases from distributed

heterogeneous sources and mining them interactively; ‒ developing efficient work and dataflow solution for

simulations generating ~100 TB of persistent data per 24-hour run

• Deliverable: ≥20 projects completed per year

Cross-cutting; Novel and Innovative ProjectsSergiu Sanielevici, PSC

• Proactive technical effort to broaden participation in XD‒ novel science areas e.g. biodiversity, linguistics, and

social networks.‒ demographic diversity e.g. researchers based at MSIs

and EPSCoR institutions, SBIR recipients‒ innovative technologies e.g. supporting mobile

computing clients, seamless integration of distributed, heterogeneous databases; development and operation of science gateways, data repositories, and campus bridging

• Ability to quickly hire consultants if new expertise is needed

Advanced Support of Community CodesJohn Cazes, TACC

• Deploying, hardening, and optimizing useful software systems ‒ collaborate with the developers of widely used community

codes and tools,including PetaApps, SDCI, STCI, SI2, MREFC and industrial partners

• Deliverable: ≥10 projects completed per year

Advanced Support of Science GatewaysSuresh Marru, IU

• Support communities that wish to use XSEDE resources via science gateways and/or data repositories

• Gateway Software Incubator: Evaluates new software and makes recommendation to gateway community. Assist with integration of emerging software like Information Services and gateway-user-attributes.

• Gateway community building: Actively engage gateway developers in sharing experiences and learning from each other.

• Gateway Helpdesk: Specialized personnel assist in gateway tickets. Many a times, involves in breaking broad gateway problems into focused tickets for relevant support teams.

• Interface between gateway developers and XSEDE software and operations groups. Provide usage patterns and help define requirements.

• Deliverable: ≥10 projects completed per year

Advanced Support for Training, Education and OutreachGalen Arnold, NCSA• Examples:

‒ development and delivery (in person and/or online) of training modules on petascale programming techniques, both general and specific to each XSEDE system;

‒ modules on workflow building, using co-scheduled data transfers, data reduction concurrent with simulation, and algorithms for petascale data mining;

‒ participation in scientific conferences to present the results of relevant advanced user support projects.

• With demonstrated interest, researchers can request training events at their institutions via help@xsede.org

• Deliverables: ≥50 events per year

New Campus Champion Fellows programLaura McGinnis, PSC• Campus Champions

‒ http://www.xsede.org/campus-champions‒ Campus reps who provide local source of knowledge about

XSEDE• Campus Champions paired with AUSS staff on real-world

projects • Professional development

‒ Expertise with new technologies, new domains on XD resources‒ Bring expertise back to campuses

• ~40 AUSS-trained Campus Champions in the community at the end of 5 years

• Alumni program, regional directory of expertise envisioned• Annual symposium at XSEDE conference to feature Fellows

We’re here to help with your Gordon work

• Questions?• wilkinsn@sdsc.edu