LBNL VACET Activities Hank Childs Computer Systems Engineer - Visualization Group August 24, 2009

LBNL VACET Activities

Hank ChildsComputer Systems Engineer - Visualization Group

August 24, 2009

Director’s Review of CRD | August 24 - 26, 2009

Outline• Overview: VACET & VisIt

• Deployment & Outreach: math infrastructure

• Research: QDV & parallel streamlines

• Preparing for the Future: hero runs & VisIt infrastructure







VACET Mission and Vision

• Mission: enable scientific insight for petascale data.• Strategy: Leverage sci-vis and analytics software

technology as an enabling technology. • Vision: adapt, extend, create, and deploy data

understanding technologies for science stakeholders• Why are we a center?

– As a center, well positioned to respond to diverse needs/objectives through coordinated R&D, software engineering, outreach efforts.


VACET Organization

• Teams: stakeholder projects, R&D projects, software engineering projects.

• Executive committee: cross-institutional, cross-team coordination.

PIsBethel/LBNL, Johnson/Utah

Executive CommitteeBethel/LBNL, Brugger/LLNL, Johnson/Utah, Joy/UCD, Ahern/ORNL

+ Pascucci/Utah, Childs/LBNL

R&D TeamsStakeholder Projects Software Engineering Teams (per site)

Chief Software Engineer, Childs/LBNL


VisIt is a richly featured, turnkey application for large data.

• VisIt is an open source, end user visualization and analysis tool for simulated and experimental data– Used by: physicists, engineers,

code developers, vis experts– >100K downloads on web

• R&D 100 award in 2005• Used “heavily to exclusively” on 8 of

world’s top 12 supercomputers

27B elementRayleigh-Taylor Instability(MIRANDA, BG/L)


VisIt has a rich feature set that can impact many science areas.

• Meshes: rectilinear, curvilinear, unstructured, point, AMR• Data: scalar, vector, tensor, material, species• Dimension: 1D, 2D, 3D, time varying• Rendering (~15): pseudocolor, volume rendering,

hedgehogs, glyphs, mesh lines, etc…• Data manipulation (~40): slicing, contouring, clipping,

thresholding, restrict to box, reflect, project, revolve, …• File formats (~85)• Derived quantities: >100 interoperable building blocks• Many general features: position lights, make movie, etc• Queries (~50): ways to pull out quantitative information,

debugging, comparative analysis


VisIt and VACET provide significant mutual leverage.

• VisIt represented over 50 person-years of effort at the time of VACET being funded

– VisIt contains over one million lines of code• Eric Brugger, NNSA VisIt lead: “VACET has assumed the lead

role in ensuring that VisIt will be able to handle the largest data sets.”

2004-6

User communitygrows, includingAWE & ASC Alliance schools

Fall ‘06

VACET is funded

Spring ‘08

AWE enters repo

2003

LLNL user communitytransitioned to VisIt

2005

2005 R&D100

2007

SciDAC Outreach Center enablesPublic SW repo

2007

Saudi Aramcofunds LLNL to support VisIt

Spring ‘07

GNEP funds LLNL to support GNEP codes at Argonne

Summer‘07

Developers from LLNL, LBL, & ORNLStart dev in repo

‘07-’08

UC Davis & UUtah research done in VisIt repo

2000

Project started

‘07-’08

Partnership withCEA is developed

2008

Institutional supportleverages effort from many labs

Spring ‘09

More developersEntering repo allthe time







We have made an impact for APDEC• PI: Phil Colella (LBNL), SciDAC Applied

Partial Differential Equations Center• Accomplishment(s)

– Software engineering to “bring product to market”. Performance improvements, interface enhancements, file readers, visual data exploration techniques.

• Science Impact– Visualization on large AMR data sets, and

using parallel platforms.– Trail blazed for future VACET work.


VACET has improved VisIt’s AMR capabilities significantly.

• Improvements:– Optimized many, many

routines, resulting in end-to-end speedups of >10X

– Added critical debugging functionality, such as spreadsheets and the ability to connect with a debugger.

– Mapped AMR grids

- Macros and python callbacks for customizability.

- Responded to over 30 requests for interface changes and bug fixes.


VACET’s efforts have led to VisIt being adopted by important ASCR stakeholders.

+ see our review document for 9 more letters of support from SciDAC-funded

groups using VisIt


Outline• Overview: VACET & VisIt.

• Deployment & Outreach: math infrastructure.




QDV and Accelerator Modeling• Accomplishment:

– Algorithms + deployment in VisIt to perform interactive visual data analysis (identify, track, analyze beam particles) in multi-TB simulation data.

• Science Impact:– Replace serial process that took hours with

one that takes seconds.– New capability: rapid data exploration and

analysis.• SC08 paper• Customer: C. Geddes (LBNL)/COMPASS• Collaborators: SciDAC SDM Center (FastBit)

Tech-X (Accelerator scientists)


Streamlines represent an activity spanning research to SWE to data insight.

Stakeholders:“VisIt is bad at

streamlines”

Stakeholders:“VisIt is bad at

streamlines”

“We need parallel streamlines” / “Wow! Parallel streamlines

is hard”

“We need parallel streamlines” / “Wow! Parallel streamlines

is hard”

Deployment effort in VisIt by SEG

Research effort:Efficient parallel

streamline generation

This work has had a broad and varied impact.

Used in analysis by SHOCKS center (image

courtesy SHOCKS website)

Used in analysis by SHOCKS center (image

courtesy SHOCKS website)

Poincare analysis for fusion community

Poincare analysis for fusion community

Streamlines used in visualization of type II

supernova collapse

Streamlines used in visualization of type II

supernova collapseResearch vehicle (and delivery vehicle) on streamline generation of AMR data sets.

Research vehicle (and delivery vehicle) on streamline generation of AMR data sets.

Level 0 only (incorrect)

Correctly traversing all AMR levels

217 pin reactorcooling simulation.Run on ¼ of Argonne BG/P.


This work has had a broad and varied impact.

“First light” picture showing mixing of cold and warm air inlets. (Nek5000/Fischer, Argonne, INCITE run)

“First light” picture showing mixing of cold and warm air inlets. (Nek5000/Fischer, Argonne, INCITE run)


Existing parallel integral curve techniques have suffered from load imbalance.

Two extremes:• Partition data over processors

and pass particles amongst processors Parallel inefficiency!

• Partition seed points over processors and process necessary data for advection Redundant I/O!

Notional streamlineexample


P0 P0 P0 P0 P0

P1 P1 P1 P1 P1

P2 P2 P2 P2 P2

P3 P3 P3 P3 P3

P4 P4 P4 P4 P4

P0

P1P2

P3P4


We have greatly advanced the state of the art for parallel integral curve techniques. Hybrid solution:• Master-slave approach that

adapts between parallel inefficiencies and redundant I/O

P0P0

P1

P1P2

P2P3

P4

Iteration Action

0 P0 reads B0,P3 reads B1

1 P1 passes points to P0,P4 passes points to P3,P2 reads B0

0: Read

0: Read



1: Pass

1: Pass1: Read

- Decision of when to pass or read is simplified here and based on load of processors owning data. - Heuristic weights against I/O, but allows for redundant I/O- All coordination done by slave masters.







Trillion-cell experiment: objectives• Research questions:

– Is it possible/feasible to run production-quality visual data analysis s/w on large machines and on large data sets?

– What obstacles/bottlenecks do we encounter at this level of scale?

• Why?– VACET’s job: provide production-quality tools for

large data. • This is demonstrating that these tools are

viable.


Trillion cell experiment methodology:

What tools, what machines, what data?• Application: VisIt 1.11.1

– VisIt is the first and only visualization application that is part of the “Joule” metric

• Machines: Cray (franklin/LBL, jaguar/ORNL), BG/P (dawn/LLNL), AIX (purple/LLNL), Linux (Juno/LLNL), Sun Linux (ranger/UTexas)

• Data: – 5123 sample data, astrophysics simulation (courtesy T.

Mezzacappa, B. Messer, S. Bruenn, R. Budjiara)– Upsampled to target problem size– Data sizes ranged to 1T (for 16K cores) to 4T (for 64K

cores), with 0.5T/8K for AIX/Purple


Trillion cell experiment methodology:What techniques?

• Two common visualization techniques:– Isocontouring, volume rendering

2T zones, 32K procs on Jaguar

2T zones, 32K procs on Franklin


Trillion cell experiment “speed bumps”

• Application bottleneck: many-to-one status update

– Workaround for study, fix to appear in future release of VisIt

• Application optimization: an NxN buffer for communication, which works well at small scale, proved problematic at large scale.

– Workaround: remove optimization, evaluate best course of action for future VisIt release.

• System issues– Loading shared libraries takes a long time, as much as 5

minutes. Potential fix: implement VisIt plugins as static libraries.


Trillion cell experiment: Significance of Results

• Production tool (VisIt) runs effectively at high concurrency, on large problem sizes, and on diverse platforms.– Test of visual data analysis infrastructure– Infrastructure is the underpinning of many different

algorithms, not just isocontouring or volume rendering.

• Minor fixes to become part of production VisIt release (later this year).

• Successfully processed “tomorrow’s data today.”

~1980 ~2000 ~2020

1M 1B 1T

We are here


VACET has contributed more than just algorithms and research to VisIt.

• Production software: bug tracking, regression testing, regular releases

• Through our efforts, VisIt now feels much more like an open source project:– Transitioned software repository to NERSC; now

accessible to a large community.• ~30 developers with write access from 10

institutions– Public mailing lists, archived and searchable.

• ~300 subscribers, get ~300 posts per month– Wiki pages on usage and development.


Summary

• The LBNL portion of VACET has made a huge impact in the ASCR community– In deployment, in research, and in paving the way for

the future• VACET is partnering with many researchers in the ASCR

community.• VisIt, the production visualization tool for VACET, is being

developed by a vibrant community and has demonstrated applicability at the petascale.

• LBNL is a major center of gravity for the VisIt project.

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LBNL VACET Activities Hank Childs Computer Systems Engineer - Visualization Group August 24, 2009

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