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Visualization at NERSC Update

Visualization at NERSC Update. Ken Schwartz, LBL KSSchwartz@lbl.gov Visualization Project Leader National Energy Research Scientific Computing Division http://vis.lbl.gov. What’s New (Software). New Vis Software Escher VMD 1.7 NAMD 2.3 Garlic 1.1 RASMOL 2.6 OPENDX 4.1.3

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Visualization at NERSC Update

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  1. Visualization at NERSC Update • Ken Schwartz, LBL • KSSchwartz@lbl.gov • Visualization Project Leader • National Energy Research Scientific Computing Division • http://vis.lbl.gov

  2. What’s New (Software) • New Vis Software • Escher • VMD 1.7 • NAMD 2.3 • Garlic 1.1 • RASMOL 2.6 • OPENDX 4.1.3 • CEI Ensight 7.4 (under evaluation, available for user testing) • Seaborg • VMD 1.7 • XV 3.10a • Garlic 1.1 • OPENDX 4.1.3 • CEI EnSight 7.4 (under evaluation , available for user testing) • AVS5.5 * • IDL 5.5 * • Express 6.0 * *On seaborg, not released pending licensing problem resolution. Please ask for fully functional demo license for temporary use.

  3. Domain Specific Endeavors • VMD, Molecular Visualization Software

  4. GARLIC, Molecular Visualization Software

  5. Software Evaluation • Data Explorer (OpenDX) on Linux, IRIX and AIX

  6. Software Evaluation (cont’d) • CEI EnSight on IRIX, Linux and AIX

  7. What’s Updated (Software) • Visualization Software • Escher • AVS Express 6.0 • IDL 5.5 • AVS 5.5 • PV-Wave 7.5 • ImageMagick 5.4.5 (available not yet announced) • XV 3.10a, with postscript and pdf support • Seaborg • XV 3.10a, with postscript and pdf support

  8. Web Site Updates • Enhanced Software Support Web Pages • Emphasis on online resources – most users are remote! • Increased scope of documentation • http://vis.lbl.gov/software_support • Online Manuals (online /downloadable) • Vendor’s website linkages • Other useful related resources • Tutorials • Specific How To’s, examples • FlexLM information for remote licensing support • New linkages from NERSC HPCF site • http://hpcf.nersc.gov/software/apps • Quick descriptions of how to load individual programs on NERSC machines with specific links to vis.lbl.gov documentation for that package.

  9. New “What’s New” Web Page • http://vis.lbl.gov/whats_new.html • New software • Software Updates, New Deployments • Events • New Documentation / Examples

  10. Online Resources • Documentation from Vendors (AVS Express)

  11. Online Resources • Documentation from Vendors (IDL)

  12. Online Resources • Links to points of interest for users of visualization software • Links to Vendor’s Homepages

  13. Online Resources • Tutorials from Vendors (AVS5)

  14. Online Resources • Tutorials from Vendors (PV-Wave)

  15. Online Resources • Software Feature List (EnSight, under evaluation)

  16. Online Resources • Additional Resources (Gnuplot)

  17. Online Resources • How To’s: MPEG Generation

  18. New Search Engine • http://vis.lbl.gov/search.html

  19. Improved Interface to Nersc Consulting • Visualization group Consulting integrated into “Right Now Web” NERSC help desk functions • Allows ‘seamless’ bidirectional interface between NERSC users, Visualization Group, and NERSC USG consultants.

  20. Right Now Web Help Interface(Consultant’s view) • User Access at http://help.nersc.gov

  21. Planned Activities • NUG VIS WORKSHOP • Software Maintenance • Evaluation of New Technology • Software Evaluations • More Web updates • Hardware updates (Escher) • Pilot Projects • Application Serving • License Serving • Software Resource Utilization Tracking • Portals

  22. NUG Visualization Requirements Workshop • Focus: defining and prioritizing visualization requirements of many DOE-sponsored computational science programs being carried out at NERSC • http://vis.lbl.gov/Events/ Click on “2002 NERSC User Group Visualization Greenbook Workshop” • To be held on Wed, June 5, 2002 • Lawrence Berkeley National Laboratory, in Berkeley, California, Perserverance Hall, located in Building 54, Room 103 • One-day workshop adjacent to the NERSC User Group (NUG) meeting.

  23. Vis Workshop Focal Areas of Interest • High Energy and Nuclear Physics • Materials Sciences • Fusion Energy Sciences • Climate • Combustion • Computational Biology and Energy Biosciences • Geosciences • Chemical Sciences

  24. Previous Software Maintenance Schedule

  25. Planned Software Maintainence / Update Schedule • Software maintenance / update schedule • Current on all major packages supported. Upgrade when new releases are available. • Vtk • Tcl/Tk • NetPBM (formerly pbmplus) • ImageMagick, OPENDX • Expansion / updating of supporting libraries with improved integration to applications as helper apps • Netcdf, urt (utah raster kit), tiff, gtk+, glib, libmng, libjpeg, libz, libpng, hdf

  26. Current Software Summary • Visualization software on escher, as well as NERSC3 (IBM SP2), Cray PVP and T3E systems. • 3D Applications:AVS5 , AVS Express, MPE Express*, AVS GSHARP*, IDL, NCAR Graphics, PV-Wave, Khorosu, Xprismpro, EnSight *, IBM OpenDX , VMD, Garlic, Rasmol • 2D Imaging:xv, ImageMagick, imtools, pbmplus, GIMP* • 2D Applications:GNUplot , ghostscript ,ghostview, MPEG Tools (mpeg_encode, mpeg_play) • 2D Subroutine Libraries:tcl/tk • 3D Subroutine Libraries:netCDF,HDF,HDF5 • 2D/3D Developer Tools:Vtk,hdf • Applications with Visualization Capabilities:Matlab, Mathematica, Maple * Not for production use uUnsupported

  27. Visualization Group: Evaluation of New Technology • Objective: keep abreast of emerging visualization tools, evaluate for appropriateness for NERSC community, install and support if warranted. • Example: OpenDX • Open Source: runs on multiple platforms • Capable of taking advantage on multiprocessor hardware (IRIX, AIX, etc) • Rapid application programming environment • Example: CEI Ensight • Takes advantage of Client / Server / Server of Server Model • Allows for analysis of data ‘in place’ • More efficient than Remote X Display • Parallel processing, Multipipe, Stereo Display, Movie Generation

  28. Previous Evaluation of New Technology Schedule

  29. Software Evaluations • On Schedule for Evaluations • Rescheduled: possible future evals /no further evaluation (already partially evaluated) • OpenViz • Gsharp • MSI Insight • Current Evaluations • EnSight • MPE Express • GIMP • Near Future • VisIt • Paraview • Parallel OpenDx

  30. Sample Criteria for Evaluation: EnSight • Notify users of the eval period, and solicit feedback. • Ability to read Data • AMR, Current user’s data formats, including time varying data. Degree of difficulty, data Model • Visualization techniques • Slice, dice, volume render, streamlines, particle advection, isosurface, compute vector magnitude, compute gradient vector from scalar data, univariate statistical analysis of scalar data • Make movies directly from Ensight. • Display Capabilities • multibuffered stereo display • tiled display capability • Client Server • Eval server on the SP2 and client on escher • Eval server on escher and client on remote Linux / windows machine • Eval Server of Server architecture eg Seaborg / Escher /PDSF/ Remote Linux

  31. More Web updates • More comparisons of software packages • Triage • Strengths and weaknesses of individual packages • Higher level of Integration between NERSC and vis.lbl.gov site • More examples of using software for specific applications • App server web pages • Secure facility to download applications complete with installation instructions

  32. Escher • NERSC/Production • Visualization server (escher.nersc.gov): SGI Onyx2, 8x 195Mhz R10K CPUs, 5G RAM, 2x iR2, 2x gigE (NEW), 1x HiPPI, 1TB RAID. • Escher Replacement under evaluation

  33. Visualization Group NERSC: Pilot Projects • Application Serving • Remote Application Licensing • Application Utilization Logging • Portal: streamlined and simplified access to remote resources, • parallel and pipelined rendering for improved performance

  34. Application Serving • Concept • Download applications for remote deployment on user’s machine. • Rationale • Large monolithic applications (AVS5, IDL, etc) • extremely high latency via remote terminal display • low interactivity / usability when used from NERSC servers • New class of workstations • Recent advances in quality of Linux operating system • Low-cost hardware • Reduce interactive load on some NERSC platforms • Schedule • Currently deployed with few users

  35. Remote Licensing • Concept • Applications licensed from NERSC • Remote deployment • Distributed among NERSC resources • Rationale • Takes advantage of software resources more fully • More efficient utilization of NERSC resources for client / server computing • Process data in place • Simplifies license administration • Port blockage issues • Increased uptime • Increased reliability

  36. Software Utilization Logging (ulog) Resource Tracking • Concepts • Utilization logging: Implementing a set of tools to capture and log application usage data, and to generate an analysis of application usage. • Similar in approach to a system logging facility • Rationale • Optimization of resources • No way to determine this information from currently available data • Increased understanding of user requirements • Schedule • Currently developing methodologies to deploy ‘ulog’ server • Define a suitable network service abstraction for the ulog client and server • Design and implement prototype ulog client and server • Deploy production version monitoring Escher initially • Test and deploy for remote application serving

  37. Portal • Concept • To coalesce diverse resources related to visualization into a single web location • Applications • Supporting documentatation • Tutorials for applications • Rationale • Provide an important role in online communities • Organized, easy access to diverse services • Simplifying and streamlining access of visualization resources to remote NERSC users • Integrated portal services are designed using "n-tiered" architecture. • Client and server interaction brokered by portal • Allows integrated, centralized access to distributed hardware, software, data and knowledge resources

  38. Portal Projects • A framework to transition visualization research prototype applications into production use • The first such target will be • a viewer to be run on the user's workstation • a computational backend component which runs on a high performance parallel computer • Additional Possible Future Targets • One button MPEG • Visualization Spreadsheets

  39. Vis Portal Example

  40. Strategic Overview

  41. Visualization Group: Close Collaboration • Domain-specific application of scientific visualization technology to domain-specific endeavors. • Recent examples of this kind of work: McCurdy, Ryne (SciDAC), Vahala, Nugent • Anticipated benefits • Better understanding of data = better science • Integral part of proposals for new money • Visualization is the most visible part of scientific research.

  42. Recent Collaborations • A 3-D spectrum synthesis model of a supernova plotting the flux versus wavelength as a function of inclination angle. • This supernova has a toroid of Calcium around it's main eject. • The absorption features due to Calcium increase in strength in the spectrum as the line of sight is moved towards the toroid. (Nugent)

  43. Recent Collaborations (con’t) • Beam Simulation Data (Ryne)

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