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Introduction to Scientific Visualization in the WestGrid Environment

Introduction to Scientific Visualization in the WestGrid Environment

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Introduction to Scientific Visualization in the WestGrid Environment

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  1. Introduction to Scientific Visualization in the WestGrid Environment Jon Johansson

  2. What is Scientific Visualization? • convert scientific data into visual form • use computer to process data • numerical algorithms such as marching cubes to extract features • add color, lights, camera view (create a 3D scene) • graphics techniques to render • the data sets can be large – many gigabytes or more • resulting image is presented to the human visual processing system for the direct analysis and interpretation of the information

  3. What is Scientific Visualization? • generally deals with data that has a natural geometric structure • MRI, CAT data (measured) • weather simulations (computed)

  4. What is Scientific Visualization? • the key point is that we can understand data in a picture much better than we can understand a bunch of numbers • WestGrid resources can generate a lot of numbers!!

  5. What is Scientific Visualization? • use well understood algorithms to extract features from data sets • goals • understand the data (exploration) • interactively examine the data looking for the parts that are interesting • communicate the data to peers • publications • conferences

  6. What is Scientific Visualization? • once we find interesting structures in the data we have the freedom to arrange • colors • lights • transparency • camera views • this should clarify what we are looking at

  7. WestGrid Visualization Resources • WestGrid provides a visualization server located at Simon Fraser University • the machine can be accessed as: • • • IP address: • Hydra is an SGI Onyx UltimateVision graphics supercomputer • 24 processors • 14 GB RAM • 10 graphics pipes

  8. WestGrid Visualization Resources • You should have access to hydra automatically by being granted access to WestGrid resources • Info about accounts: • • Apply for an account at: •

  9. WestGrid Visualization Resources Web links for more information: • WestGrid Collaboration/Visualization • • Visualization Server Usage page • • SFU Visualization Server Site •

  10. OpenGL Vizserver • SGI Vizserver is client-server software that allows you to run fully hardware-accelerated graphics applications on a remote machine and have images delivered to your desktop • the server is installed on • • the client is installed on your workstation

  11. OpenGL Vizserver • OpenGL VizServer • the server software runs on the WestGrid Visualization Server machine • the client runs on the users desktop machine • • there are currently 5 licenses for the Vizserver software on hydra

  12. OpenGL Vizserver • Application-transparent • OpenGL Vizserver runs existing OpenGL® API-based applications without modification • Shared application control • OpenGL Vizserver instantly turns existing stand-alone applications into collaborative applications with up to five remote sites sharing control of a single interactive application

  13. OpenGL Vizserver • Platform/system independent • OpenGL Vizserver gives existing workstations, personal computers, and even wireless handheld devices the power of a Silicon Graphics Prism or SGI Onyx family system, as well as direct interaction with experts on Silicon Graphics workstations.

  14. OpenGL Vizserver • you can run nearly any graphics or visualization application on the remote SGI host (, and have the resulting imagery delivered to your desktop • the client machine simply decompresses and displays the image created by the server

  15. OpenGL Vizserver • why the Vizserver approach is better: • X doesn't support hardware accelerated 3D graphics • OpenGL function calls are passed to the graphics card on your desktop • the X protocol is horribly inefficient • Vizserver uses a much more streamlined (custom) protocol to move events and payload image data • data compression is available • Vizserver lets multiple users interact simultaneously with a single application running on the graphics server • each connection has a dedicated graphics pipe

  16. OpenGL Vizserver • OpenGL Vizserver clients are available for • SGI® IRIX® OS-based systems, such as Silicon Graphics Octane2, Silicon Graphics Fuel, Silicon Graphics® O2+™, and the SGI Onyx family • Linux® • Solaris™ • Windows NT®, Windows® 2000, Windows® XP, and Windows® XP Tablet PC Edition • Mac OS X

  17. OpenGL Vizserver • the OpenGL Vizserver client is a free download from the SGI website • • note that you must create a Supportfolio ID to be able to download the client • this is free

  18. Connection to Hydra • you need to create an SSH tunnel to hydra to be able to use it. • from a Linux/Unix machine: • ssh -L -N • replace “username” with your WestGrid username and you will be prompted for your password • 7051 is the port that vizserver uses to make connections

  19. Connection to Hydra • you will need to set an environment variable to be able start a vizserver session: • VSX_SESSION_HOST = • launch the vizserver client • connect to “localhost” not to hydra • the connection is handled by the tunnel • you still need to authenticate to Hydra with your WestGrid username and password. •

  20. Connection to Hydra Sample session start • set up the SSH tunnel • ssh -L • set the environment variable (Bash shell) • export • launch the client • vizserver -h localhost

  21. OpenGL Vizserver • Sample session start (cont.) • enter your WestGrid user id and password to login to hydra • start a session • select parameters for the session • launch applications from the vizserver console window

  22. SSH tunneling • also called “port forwarding” or “port mapping” • forward a network port from one network node to another • used to carry insecure network traffic over the Internet in a secure way • users outside a firewall can access a service inside the firewall

  23. SSH tunneling • ssh connects using port 22 • connection is encrypted and secure • vizserver connects using port 7051 • connection is not encrypted • to make a vizserver session secure, wrap the vizserver session inside ssh

  24. SSH tunneling • on the source machine • ssh listens for packets addressed to port 7051 • all those packets are encrypted and addressed to the destination using port 22 • on the destination machine • when the packets are received, ssh decrypts them • packets are then sent to the destination port

  25. SSH tunneling • We can use a GUI and manually assign port forwarding • port 7051 on localhost is forwarded to 7051 on the remote host • this is an “outgoing” tunnel • we don’t need an incoming (reverse) tunnel for port 7051 - only an outgoing tunnel to the server • our big concern is that the username and password used to authenticate to hydra be encrypted

  26. Scientific Visualization • Having opened a connection to hydra we would like to use a visualization application – what’s available?

  27. Viz Packages • OpenDX, VTK are AVS use a pipelined, component-based architecture • a user can quickly assemble modular software components into a “finished application.” • these systems are flexible in the sense that components can be combined in a multitude of ways, thereby allowing an application developer to accomplish a wide variety of visualization tasks • they are extensible as they offer the means for developers to add new components to the system, thereby extending the system’s functionality

  28. Scientific Visualization • to be able to run OpenDX on hydra: • set the environment variable DXROOT to • setenv DXROOT /usr/local/dx (tcsh) • export DXROOT=/usr/local/dx (bash) • add the following directory to your library path • setenv LD_LIBRARY_PATH {LD_LIBRARY_PATH}:/usr/local/lib/ (tcsh)

  29. Scientific Visualization • In order to create a visualization: • import your data into the package • explore the data looking for the interesting features • lots of work here • having found interesting features set up the view to show them clearly. Select: • colors/surface properties • camera view • lights (these have some properties to adjust) • export images/animations

  30. Scientific Visualization • color choice can help to clarify a visualization • a handy guide is the online paper “A Rule-based Tool for Assisting Colormap Selection” by Lawrence D. Bergman, Bernice E. Rogowitz and Lloyd A. Treinish, all from IBM • • lots of interesting references at the end

  31. Scientific Visualization • another very nice online publication is “How NOT to Lie with Visualization” by Bernice E. Rogowitz and Lloyd A. Treinish, from IBM • • PRAVDA is intellectual property (IBM’s) separate from OpenDX and isn’t freely available • the papers are still worth reading

  32. Scientific Visualization Source:

  33. Sample Data Set • We have the electric potential due to a dielectric cylinder introduced into a constant electric field E0 • the parameters I used are: • E0 = 50 V/m • dielectric constant = 5 • Rcyl = 10 m • -50 m ≤ x, y, z ≤ 50 m

  34. Sample Data Set

  35. OpenDX Data Import • a data file might consist of ascii values, each line containing 4 values … -8.50000000 14.72243186 48.00000000 326.96078431 -8.50000000 14.72243186 49.00000000 326.96078431 -8.50000000 14.72243186 50.00000000 326.96078431 -9.50627936 14.09363873 -50.00000000 365.66830060 -9.50627936 14.09363873 -49.00000000 365.66830060 -9.50627936 14.09363873 -48.00000000 365.66830060 … • it’s important know how the file was written: • row major: for( i = 0; i < nx; i++){ for( j = 0; j < ny; j++){ for( k = 0; k < nz; k++){ fprintf( outfh, "%12.8f %12.8f %12.8f %12.8f \n", x, y, z, V ); } } } • row major is defined by the last index varying the fastest

  36. OpenDX Data Import • We have a data set that has regular spacings in the x, y and z directions • We don’t need to read the coordinates for each point from a file • The general header file to read in this data is: • file = ./pot_cart.dat • grid = 101 x 101 x 101 • format = ascii • interleaving = field • majority = row • header = lines 0 • field = potential • structure = scalar • type = float • dependency = positions • positions = regular, regular, regular, -50.0, 1.0, -50.0, 1.0, -50.0, 1.0 • end

  37. Sample Data Set • the connections between the points are inferred when you tell OpenDX that the data are “row major” • these are Cartesian connections

  38. Sample Data Set • you can also work in non-Cartesian coordinates • the grid is row major in cylindrical coordinates (r, phi, z) • write Cartesian coordinates in the file and connections are inferred from the cylindrical grid

  39. Sample Data Set

  40. Sample Data Set

  41. Data Import • Start with a FileSelector module to browse to the general file describing the data set and connect it to an import module which actually does the reading • Double click on the FileSelector to get a widget to browse the file system • When the data is in the package we can start applying algorithms to it and look for interesting features

  42. Components of the visualization • Isovalues of the electric potential • The lower slice shows the electric potential with contour lines to give a sense of the shape change close to the cylinder • Use a slab module to extract a slice of the potential field • Use the Isosurface module to extract contour lines at values • -1750, -1250, -750, -250, 250, 750, 1250, 1750 volts

  43. Components of the visualization • In the Slab module set the parameters: • dimension: “z” • position: 0 • thickness: (0 or 1) • this is the default • The AutoColor module generates a color map so that we have something to see

  44. Components of the visualization

  45. Components of the visualization • Take the output of the Slab module and attach it to the input of an Isosurface module • The 2D slab data will result in contour lines • Set the isovalues at • -1750, -1250, -750, -250, 250, 750, 1250, 1750 volts • The contour lines are then passed to a Tube module • Set the diameter of the tube to 1.0

  46. Components of the visualization

  47. Components of the visualization • Electric field lines • The middle slice is color mapped to the magnitude of the electric field and shows some field lines • The lines are diverted in the region of the cylinder • Use the Gradient module and the Compute module to calculate the electric field from the electric potential E = - gradj

  48. Components of the visualization • Use a Slab module to extract a slice of the electric field • Use the Streamline module to extract contour lines at values • The Streamline module needs the vector field as one input, and a set of seed points as the next input • Use the Tube module to produce lines with some thickness

  49. Components of the visualization • Use the Compute module after the gradient to negate the vector components • In the Compute module set “expression” to [-a.x, -a.y, -a.z] • In Slab set • dimension: “z” • position: 50 • thickness: (0 or 1) • this is the default

  50. Components of the visualization