introduction to scientific visualization in the …...ssh tunneling • we can use a gui and...

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Introduction to Scientific Visualization in the WestGrid Environment

Introduction to Scientific Visualization in the WestGrid Environment

Jon JohanssonJon Johansson

November 5, 2008November 5, 2008

Jon JohanssonAcademic Information and

Communication TechnologiesUniversity of Alberta

Jon JohanssonAcademic Information and

Communication TechnologiesUniversity of Alberta

Visualization in WestGridSlide 1 of 75


What is Scientific Visualization?What is Scientific Visualization?

• convert scientific data into visual form– use computers to process data

• convert scientific data into visual form– use computers to process datap p

• 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• the resulting image is presented to the human

visual processing system for the direct analysis

p p• 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• the resulting image is presented to the human

visual processing system for the direct analysis


visual processing system for the direct analysis and interpretation of the informationvisual processing system for the direct analysis and interpretation of the information



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• a successful visualization is a representation of data which

• a successful visualization is a representation of data whichrepresentation of data which– allows the user to gain some insight into the

data– communicates the insight to others

• frequently deal with data that has a natural geometric structure

representation of data which– allows the user to gain some insight into the

data– communicates the insight to others

• frequently deal with data that has a natural geometric structure


natural geometric structure • MRI, CAT data (measured)• weather simulations (computed)

natural geometric structure • MRI, CAT data (measured)• weather simulations (computed)




• the key point is that we can understand data in a picture much better than we

• the key point is that we can understand data in a picture much better than we data in a picture much better than we can understand a bunch of numbers

• WestGrid resources can generate a lot of numbers!!

data in a picture much better than we can understand a bunch of numbers

• WestGrid resources can generate a lot of numbers!!

November 5, 2008November 5, 2008Visualization in WestGrid

Slide 4 of 75Visualization in WestGrid

Slide 4 of 75

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• use well understood algorithms to extract features from data sets

• 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

• goals– understand the data (exploration)

• interactively examine the data looking for the parts that are interesting

– communicate the data to peers• publications• conferences


conferences• NOTE: the exploration phase is usually interactive

so we need to generate images in (almost) real time– humans in the loop have limited tolerance for delay

conferences• NOTE: the exploration phase is usually interactive

so we need to generate images in (almost) real time– humans in the loop have limited tolerance for delay




• once we find interesting structures in the data we have the freedom to arrange

• once we find interesting structures in the data we have the freedom to arrangehave the freedom to arrange– colors– lights– transparency– camera views

• this should clarify what we are looking at

have the freedom to arrange– colors– lights– transparency– camera views

• this should clarify what we are looking at



Slide 6 of 75

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WestGrid Visualization ResourcesWestGrid Visualization Resources

• WestGrid provides a visualization server located at Simon Fraser U i it

• WestGrid provides a visualization server located at Simon Fraser U i itUniversity

• the machine can be accessed as:–– hydra.westgrid.cahydra.westgrid.ca–– vizserver.westgrid.cavizserver.westgrid.ca–– IP address: 206.12.24.8IP address: 206.12.24.8

• Hydra is an SGI Onyx UltimateVision graphics supercomputer

University• the machine can be accessed as:

–– hydra.westgrid.cahydra.westgrid.ca–– vizserver.westgrid.cavizserver.westgrid.ca–– IP address: 206.12.24.8IP address: 206.12.24.8

• Hydra is an SGI Onyx UltimateVision graphics supercomputer

– 24 processors– 14 GB RAM – 10 graphics pipes

– 24 processors– 14 GB RAM – 10 graphics pipes



Slide 7 of 75


• You should have access to hydra automatically by being granted access

• You should have access to hydra automatically by being granted access automatically by being granted access to WestGrid resources

• Info about accounts:– http://www.westgrid.ca/support/accounts

• Apply for an account at:– http://www.westgrid.ca/support/accounts/applying for an a

automatically by being granted access to WestGrid resources

• Info about accounts:– http://www.westgrid.ca/support/accounts

• Apply for an account at:– http://www.westgrid.ca/support/accounts/applying for an a


p // g / pp / / pp y g_ _ _ccount

p // g / pp / / pp y g_ _ _ccount



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Web links for more information:Web links for more information:• WestGrid Collaboration/VisualizationWeb links for more information:Web links for more information:• WestGrid Collaboration/VisualizationWestGrid Collaboration/Visualization

– http://www.westgrid.ca/support/visualization/• Visualization Visualization Server Page

– http://www.westgrid.ca/support/visualization/visualization_server/using_vizserver

• WestGrid Visualization Facilities– http://www.westgrid.ca/support/visualization/visualizati

on_facilities

WestGrid Collaboration/Visualization– http://www.westgrid.ca/support/visualization/

• Visualization Visualization Server Page – http://www.westgrid.ca/support/visualization/visualizati

on_server/using_vizserver• WestGrid Visualization Facilities

– http://www.westgrid.ca/support/visualization/visualization_facilities



Slide 9 of 75

Visual ServingVisual Serving

• OpenGL Vizserver 1.1 released by SGI in April 2000

• OpenGL Vizserver 1.1 released by SGI in April 2000April 2000

• users are able to interact with visualization supercomputers from anywhere in the world – connect individually

connect as a collaborative community

April 2000• users are able to interact with

visualization supercomputers from anywhere in the world – connect individually

connect as a collaborative community


– connect as a collaborative community• rebranded as Visual Area Networking

(VAN) in 2002– hardware coupled with OpenGL Vizserver 2.0

– connect as a collaborative community• rebranded as Visual Area Networking

(VAN) in 2002– hardware coupled with OpenGL Vizserver 2.0



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WestGrid Visual Area NetworkWestGrid Visual Area Network



Slide 11 of 75

SGI OpenGL VizserverSGI OpenGL Vizserver

• SGI Vizserver is client-server software that allows you to run fully hardware

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

• the server is installed on – hydra westgrid ca

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 – hydra westgrid ca


– hydra.westgrid.ca • the client is installed on your workstation

– hydra.westgrid.ca • the client is installed on your workstation



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• OpenGL VizServerthe server software runs on the WestGrid

• OpenGL VizServerthe server software runs on the WestGrid – the server software runs on the WestGrid Visualization Server machine

– the client runs on the users desktop machine– http://www.sgi.com/products/software/vizserver/

• there are currently 5 licenses for the Vizserver software on hydra

– the server software runs on the WestGrid Visualization Server machine

– the client runs on the users desktop machine– http://www.sgi.com/products/software/vizserver/

• there are currently 5 licenses for the Vizserver software on hydra


yy




• Application-transparentOpenGL Vizserver runs existing OpenGL® API

• Application-transparentOpenGL Vizserver runs existing OpenGL® API– 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

– 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 sharing control of a single interactive application



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• Platform/system independentOpenGL Vizserver gives existing workstations

• Platform/system independentOpenGL Vizserver gives existing workstations – OpenGL Vizserver gives existing workstations, personal computers, and even wireless handheld devices the power of a Silicon Graphics Prism or SGI Onyx family system

– the application uses the resources on the server

CPU d hi i

– OpenGL Vizserver gives existing workstations, personal computers, and even wireless handheld devices the power of a Silicon Graphics Prism or SGI Onyx family system

– the application uses the resources on the server

CPU d hi i


• CPUs and graphics pipes– images are sent to the client machine

• no need for much graphic power

• CPUs and graphics pipes– images are sent to the client machine

• no need for much graphic power




• you can run nearly any graphics or visualization application on the remote

• you can run nearly any graphics or visualization application on the remote visualization application on the remote SGI host (hydra.westgrid.ca), and have the resulting imagery delivered to your desktop

• the client machine simply decompresses and displays the image created by the

visualization application on the remote SGI host (hydra.westgrid.ca), and have the resulting imagery delivered to your desktop

• the client machine simply decompresses and displays the image created by the


and displays the image created by the serverand displays the image created by the server



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• why the Vizserver approach is better:– X doesn't support hardware accelerated 3D graphics

• why the Vizserver approach is better:– X doesn't support hardware accelerated 3D graphicspp g p

• 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 i l li ti i th hi

pp g p• 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

i l li ti i th hi


a single application running on the graphics server• each connection has a dedicated graphics pipe

a single application running on the graphics server• each connection has a dedicated graphics pipe




• OpenGL Vizserver clients are available for – SGI® IRIX® OS-based systems such as Silicon

• OpenGL Vizserver clients are available for – SGI® IRIX® OS-based systems such as Silicon – 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,

– 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

, , ,and Windows® XP Tablet PC Edition

– Mac OS X



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• the OpenGL Vizserver client is a free download from the SGI website

• the OpenGL Vizserver client is a free download from the SGI websitedownload from the SGI website– https://support.sgi.com/login

• note that you must create a Supportfolio ID to be able to download the client– this is free

download from the SGI website– https://support.sgi.com/login

• note that you must create a Supportfolio ID to be able to download the client– this is free



Slide 19 of 75

Connection to HydraConnection to Hydra

• you need to create an SSH tunnel to hydra to be able to use it

• you need to create an SSH tunnel to hydra to be able to use ithydra to be able to use it.

• from a Linux/Unix machine:–– sshssh --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051

--N [email protected] [email protected]– replace “username” with your WestGrid

username and you will be prompted for your password

hydra to be able to use it.• from a Linux/Unix machine:

–– sshssh --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051--N [email protected] [email protected]

– replace “username” with your WestGrid username and you will be prompted for your password


password• 7051 is the port that vizserver uses to

make connections

password• 7051 is the port that vizserver uses to

make connections



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• look at this connection command:–– sshssh --L 7051:hydra westgrid ca:7051L 7051:hydra westgrid ca:7051

• look at this connection command:–– sshssh --L 7051:hydra westgrid ca:7051L 7051:hydra westgrid ca:7051–– sshssh --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051

--N [email protected] [email protected]•• --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051

– specifies that port 7051 on the local (client) machine is to be forwarded to the given host and port on the remote machine

– this is an “outgoing tunnel”•• --NN means “do not execute a remote command”

– for an “incoming tunnel” (the given port on

–– sshssh --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051--N [email protected] [email protected]

•• --L 7051:hydra.westgrid.ca:7051L 7051:hydra.westgrid.ca:7051– specifies that port 7051 on the local (client) machine is to be

forwarded to the given host and port on the remote machine– this is an “outgoing tunnel”

•• --NN means “do not execute a remote command” – for an “incoming tunnel” (the given port on


for an incoming tunnel (the given port on the remote (server) machine is to be forwarded to the given port on the local machine) use --RR instead of --LL

for an incoming tunnel (the given port on the remote (server) machine is to be forwarded to the given port on the local machine) use --RR instead of --LL



Connection to HydraConnection to Hydra• you will need to set an environment

variable to be able start a vizserversession:

• you will need to set an environment variable to be able start a vizserversession:session:– VSX_SESSION_HOST = hydra.westgrid.ca

• launch the vizserver client– connect to “localhost” not to hydra– the connection is handled by the tunnel

• you still need to authenticate to Hydra

session:– VSX_SESSION_HOST = hydra.westgrid.ca

• launch the vizserver client– connect to “localhost” not to hydra– the connection is handled by the tunnel

• you still need to authenticate to Hydra


y ywith your WestGrid username and password.– http://www.westgrid.ca/files/webfm/support/visualizati

on/vizserver_tunnel.pdf

y ywith your WestGrid username and password.– http://www.westgrid.ca/files/webfm/support/visualizati

on/vizserver_tunnel.pdfVisualization in WestGrid


Slide 22 of 75

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Sample session startSample session start• set up the SSH tunnel

–– sshssh --L 7051:hydra.westgrid.ca:7051 L 7051:hydra.westgrid.ca:7051 --N [email protected] [email protected]

• set the environment variable (Bash shell)–– export VSX_SESSION_HOST=hydra.westgrid.caexport VSX_SESSION_HOST=hydra.westgrid.ca

i

• set up the SSH tunnel–– sshssh --L 7051:hydra.westgrid.ca:7051 L 7051:hydra.westgrid.ca:7051

--N [email protected] [email protected]• set the environment variable (Bash shell)

–– export VSX_SESSION_HOST=hydra.westgrid.caexport VSX_SESSION_HOST=hydra.westgrid.ca

i


• launch the client–– vizservervizserver --h h localhostlocalhost

• launch the client–– vizservervizserver --h h localhostlocalhost



OpenGL VizserverOpenGL Vizserver

• Sample session start (cont.)• enter your WestGrid user id and password • Sample session start (cont.)• enter your WestGrid user id and password • 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

• 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


console windowconsole window



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SSH tunnelingSSH tunneling

• also called “port forwarding” or “port mapping”

• also called “port forwarding” or “port mapping”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

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 firewallservice inside the firewall




• ssh connects using port 22 – connection is encrypted and secure

• vizserver connects using port 7051

• ssh connects using port 22 – connection is encrypted and secure

• vizserver connects using port 7051


• vizserver connects using port 7051– connection is not encrypted

• to make a vizserver session secure, wrap the vizserver session inside ssh

• vizserver connects using port 7051– connection is not encrypted

• to make a vizserver session secure, wrap the vizserver session inside ssh



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• on the source machine – ssh listens for packets addressed to port 7051

• 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

– 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



SSH tunnelingSSH tunneling• We can use a GUI and manually assign port

forwarding – port 7051 on localhost is forwarded to 7051 on the

• We can use a GUI and manually assign port forwarding – port 7051 on localhost is forwarded to 7051 on the p

remote host• this is an “outgoing tunnel”• outgoing tunnels protect the data that your local

computer sends to the remote host computer– we don’t need an incoming (reverse) tunnel for port

7051 - only an outgoing tunnel to the server• incoming tunnels protect the data that your local

t i i i f th t h t

premote host

• this is an “outgoing tunnel”• outgoing tunnels protect the data that your local

computer sends to the remote host computer– we don’t need an incoming (reverse) tunnel for port

7051 - only an outgoing tunnel to the server• incoming tunnels protect the data that your local

t i i i f th t h t


computer is receiving from the remote host computer.

• our main concern is that the username and password used to authenticate to hydra be encrypted

computer is receiving from the remote host computer.

• our main concern is that the username and password used to authenticate to hydra be encrypted



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Scientific VisualizationScientific Visualization

• Having opened a connection to hydra we would like to use a visualization application – what’s

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

Package Name Start Command

AVS/Express 6.2 express

OpenDX 4.3.2 dx


• if something is not configured correctly, please send a message to [email protected]

• if something is not configured correctly, please send a message to [email protected]

VTK vtk (the tcl shell for vtk)



Viz PackagesViz Packages

• OpenDX, VTK and AVS Express use a pipelined, component-based architecture

• OpenDX, VTK and AVS Express use a pipelined, component-based architecture

• a user can quickly assemble modular software components into a “finished application.”

• these systems are flexible - 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 - they offer the means for developers to add new components to the

• a user can quickly assemble modular software components into a “finished application.”

• these systems are flexible - 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 - they offer the means for developers to add new components to the


developers to add new components to the system, thereby extending the system’s functionality

developers to add new components to the system, thereby extending the system’s functionality



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OpenDXOpenDX

• to be able to run OpenDX on hydra:set the environment variable DXROOT to

• to be able to run OpenDX on hydra:set the environment variable DXROOT to – 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)– add the bin directories to your path

– 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)– add the bin directories to your path


• setenv PATH {$PATH}:/usr/local/dx/bin:/usr/local/dx/bin_sgi

• setenv PATH {$PATH}:/usr/local/dx/bin:/usr/local/dx/bin_sgi




• In order to create a visualization:– import your data into the package

• In order to create a visualization:– import your data into the packageimport 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

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

• lights (these have some properties to adjust)– export images/animations



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• color choice can help to clarify a visualization• a handy guide is the online paper “A Rule based • color choice can help to clarify a visualization• a handy guide is the online paper “A Rule based • 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

• http://www.research.ibm.com/dx/proceedings/pravda/index.htm

• lots of interesting references at the end

• 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

• http://www.research.ibm.com/dx/proceedings/pravda/index.htm

• lots of interesting references at the end


• lots of interesting references at the end• lots of interesting references at the end




• another very nice online publication is “How NOT to Lie with Visualization” by Bernice E. Rogowitz

• another very nice online publication is “How NOT to Lie with Visualization” by Bernice E. Rogowitzto Lie with Visualization by Bernice E. Rogowitzand Lloyd A. Treinish, from IBM

• http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm– PRAVDA is intellectual property (IBM’s) separate from

OpenDX and isn’t freely available– the papers are still worth reading

to Lie with Visualization by Bernice E. Rogowitzand Lloyd A. Treinish, from IBM

• http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm– PRAVDA is intellectual property (IBM’s) separate from

OpenDX and isn’t freely available– the papers are still worth reading


p p gp p g



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November 5, 2008November 5, 2008Source: http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm



Sample Data SetSample Data Set

• We have the electric potential due to a dielectric cylinder introduced into a

• We have the electric potential due to a dielectric cylinder introduced into a dielectric cylinder introduced into a constant electric field E0

• the parameters I used are:– E0 = 50 V/m– dielectric constant = 5 F/m

R = 10 m

dielectric cylinder introduced into a constant electric field E0

• the parameters I used are:– E0 = 50 V/m– dielectric constant = 5 F/m

R = 10 m


– Rcyl = 10 m– -50 m ≤ x, y, z ≤ 50 m– Rcyl = 10 m– -50 m ≤ x, y, z ≤ 50 m



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Slide 37 of 75

OpenDX Data ImportOpenDX 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

• 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 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 );

-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 );


p ( , \ , , y, , );}

}}

• row major is defined by the last index varying the fastest

p ( , \ , , y, , );}

}}

• row major is defined by the last index varying the fastest



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OpenDX Data ImportOpenDX 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:

• 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:e ge e a eade e o ead s da a s:

• 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

i i

e ge e a eade e o ead s da a s:• 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

i i


• dependency = positions• positions = regular, regular, regular, -50.0, 1.0, -50.0, 1.0, -50.0, 1.0• end

• dependency = positions• positions = regular, regular, regular, -50.0, 1.0, -50.0, 1.0, -50.0, 1.0• end




• the connections between the points

• the connections between the points between the points are inferred when you tell OpenDX that the data are “row major”

• these are Cartesian connections

between the points are inferred when you tell OpenDX that the data are “row major”

• these are Cartesian connections



Slide 40 of 75

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• you can also work in non-Cartesian

• you can also work in non-Cartesian non Cartesian coordinates

• the grid is row major in cylindrical coordinates (r, phi, z)

• write Cartesian coordinates in the file

non Cartesian coordinates

• the grid is row major in cylindrical coordinates (r, phi, z)

• write Cartesian coordinates in the file


coordinates in the file and connections are inferred from the cylindrical grid

coordinates in the file and connections are inferred from the cylindrical grid






Slide 42 of 75

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Slide 43 of 75

Data ImportData Import

• Start with a FileSelector module to browse to the general file describing the data set

• 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

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



Slide 44 of 75

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Components of the visualizationComponents of the visualization

• Isovalues of the electric potential• The lower slice shows the electric • Isovalues of the electric potential• The lower slice shows the electric • 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 fieldUse the Isosurface module to extract contour

• 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 fieldUse the Isosurface module to extract contour


– Use the Isosurface module to extract contour lines at values

• -1750, -1250, -750, -250, 250, 750, 1250, 1750 volts

– Use the Isosurface module to extract contour lines at values

• -1750, -1250, -750, -250, 250, 750, 1250, 1750 volts




• In the Slab module set the parameters:

• In the Slab module set the parameters:parameters:– dimension: “z”– position: 0– thickness: (0 or 1)

• this is the default• The AutoColor module generates

a color map so that we have

parameters:– dimension: “z”– position: 0– thickness: (0 or 1)

• this is the default• The AutoColor module generates

a color map so that we have


a color map so that we have something to seea color map so that we have something to see



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• Take the output of the Slab module and attach it to the input of an Isosurface

• 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

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– Set the diameter of the tube to 1.0



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• Electric field linesTh iddl li i l d t th

• Electric field linesTh iddl li i l d t th • 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

• 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


• Use the Gradient module and the Compute module to calculate the electric field from the electric potential

E = - grad ϕ

• Use the Gradient module and the Compute module to calculate the electric field from the electric potential

E = - grad ϕ



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– Use a Slab module to extract a slice of the electric field

– Use a Slab module to extract a slice of the electric fieldelectric 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

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


– Use the Tube module to produce lines with some thickness

– Use the Tube module to produce lines with some thickness




• Use the Compute module after the gradient to negate the vector

• Use the Compute module after the gradient to negate the vector gradient to negate the vector components

• In the Compute module set “expression” to

[-a.x, -a.y, -a.z]• In Slab set

dimension: “z”

gradient to negate the vector components

• In the Compute module set “expression” to

[-a.x, -a.y, -a.z]• In Slab set

dimension: “z”


– dimension: z– position: 50– thickness: (0 or 1)

• this is the default

– dimension: z– position: 50– thickness: (0 or 1)

• this is the default



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• To calculate streamlines connect the Electric Field (output of

• To calculate streamlines connect the Electric Field (output of Compute) to the left input of the Streamlines module

• Use another Slab module to extract a line of points to use as seeds for the stream line– Dimension: “x”– Position: 0

Compute) to the left input of the Streamlines module

• Use another Slab module to extract a line of points to use as seeds for the stream line– Dimension: “x”– Position: 0


• Use Reduce to decrease the number of points by 4

• Use Tube with diameter 1.0

• Use Reduce to decrease the number of points by 4

• Use Tube with diameter 1.0



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• The top slice shows vector glyphs at some grid points of the electric field

• The top slice shows vector glyphs at some grid points of the electric fieldgrid points of the electric field– The glyphs show the direction of the field– The size of the glyphs is scaled to the

magnitude of the field

grid points of the electric field– The glyphs show the direction of the field– The size of the glyphs is scaled to the

magnitude of the field



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• Insert a Reduce module and a Glyph module between Slab and Collect

• Insert a Reduce module and a Glyph module between Slab and Collect

• The Slab module parameters:– Dimension: “z”– Position: 100

• The Reduce module has – Factor: 4.0

• In the Glyph module– Type: “rocket”

• The Slab module parameters:– Dimension: “z”– Position: 100

• The Reduce module has – Factor: 4.0

• In the Glyph module– Type: “rocket”


Type: rocket– Shape: 1.0– Scale: 0.15– Ratio: 0.1

Type: rocket– Shape: 1.0– Scale: 0.15– Ratio: 0.1






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• We have applied some visualization techniques to

• We have applied some visualization techniques to the data and created 3 slices

• pretty, but what does it mean??

• this lacks context• need some information to

help the viewer

the data and created 3 slices

• pretty, but what does it mean??

• this lacks context• need some information to

help the viewer


understand what we are looking atunderstand what we are looking at




• Annotations – add these to provide the context for the visualization

• Annotations – add these to provide the context for the visualization

• ShowBox lets the viewer know the volume of space occupied by the data

• Text: titles, labels – explain a bit• Axes provide orientation and scale• ColorBar – shows how the numbers are mapped

to color• Draw the cylinder so we see the cause of all the

• ShowBox lets the viewer know the volume of space occupied by the data

• Text: titles, labels – explain a bit• Axes provide orientation and scale• ColorBar – shows how the numbers are mapped

to color• Draw the cylinder so we see the cause of all the


Draw the cylinder so we see the cause of all the trouble in the fieldDraw the cylinder so we see the cause of all the trouble in the field



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• The ShowBox module draws a box around the extents of

• The ShowBox module draws a box around the extents of the data set– Use a Tube module to get

nicely rendered lines• Caption modules allow you

to place text in the 2D plane of the screen– Set the text and location in the

the data set– Use a Tube module to get

nicely rendered lines• Caption modules allow you

to place text in the 2D plane of the screen– Set the text and location in the


Set the text and location in the interfaceSet the text and location in the interface






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• A very useful annotation in this

• A very useful annotation in this annotation in this visualization is some indication of where the cylinder actually is– It is, after all, the

source of all the i i i fi

annotation in this visualization is some indication of where the cylinder actually is– It is, after all, the

source of all the i i i fi


disruption in the fielddisruption in the field




• Use the Construct module to create a line– Origin: {[0 0 -50]}

• Use the Construct module to create a line– Origin: {[0 0 -50]}– Deltas: {[0 0 1]}– Counts: [1 1 101]– Data: {1}

• The Tube module creates a cylinder around the line– Diameter: 20.0– Ngon: 25

– Deltas: {[0 0 1]}– Counts: [1 1 101]– Data: {1}

• The Tube module creates a cylinder around the line– Diameter: 20.0– Ngon: 25


g• The Color module does just that

– Color: “purple”– Opacity: 0.3

g• The Color module does just that

– Color: “purple”– Opacity: 0.3



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• When we put it all together and select the camera angle that we want we hopefully

• When we put it all together and select the camera angle that we want we hopefully camera angle that we want we hopefully have what we want …

• My goals– Show a variety of techniques that I can apply

to this data set– Provide enough annotation to orient the

camera angle that we want we hopefully have what we want …

• My goals– Show a variety of techniques that I can apply

to this data set– Provide enough annotation to orient the


Provide enough annotation to orient the viewer

– Make it look nice

Provide enough annotation to orient the viewer

– Make it look nice



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DebuggingDebugging

• Debugging• Sometimes things aren’t working and you • Debugging• Sometimes things aren’t working and you • Sometimes things aren t working and you

just don’t know why• OpenDX’s equivalent of the “print”

statement is the Describe module• Attach the Describe module to the output

port of any module that is providing a

• Sometimes things aren t working and you just don’t know why

• OpenDX’s equivalent of the “print” statement is the Describe module

• Attach the Describe module to the output port of any module that is providing a


p y p gfield and Describe will give you a summary of what the module is providing in the Message Window.

p y p gfield and Describe will give you a summary of what the module is providing in the Message Window.



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DebuggingDebugging



Slide 69 of 75


• lots of info on the web h i t d t t

• lots of info on the web h i t d t t• we have some introductory pages at

– http://sciviz.aict.ualberta.ca• we have some introductory pages at

– http://sciviz.aict.ualberta.ca



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WestGrid Future VisualizationWestGrid Future Visualization

• nothing definite yet• vendors are supplying Viz Clusters to • nothing definite yet• vendors are supplying Viz Clusters to vendors are supplying Viz Clusters to

provide the functionality of the VAN• a Viz Cluster is:

– a bunch of PC parts– graphics processing units (GPUs) for rendering– software to tie it all together

vendors are supplying Viz Clusters to provide the functionality of the VAN

• a Viz Cluster is:– a bunch of PC parts– graphics processing units (GPUs) for rendering– software to tie it all togethersoftware to tie it all together

• a Viz Cluster– combines cpus for numerical computations– combines gpus for graphics rendering

software to tie it all together• a Viz Cluster

– combines cpus for numerical computations– combines gpus for graphics rendering



Slide 71 of 75

WestGrid Future VisualizationWestGrid Future Visualization• a viz cluster is generally running a version

of Linux with• a viz cluster is generally running a version

of Linux with– Message Passing Interface (MPI/Pro, Mpich or

LAM/MPI) for inter-process communication– Distributed MultiHead X (DMX) to create a

single X Windows session across multiple displays

– Chromium is used to distribute OpenGL work

– Message Passing Interface (MPI/Pro, Mpich or LAM/MPI) for inter-process communication

– Distributed MultiHead X (DMX) to create a single X Windows session across multiple displays

– Chromium is used to distribute OpenGL workChromium is used to distribute OpenGL work– VNC for remote access to the server

Chromium is used to distribute OpenGL work– VNC for remote access to the server



Slide 72 of 75

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WestGrid Future VisualizationWestGrid Future Visualization

Distributed Rendering Tile Display


Remote CollaborationVisualization in WestGrid


Slide 73 of 75

VendorsVendors• HP Scalable Visualization Array

– http://h20311.www2.hp.com/HPC/cache/281• HP Scalable Visualization Array

– http://h20311.www2.hp.com/HPC/cache/281455-0-0-0-121.html

• IBM Deep Computing Visualization– http://www-

03.ibm.com/systems/deepcomputing/visualization/

S Vi li ti S t

455-0-0-0-121.html• IBM Deep Computing Visualization

– http://www-03.ibm.com/systems/deepcomputing/visualization/

S Vi li ti S t• Sun Visualization System– http://www.sun.com/servers/visualization/

• Sun Visualization System– http://www.sun.com/servers/visualization/



Slide 74 of 75

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The EndThe EndThe EndThe End•• Questions?Questions?•• Questions?Questions?



Slide 75 of 75

introduction to scientific visualization in the …...ssh tunneling • we can use a gui and...

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