Please note: The FAQ pages at the HPCVL website are continuously being revised. Some pages might pertain to an older configuration of the system. Please let us know if you encounter problems or inaccuracies, and we will correct the entries.
This is a simple introduction to the HPCVL installation of the Numerical Algorithms Group (NAG) visualization software called "Iris Explorer". Documentation for this system is available online on our machines, and this FAQ is only meant as a basic introduction to its use on HPCVL computers.
The Iris Explorer is a very powerful visualization tool. It is designed in a modular manner to offer maximum flexibility. The Iris Explorer is provided and licensed by the Numerical Algorithms Group (NAG). In this FAQ we can only scratch the surface of its capabilities, and have to refer to the User's Guide for a more detailed treatment.
The current version of the Iris Explorer software on HPCVL machines is Release 5.0
Like most "optional" software on SUN systems, the Iris Explorer is located in the /optdirectory hierarchy. The directory root is shared with the other NAG software (i.e., libraries): /opt/nag/
The software itself is located in /opt/nag/explorer/bin.
The program requires the setting of the environment variable LM_LICENSE_FILE to work. Since it calls a Graphical User Interface, you will also have to set DISPLAY to make sure the graphics goes to your terminal. For csh:
setenv LM_LICENSE_FILE /opt/nag/license/license.dat
setenv DISPLAY ip_address:0
where ip_address stands for the IP address of your terminal, workstation, or PC.
Often it is necessary to set the following graphics variable to ensure proper operation:
setenv CXGLTYPE mesagl
This might not be necessary if your client machine has the proper graphic libraries installed. To be on the save side, it is best to include it.
It is also necessary to set several other enviroment variables. Those are collected in thesample.cshrc file in /opt/nag/explorer, and may be accessed by "sourcing" that file; in csh:
Then, the program can be started by typing
Alternatively to this sequence of setup commands, you may rely on the usepackagefacility to set up your system for Iris Explorer. By typing
at the command prompt, or including this command in your .login or .profile file, the above setup commands will automatically be applied to your shell and Iris Explorer can then just be started by typing "explorer &". Note that the DISPLAY environment variable may still have to be set manually.
HPCVL has a license agreement with the Numerical Algorithms Group. This license allows Iris Explorer to be executed on our machines without restrictions on the number of processes or seats.
The presence of a valid license is checked at runtime. This means that a license manager is automatically invoked everytime Iris Explorer is executed. This license manager will then check the system for a presence of a license file which uniquely identifies the machine.
Our agreement with NAG includes the unique opportunity for HPCVL users to download and use the Iris Explorer on their own workstations. Individual license keys will be required for this, and will be issued by us on a temporary basis. The validity of the license key is limited by the duration of our agreement with NAG, and of your access with HPCVL. Within these terms, you can freely use the software on an arbitrary number of machines. Note that we also require our users to sign a statement that they are HPCVL users, that the license keys will not be copied and passed on to third parties, and that the usage of the software will be non-commercial and serves research purposes. Find a copy of the statement here, and return it to us signed to be issued a license key. Note that the statement extends to all NAG software, i.e. it includes the NAG libraries as well. All NAG Software can be downloaded here.
After the program was set up properly, it can be started by simply typing
The ampersand enures that the explorer process is detached from the command prompt, i.e. it runs in the background and your terminal may still be used.
When you start the program, you will be presented with three windows: the Librarian, the Editor and a Log window. The program uses a "toolbox" principle.
In the librarian window you will find a large number of modules, which perform certain simple tasks, such as reading in data from a file, or calculating a function of several variables, or displaying graphics. You can click-and-drag those modules to the editor window to build a map. The librarian window also includes quite a few fully developed task maps that can serve as examples.
The editor window is the main component of Iris Explorer. Here you arrange modules that perform simple tasks to a network called a map. The output of one module may be connected to the input of another, and with this map you are able to specify the overall visualization tasks that you may want to have performed. Here is an example (from the pre-made maps that come with the program):
The map "Simple" is meant to display a so-called isosurface of a three-dimensional distribution, ie, the set of all points that share a specific value of that distribution. This is done in the simplest possible manner by reading the distribution in from disk and constructing the isosurface from those data. The map consists of three component modules: ReadLat, IsosurfaceLat, Render.
ReadLat has no input channel, and consists only of a GUI that lets the user specify which â€œlatticeâ€ file contains the needed data for the distribution. A lattice is a special data structure used in Iris Explorer to specify data of various complexity, dimensionality and connectivity. Such data might be generated by a program or by another module. ReadLathas one output channel through which it passes the lattice on to the next module.
IsosurfaceLat produces a specified isosurface from a 3D lattice. It has one input channel for a 3D lattice representing a three-dimensional distribution, and one output channel for asurface geometry. A surface geometry is a graphical object which may be displayed. There are a few adjustable parameters which might be passed to this module via a GUI, e.g. To specify the value of the isosurface.
Render is the standard renderer in Iris Explorer, and excepts several types of input, one of them being geometries. It has a variety of adjustable parameters which may be adjusted via a GUI, and have to do with the rendering of objects that are being displayed by this module, for instance colors, light sources, orientation, size, perspective, etc.
The output of each of these modulkes is connected to the input of the next one, giving a chain ReadLat > IsosurfaceLat > Render. It is at any point possible to switch in or add additional modules, for example to produce a bounding box, axes, cuts, annotations, etc.Iris Explorer comes with a large number of example maps a prepared modules. However, it is relatively simple to write additional modules and integrate them into the program, for example to let you convert the output data from your favourite program into a "lattice" that can be processed by Iris Explorer's modules.
NAG software is very well documented. For Iris Explorer online documentation is available in form of the User's Guide . We are holding a hard copy of the entire NAG doumentation at our Kingston office as well.
Some level of support is also part of our agreement with NAG, so if you contact us we can forward your questions and concerns.
HPCVL also offers user support; for questions about this FAQ and the usage of the NAG libraries on HPCVL machines contact us .