Data Visualization on the SGI Onyx4

The CSB maintains state-of-the-art data visualization facilities funded by ACCRE. These facilities are accessible to all Vanderbilt research faculty, students, and staff and are currently colocated in 5119 Stevenson Center with the A&S Molecular Modeling Teaching Lab.


The facility offers an SGI Onyx4 "graphics supercomputer" with three methods of displaying visual data. The Onyx4 is an SMP-style shared-memory system with 8 CPUs, 4GB of RAM, a 3TB disk array, and four "UltimateVision" graphics boards, configured as follows:

  • Two of the graphics boards each drive their own active-stereo 1600x1024 widescreen 24" CRT for multiheaded local console login sessions.
  • A third graphics board drives a Cyviz SXGA passive-stereo projector for creating life-size stereo visualizations in 5119 Stevenson.
  • The fourth graphics board is dedicated to SGI OpenGL Vizserver software, which allows you to run standard OpenGL software applications on the Onyx4 from your office via a Windows, Macintosh, Linux, SGI, or Sun workstation connected to the Vanderbilt network backbone.


The Onyx4 uses MIPS CPUs and runs the IRIX operating system. In general, most any OpenGL software that runs on the IRIX/MIPS platform will run on the Onyx4. Older applications that use the IRIS GL API (instead of OpenGL) will not run due to the new ATI-based graphics architecture used on the Onyx4.

  • Compilers and Libraries: We are currently working on getting licenses for the SGI MIPS compilers from SGI so that you can compile software using the native commercial compilers for this platform. gcc and g77 compilers are available in /usr/freeware/bin. SGI's native MPI over ccNUMA implementation is installed. The MPI libs, headers, and executables are installed in system-default places (/usr/lib, /usr/include, and /usr/bin respectively) which makes it relatively easy to compile and link MPI applications without complicated modifications to Makefiles.
  • Amira: The primary commercial visualization application that is installed on the Onyx is Amira. Amira is a powerful application that allows one to quickly create complex, detailed visualizations of a wide variety of data. We currently have a single license of Amira on the system, so only one copy can be active at any one time although the system can handle more if such a demand is created. Amira documentation in PDF format is here. There are several demo visualizations located in /sb/apps/Amira-3.1.1/data/amira3.0Demos
  • Molecular Visualization: We have the AmiraMol module as well as a large selection of the most standard molecular modeling/visualization software packages installed on the system. AmiraMol documentation in PDF format is here.
  • Vizserver: SGI's OpenGL Vizserver software allows you to run OpenGL-based software on the Onyx and display the results over the network back on your Windows, Macintosh, Linux, SGI, or Sun workstation. This capability allows one to use the Onyx4 to create visualizations without leaving your office. In order to make this work, you need the Vizserver Client software installed on your workstation and a CSB login to gain access to the Onyx. See the using vizserver page for details.

Access & Usage Policies

These facilities are accessible to all Vanderbilt research faculty, students, and staff and are currently colocated in 5119 Stevenson Center with the A&S Molecular Modeling Teaching Lab. The Onyx4 and its software applications can be accessed remotely via Vizserver as described above.

At the moment there is no signup for the system so it is available on a first-come, first-served basis. As such, be considerate of other users and log yourself out when you are not using the system. For physical access to the facility (for multihead stereo graphics and/or stereo projection capability), contact Jarrod Smith for the door code.

For performance reasons, all data I/O should be performed from the local disk array, which is mounted in the filesystem as /sb/onyx/accre. You can create yourself a directory under this location and put your visualization datasets there. Note that this is treated as scratch space, which means it will not be backed up and files can be removed after 30 days of disuse, without warning. Once you create data files you wish to save, you must move them back to a known safe location.