Computational Facility Spotlights

We are continually adding new features to our Computational Facility (and expanding the spotlight to highlight more of the existing features of the Facility) so come here often.

VMD and a Crowd
Since 1993 we have maintained a stereo projection facility to create an interactive visual environment for computational molecular modelling. A projected computer screen serves as a window to three dimensional images which are easily viewed by groups of people. In addition, a haptic input device allows for users to actually feel the forces as they are applied to the molecular systems. More information on the facility is available here.
Public Visualization Workstations
When the power of our desktop workstations is not adequate to properly view and manipulate the molecules we study, we must use larger systems with additional memory, processing power, video, and input devices. Our primary visualization workstations are a Sun Ultra 40 workstation featuring nVidia Quadro FX 5800 graphics and 32 gigabytes of memory and Supermicro workstations featuring nVidia Quadro FX 5800 graphics and 48 or 72 gigabytes of memory; equipped with stereo emitters, dual monitors or a 30" display, and SpaceNavigator input devices for the best user experience; one of these also runs our 3D projection facility. We also have additional Sun Ultra 40s, Supermicro workstations, and an Apple Mac Pro available for public visualization use. The full list is available here.
User Desktops
In order to properly analyze our data, each user must have a powerful graphics workstation on their desktop. These desktops are custom built Xeon W3520 workstations housing 24GB of memory and a nVidia GTX 470 graphics graphics board. Intel based Apple iMacs are used for administrative work. The full list is available here.
As the Resource simulates larger and larger molecules for increasingly long times, the need for disk space has grown exponentially. Our local network currently hosts 500 terabytes of hard drives, divided across seven file servers. In addition to a five gigabyte disk quota for their home directories, users can store up to three hundred gigabytes of regularly backed-up data in a shared Projects space. An additional terabyte of shared space available as scratch space for all users. More information on our disk space partitioning is available here.
titania cluster
Since 1993 the Resource has been using compute clusters to cost-effectively perform Molecular Dynamics simulations. We built our first Linux PC cluster in 1998, and have continued to configure newer, faster, and larger systems approximately every two years since. More information is available here.
Wide Variety of Systems
To properly develop, maintain, and test our software for our diverse user base, our developers need access a broad variety of hardware and operating systems. On the hardware side, in addition to our standard Linux workstations we maintain development systems that allow us to develop software on multiple operating systems on ARM, x86, SPARC, and other desktop hardware platforms, and for various makes and models of mobile phone and tablet devices. The full list is available here.
File Servers
Servers that store data and serve content to the outside world must be as stable as possible. As such, we rely on three classes of stable servers to store our data and share our work. Two SunFire X4200s and five SunFire X4270s store and share our data throughout the Resource's machines and beyond, acting as file, web, and mail servers; seven SunFire X4500 class servers offer additional file storage capacity with years of uptime; and five SunFire V100s/Netra X1s offer additional services, such as name service, printing, SMB, and external logins. The full list is available here.
System Security
While many research groups choose to work behind a firewall, the Resource has chosen to stay open to the world and instead focus on making sure each system on the network is well-defended. Generally, the only service open on a given system is SSH, for remote access. User passwords never go over the network in the clear, where they could be intercepted; instead, all relevant connections are encrypted using SSL or similar technologies (IMAP/S, SSH, SFTP, etc), and the only unencrypted traffic is web, mail, and other unauthenticated traffic (and even these protocols offer SSL capabilities). Systems and services which cannot be fully secured are TCP wrapped, to remove access from unapproved systems. New systems are scanned to ensure that no unauthorized ports are open. Our system administration team generally patches holes in our open services within six hours of their discovery. Windows systems are patched nightly with SUS.
Backup System
In a research environement, data integrity is at least as important as creating the data in the first place. To ensure that files are not lost to user or hardware error, we have developed an in-house backup solution, based on Sun's ufsdump and ufsrestore commands for UFS filesystems. We also have an in-house solution for Sun's ZFS filesystem. Files are dumped nightly to disk, and monthly to external disk; several copies are kept of each. These dumps allow us to easily restore lost user files, as well as recover from catastrophic disk failures. Additionally, we structure our backups so that the data can be read back from any system ten years from now.