For data processing, image analysis, and computer simulation, the CABI has several workstations running SuSE Linux. Four of them (kryten, rimmer, zaphod, and zarquon) are in the Image Analysis Lab and three others (wonko, lister, and ghana) are in CABI West. Several researchers have Linux workstations in their offices. In addition a Sun Ultra 10 workstation (sulcus) and a Windows PC (Alborg) are in the Image Analysis Lab, and the SMIS simulator is usually in Raj's office or the 3T suite.
The CABI also has two IBM RS/6000 F50 file and print servers, a PogoLinux StorageWare 3800 file server, and a Dell Precision 420 web and ftp server (claymore). Several printers, jaz drives, CD writers, and DVD writers are available to CABI computer users.
Currently (December 2006) most CABI workstations are running SuSE Linux 9.0. However, there are some exceptions: (1) kryten has the MEDx image analysis software, which does not run under SuSE 9.0, so kryten is still running SuSE 7.3; (2) zaphod is now running SuSE 10.1, which we have installed for evaluation. Note that zarquon has temporarily been modified so that people can evaluate the AFNI diffusion plugin of Dr. LR Frank of UCSD; other software (FSL, slicer, etc.) has been disabled on zarquon for the time being.
If you need help with any computer problems please contact the Helpdesk of the Information Sciences Division (ISD, phone x6521). If the problem is related to Linux or AFS they will contact the CABI Computer Administrator.
Typically those who work in CABI get an NKI domain account and an AFS account. The NKI domain account lets you login to the Windows computers on the network and includes an email account. The AFS account lets you login to the CABI Linux computers and also gives you access to shared CABI directories (in /afs/cabi/common for example).
The NKI domain account (Windows account) is set up by ISD, and the AFS account is set up by the CABI computer administrator. Accounts can be requested by contacting the Helpdesk (phone x6521). It is most convenient when the usernames of both accounts are identical, so if you have one account and are requesting the other let them know your username. Note that AFS usernames are limited to 8 characters, so if you have a long surname (8 letters or more) be sure to ask that your username be no longer than 8 letters.
You should have the Windows AFS client installed if you want to access AFS files on your PC. To install it yourself see the webpage on Installing the Windows AFS client. Otherwise please contact the Helpdesk.
You can also access AFS files via the Network Neighborhood in Windows if you enable plain text passwords. This is described in the Frequently Asked Questions. However, since the access is through a workstation rather than one of the fileservers, it is slower, especially when the workstation is being heavily used by someone else. In addition, if the workstation crashes you can lose changes to the file that you're working on. The AFS client avoids these problems.
When your windows PC is setup, ISD will install printers accessible through the NKI print server. Follow the instructions for installing a CABI printer in Windows if you want to install additional printers, or contact the Helpdesk.
The CABI Unix computers use the Andrew File System (AFS), which resides on the IBM servers golem and balrog. MRI data acquired on any of our MR systems can be saved to the AFS filespace and accessed from a Linux workstation or a Windows PC for subsequent image processing and display. Data can be shared between users collaborating on projects, without the inconvenience of having to copy data from computer to computer.
When you login to a CABI Linux workstation, your home directory is your AFS home directory. On a Windows PC, you can access the files in your AFS home directory using the Windows AFS client which can be installed on your PC.
AFS provides enhancements over the conventional Unix NFS file system, including file caching for increased speed, greater flexibility in file sharing and increased protection of data. However, with the new file system come some new commands, which are described in great detail in IBM's AFS User Guide, in less detail in the CABI Short Introduction to AFS, and in the briefer CABI Useful AFS Information.
| /afs/cabi | start of the AFS directory tree |
| /media/jaz | mount point for jaz drives |
| /temp | local directory on computer for temporary data |
| /usr/local/dmp | contains programs written or installed by CABI users |
| common | contains subdirectories for useful IDL programs, MATLAB startup files, the website, and other files |
| download | contains some software downloaded from the internet |
| temp | you can create a subdirectory in /afs/cabi/temp and store data there temporarily |
| usr | contains users' home directories |
For example, /afs/cabi/usr/lewis. Home directories are 1-2GB in size. The symbol ~ refers to your home directory. For example, to change to the public_html subdirectory of your home directory you could type cd ~/public_html.
Your AFS home directory contains the following subdirectories:
In addition, some users have 5 GB data volumes mounted as subdirectories dv01, dv02, ... of their home directories. If you need more disk space you can ask for one or more of these volumes, but be aware that disk space is limited. Note that data in these data volumes are not backed up. Principal investigators who need a lot of disk space for a project can purchase extra disks to be installed on our file servers, and we will allocate extra disk space for them and those who work with them. We prefer to buy 6-7 identical disks at the same time and install them as a RAID array for extra protection of your data. Previously, various PI's have pooled together money to buy disks. If you are interested, please contact the CABI system administrator (Dave Lewis).
The temp directory /afs/cabi/temp has 7.5 GB of disk space for temporary storage of data. If you run out of disk space in your home directory, you can create a subdirectory of /afs/cabi/temp and store data in it. Because of the temptation of most of us to store data there indefinitely and because many people have to deal with large amounts of data, data is "cleaned" from the temp directory automatically every night. The "cleaning" program deletes files based on their size and modification date; how long your files stay there is therefore dependent on what other files are there (and thus is hard to predict). We do not backup this temp directory.
Each user home directory has a temp subdirectory. The permissions are set on it to be writable by all users. If others want to give you data, you can have them put it in your temp subdirectory.
Each Linux workstation has about 8 GB of disk space available in /temp. However, it is not backed up. If you use it, please create your own subdirectory for your data, and please delete it when it is no longer needed. Please do not rely on it staying there for any period of time, since others may need the space. And if they really really need the space, they might delete your data if they think that it is old. (Exception: Linux computers in people's offices instead have the directory /home which they can use as they please.)
All AFS home directories are backed up to tape nightly. Up to two versions of each file are kept indefinitely.
Users are responsible for backing up their own raw MR data. It is highly recommended that you do this soon after the data is acquired. While we have successfully retrieved from tape every file that users wanted that had been previously backed up to tape, the process is not perfect. You can burn data to CD on the 3T and 7T servers, most of the Linux computers, and on Alborg. The 7T server and some of the Linux computers (marvin, wonko, and zarquon) have DVD burners. The Linux CD/DVD writing program k3b has a nice graphical interface and is easy to use. (See the tips for burning CDs on our Linux computers.)
Note that the data volumes, which are mounted as subdirectories of some users' home directories as dv01, dv02, etc., are not backed up. We don't have the resources for it. Users are responsible for making their own backups of these volumes (on CDs or DVDs, for example).
The temp directories /afs/cabi/temp and /temp, as well as data on the ftp site, are not backed up either.
Since we store patient/subject data on our computers, it is especially important that our computer accounts be protected with good passwords. Hackers do try to gain unauthorized access to computers. Please use a good password even if you don't have patient data and even if you don't mind having your own files stolen or deleted by another person. Once on a computer, hackers can often figure out how to get superuser privileges and have access to all files. In addition, hackers could use our computers as a stepping stone to other systems or to launch denial of service attacks to your favorite websites.
When we create AFS accounts, we use a method that gives passwords that are easy to remember but not easily guessed. You are free to change your password with the kpasswd command, but please choose something that is not easily guessed. Also, your password must be between 6 and 8 characters in length.
Any word (English or otherwise) or name is not a good password. The first letter of each word in a sentence is a good way to generate a password, as long as the resulting password is not a normal word. But please avoid common acronyms or well known sentences. The first letter of each word in a line of a song is easy to remember, but try not to hum it when you log in. Intermixing words (for example, mixing CABI and fmri gives CfAmBrIi) is another good method, but more difficult to remember. Use of capitalization, numbers, and nonalphanumeric characters is good.
Please log out of computers when you are done with them so that other people can log in to them. Also, do not reboot a Linux workstation, since others may be logged into it remotely or may be running simulations or data processing programs in the background. For more information, see the webpage on CABI computer etiquette.
| Data Handling | How to transfer and archive data acquired at CABI |
| Software Resources | Description of CABI software resources and access from the internet |
| Hardware Resources | Description of CABI hardware resources including printers, jaz drives, and CDROM writers |
| Unix Commands | Some useful unix commands |
| Unix Techniques | Some useful unix techniques |
|
This page was last updated on 1/3/2007. |