Hardware Computer Resources

Contents

• Overview

• Printers

• JAZ drives

• CDROM writer

Overview

The CABI computer resources include two IBM RS/6000 F50 file and print servers, a Linux file server, a Linux web and ftp server (claymore), four 700 MHz - 1GHz Dell Precision 410/420 Linux workstations (kryten, lister, rimmer, and zaphod), two 3 GHz dual processor PogoLinux workstations with 2 GB memory (wonko and zarquon), a Sun Ultra 10 workstation (sulcus), a Windows NT workstation (Alborg), and various other Windows PCs. The following workstations are located in the Image Analysis Lab: Alborg, kryten, rimmer, sulcus, zaphod, and zarquon. The following workstations are located in CABI West: marvin and wonko.

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.

Users' data are stored on RAID 5 disk arrays, and home directories are backed up every night. The total unix disk space available to users is about two terabytes. Several printers, jaz drives, and CD writers and DVD writers are available to CABI computer users.

Printers

Several printers are available to CABI users. Follow the instructions for installing a CABI printer in Windows if you want to install a printer on your PC, or contact the Helpdesk.

JAZ drives

2 GB Jaz drives are available on the linux workstations kryten, marvin, trillian, and zaphod. They will read and write to 1 and 2 GB Jaz cartridges formatted for PC or formatted with the linux ext2 file system. They will also read Jaz disks formatted for sun.

Mounting

To mount a cartridge on the Jaz drive, first insert it gently into the empty drive. If you encounter resistance, pull the cartridge out and realign it with the drive opening before reinserting. After the cartridge has been inserted, mount it by left-clicking the Jaz icon on the desktop (opens the Konqueror file manager) or by right-clicking the Jaz icon and choosing 'Mount'. Alternatively, enter the following command:

mount /media/jaz

The jaz drive will be mounted at /media/jaz, so you can get to your files with "cd /media/jaz" or through the Konqueror file manager.

Unmounting

To unmount the cartridge, first make sure that you are not working in /media/jaz or any of its subdirectories. Then right-click the Jaz icon and choose 'Unmount'. Alternatively, enter the following command:

umount /media/jaz

This will unmount the drive, after which you will be able to eject the cartridge by pressing the small round button on the front right corner of the drive. If you get an error message saying that the Jaz is busy, make sure that none of the files on the Jaz disk are open and that your current working directory is not /media/jaz or any of its subdirectories.

CDROM Writers

The CABI has HP CD writers available on the linux workstations kryten, marvin, trillian, and zaphod.  The CD writers are capable of writing both CD-R and CD-RW media at speeds up to 12x. The CDROMs created on these drives are readable on other unix workstations as well as Windows and Macintosh computers. We use a GUI-based application for writing CDs called "xcdroast" (see instructions below). 

The advantage of the CDROM is that it is relatively inexpensive and random access media for archiving data and other important files that you might have. We highly recommend it for making archival copies of the precious data that you collect at the CABI. CD-R blanks are available at most computer stores such as CompUSA in West Nyack (10 minutes away in Palisades Center at Route 303 and the New York State Thruway) for $1-2 each.

Instructions to users of SuSE Linux 8.2 and 9.0

Use k3b instead of xcdroast. It is much more intuitive - with its graphical interface you can drag and drop the files you want for example. See the tips below.

Instructions for writing files to a CD with xcdroast version 0.98

1. On a linux machine with a CD-RW drive, type "xcdroast" to start the application.
2. Read the Disclaimer message and click "Accept".
3. If this is the first time you are running this version of xcdroast, click "Setup", then "Save Configuration", then "OK".
4. Click "Create CD" and then "Master tracks".
5. In the "Master source" tab, select the files and directories that you want to copy to CD from the "File/Directory view" area. Either navigate to a file or directory through the small browser (may be slow; see below) or type in the file or directory path below the browser. Then click "Add" and specify the path on the CD on the CD to be burned (see below). The files and directories will be listed in "Session view".
   • if you navigate to the directory, go through "cabi.rfmh.org" or "cabi" rather than ".cabi.rfmh.org", which can be slower
   • navigating to a directory will be slow if there are thousands of files in the directory or if you just have "l" ("list") permissions in that directory (or a higher-level directory in the directory tree)
   • you can add multiple files or directories; you can remove them with "Remove"
   • if you add just one file or directory, you can add it to the root directory of the CD ("/"). If you instead choose "Add with full path", it will put the whole directory structure on the CD; then later when you want to use the CD you will have to navigate through through the whole directory structure
   • for multiple directories: choose "Add with custom path", and then specify a path. For example, if I wanted to copy two directories, /afs/cabi/usr/lewis/Siemens and /afs/cabi/usr/lewis/SMIS, I would use the custom paths "Siemens" and "SMIS" respectively. When the CD is burned, two directories, /Siemens and /SMIS, will be created. If instead you choose "Add to root directory", xcdroast will try to combine all of the directories into the root directory (top directory) on the CD, which can cause confusion or filename conflicts
   • to change the pathname(s) on the CD: select the path in "Session view" (click on it once), click on "Redirect", and type the desired name of that directory on the CD
6. Click on the "ISO9660 options" tab to specify the image type. We suggest "Rock Ridge + Joliet".
7. Click on the "ISO9660 header" tab. You can set the various ID fields. The most important one is the Volume-ID since this will be the label of the volume when you mount it on Windows or Unix.
8. Click on the "Create session/image" tab. Click on "Calculate size" and verify that the "New session size" is not too big to fit on the CD.
9. Choose either "Master to image file" (recommended in most cases, such as from your home directory or /afs/cabi/temp) or "Master and write on-the-fly" (recommended if you are writing data locally, such as from a Jaz disk, CD, or /temp).
   1. Mastering an image file -- useful if access to your files is slower than the CD writing speed (e.g., accessing your files over the network, which is normally the case). xcdroast will first write your data to an ISO file in /temp. The name of this file is determined by the "File prefix". Then you write the ISO file to a CD.
      1. Make sure that the "biggest available block" is larger than the "New session size". If there is insufficent disk space, you will need to delete old ISO files - see step v below.
      2. Choose a name for the "File prefix". By default it will be "track", which means that it will try to create an ISO file called "track-01.img" in /temp. If someone else already created this file, you will get an error message. In that case, use a different file prefix.
      3. Create the ISO file: Click "Master to image file". A CD image file in ISO format will be created in /temp with a name like "track-01.img"
      4. Write the ISO file to a CD: Click "Write Tracks", then click on the "Layout tracks" tab. Click the image file name (under Image-Information) to select it, then click "Add". Then click "Accept track layout", then the "Write tracks" button at the bottom of the window.
      5. Verify the CD writing (optional): Click on "Verify Tracks", then "Start Verify Image". A progress meter will appear to document the progress of the verify. Click "OK" when this is done.
      6. Delete the ISO file from /temp: Click on "Delete Tracks". Select the image file you wish to delete by clicking on the checkbox. Click on "Delete selected Tracks". You will be prompted if you really want to delete the track, then click "Yes".
   2. Mastering and writing on-the-fly -- write data directly to CD without creating the ISO file first. Note that if you are writing data from your home directory or from /afs/cabi/temp, the data has to travel across the network, which generally is not able to keep up with writing on-the-fly at fast speeds such as 12x.
      1. Click "Master and write on-the-fly".
      2. A progress meter will then appear indicating the percentage of the data that has been written. If the "FIFO" bar reaches 0%, the file access was not fast enough to keep up with the CD writer.
      3. When the write is complete, click "Ok".
10. Click on "Back to Main" and then "Exit"

Tips for xcdroast

• In step 5 above (specifying the directory), navigating to the file or directory may be slow if there are thousands of files in any part of the path. (When you navigate to a directory, Xcdroast checks every file in that directory to see whether it is another directory.) It will also be slow if you just have "l" permission in any part of the path. It will be faster if you type in the path.
• When you add a directory in step 5 above, everything in that directory will go to the root directory of the CD by default. (The root directory is the top-level directory on the CD.) For example if you add the directory /afs/cabi/usr/doe/data, all the files and subdirectories in /afs/cabi/usr/doe/data will be added to the CD, but there will be no directory on the CD named /afs/cabi/usr/doe/data. You can specify a directory to put the files in with "Redirect".
• Hence if you add multiple directories (step 5 above), by default their contents will be added to the root directory of the CD, i.e. they will all be combined into one directory. This can be confusing and there is a potential for filename conflict. "Redirect" will avoid the problem.

Tips for both k3b and xcdroast

• Don't use cheap CD's, because they may go bad over time.
• We suggest using Rock Ridge and Joliet for compatibility with CDROM reading in both Unix and Windows.
• After writing to CD, look at it in Windows or Linux to double-check that it came out OK.
• Writing on-the-fly: If you want to write on the fly, we suggest that you first try it in simulation mode to make sure that file access is fast enough to keep up with the CD writing. (Remember that your AFS files are stored on the file servers, so the files have to travel over the network, which is often slow compared to the CD writing speed.) If it fails simulation mode, either decrease the writing speed (default is 12x) or master to an image file.
• Writing to CD on-the-fly from Jaz disks: If the files are fragmented, file access for your files on the Jaz disk may be slow. Again we suggest first testing in simulation mode.

This page was last updated on 12/5/2006.