Hardware Computer Resources
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.
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.
|Printer Name (Windows)
||Printer Name (Linux)
||HP LaserJet 4M, PostScript, 600 dpi, plain paper
||Default printer for CABI West
||HP LaserJet 4050N, PostScript, 600 dpi, plain paper
||Image Analysis Lab
||Default printer for Image Analysis Lab
||Dell Color Laser 5100cn, PostScript, 600 dpi, plain
||up to 25ppm full-page color, 35ppm B&W
||HP LaserJet 4si, PostScript, 600 dpi, plain paper
||DMP Main Office
||Not accessible from Linux
||HP Color LaserJet 4550N, PostScript, 600 dpi, plain
||Information Systems Division (ISD) Teaching Area
||Not accessible from Linux; 4ppm full-page color, 16ppm B&W
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
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:
The jaz drive will be mounted at /media/jaz, so you can get to
your files with "cd /media/jaz" or through the Konqueror
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:
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.
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
- On a linux machine with a CD-RW drive, type "xcdroast"
to start the application.
- Read the Disclaimer message and click "Accept".
- If this is the first time you are running this version of
xcdroast, click "Setup", then "Save
Configuration", then "OK".
- Click "Create CD" and then
- 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
- if you navigate to the directory, go through
"cabi.rfmh.org" or "cabi"
rather than ".cabi.rfmh.org", which can
- 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/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
- Click on the "ISO9660 options"
tab to specify the image type. We suggest "Rock
Ridge + Joliet".
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- 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"
- 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.
- 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.
- 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".
- 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.
- Click "Master and write
- 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.
- When the write is complete, click
- Click on "Back to Main" and then
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
- 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
||This page was last updated on 12/5/2006.