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The three genomics servers are:
- Silverjack - Mainly
used by Phillip SanMiguel and other
'wetlab' people.
- Fermat - General
use; has most of the 'wetlab' programs on it as well as the
statistical programs.
- Descartes – Used mostly
for Oracle database production.
- Sapporo
– General use. Used mostly for
large statistical programs.
Silverjack, Fermat, and Descartes are similar in power and
capability. They are all Sun model E-450 computers with 4 processors
and 4 GB of physical memory. They all run the Unix-based Solaris 8
operating system and are clustered together so that when you log into any
of them you will be connected to your home directory and have a similar
working environment.
Sapporo is a SunFire V-880
computer with 8 proccessors and 32GB of physical memory. It runs the UNIX based Solaris 9
operating system and is clustered together with the other three Sun
servers.
Because of software licensing restrictions, there are some significant
differences on the servers.
- The GCG package runs
only on Fermat and Silverjack
- The SAS statistical
package runs on Fermat, Sapporo
and Descartes.
And there are some other small operational differences. In
general:
- If you want to run
'wet-lab' programs such as GCG, Lucy, the Staden package, etc. use
Silverjack.
- If you want to run
normal statistical packages or normal Unix programs use Fermat or Sapporo.
For web services, Silverjack is also known as "data.genomics.purdue.edu"
and Fermat as "www.genomics.purdue.edu".
There are two printers located in WSLR 204. A black & white HP
laserjet and a color Epson inkjet.
The Genomics center is open to anyone at Purdue who has an interest in
genomics. We will soon have an on-line form that you can fill out in
order to get an account. In the meantime please see the secretary in
WSLR 206 or one of the system administrators.
You can connect to the servers to run programs via four different
methods:
- Web -- for the GCG
package only. See below.
- Secure-telnet (SSH)
for a command line interface. http://www.freessh.org/
has several SSH client programs available. For PCs the 'putty'
program is adequate for simple use and is available here
but look at the above mentioned site for more powerful programs.
One of these is the FiSSH
program. We can not legally redistribute the FiSSH program so you
must download it on your own. For Macs we recommend the program
called 'nifty'.
- X-windows for a windowing
interface. Purdue has a site license for a PC and Mac X-windows
server. See the PACE
project. For the PC make sure you pick up the Hummingbird
program.
- VNC -- a simple
X-windows interface.
In general, if you are using the GCG package and are not a
"power" user, we suggest the web interface. If you are
comfortable with a command-line interface to the system, use an SSH
connection. Unless you really want to get mired into the Unix world,
using VNC instead of a straight X-windows program will be good for everyone
else.
To transfer files there are three different methods:
- The venerable FTP
(file transfer program). On the Mac a popular FTP program is
called 'Fetch', on the PCs a command program is 'WS_FTP' along with
many other good ones.
- From a PC, mapping a
network drive. If you are running WindowsNT or Windows2000 from
the file explorer you can 'map a network drive' to
'\\fermat.genomics.purdue.edu\yourname' where 'yourname' is your
Genomics login name. You do need to get pre-authorized for
this so talk to a sysadmin.
- From a Mac via the
'chooser' and 'appleshare'. The Genomics center is in the
'horticulture' zone and you can connect to one of the servers (fermat
or silverjack) using your Genomics login name.
Note: For all of the above, if you are not using a Purdue
computer then you will need use a proxy connection. This is simple to do if
you have a PC. See directory.purdue.edu/MAIL-HUB/md/pptp.html.
The main printer for the center is a black & white laser printer
called 'wslr' that is located in room 204 of the WSLR building. By
default this is where your printouts will go to.
To obtain a list of available printers type either:
lpstat -s lpstat -p -D
To print a file to a printer use either the "lp" or
"lpr" command. In order to print to the non-default printer
you must append either "-d" or "-P". As example,
to print to the printer 'color' one would use:
lp -d color myfile(s) lpr –P color myfile(s)
It is possible to define your own default printer via modifying the
'LPDEST' variable. As an example, to set the default printer to
'hans311', most people would type:
setenv LPDEST hans311
This can be done either at a command prompt or, in order to make the
modification permanent, via editing your '.cshrc' file.
For GCG users, you can set your plotting device via 'setplot' command.
We can also add printers to global list. These printers should
either be on the Macintosh network (e.g., viewable via the 'chooser') or
have an IP address. Most modern printers that are hooked directly to
network are of the latter sort. It may also be possible to hookup a
PC-only printer. It depends a lot on the PC and the printer. In
any case please get hold of one of the sysadmins.
The preferred method of contacting both system
administrators is via email to:
genomicssysadmin@purdue.edu
(both go to the same shared mail box.)
Rick
Westerman is the backup sysadmin and the
main person for the 'wet-lab' or biocomputing packages.
Email: westerman@purdue.edu.
Phone: 49-40505. Home phone: 743-6596.
Doug Yatcilla is the main sysadmin and
statistical package person. Phone: 49-41429. Email yatcilla@purdue.edu.
If you need a new account created, other system work done, or need help
on a statistics package then please contact Doug first. If you need
help on the GCG, VectorNTI, or other wetlab programs please contact
Rick. While we both can provide help in any area it is best to go
directly to area specialist.
If it is an emergency (e.g., the system is non-functional) get hold of
Doug first if possible and then Rick. Or simply send us both email
at gadmin@purdue.edu and then call.
Purdue
University and School
of Agriculture
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