UNIX/Linux COMPUTERSTable of Contents
Here we present a small collection of useful pieces of information, which, where appropriate, are Narrabri specific.
The software for analyzing ATCA data is run on the server Kaputar or the desktop Linux PC's. For information about this software see the section on ATCA Data Analysis Software in the chapter on Application Software.
The main compute server Kaputar is a dual Quad core Xeon processor Linux machine with 96GB of memory and in excess of 20 TB publicly available data disk, however the Linux Workstations are also capable of running the data reduction packages locally. Kaputar and the workstations handle nearly all the general data reduction and analysis by vistors.
To access Kaputar simply connect via ssh from the workstations, there is a choice of 4 Dell PCs running Windows7 or Linux. All these provide display facilities (the X-terminal and PC via Xming). Their main use is for working on ATCA data with Miriad or AIPS. They are located in the observers areas in the control building in the region adjacent to the control room and the the library.
Local Home directories are hosted on a server called Zephir. It should NOT BE USED for data reduction at any time. Its main use is as a server of software packages to all other machines, and providing network services e.g. DNS.
Note again that most data reduction is done on Kaputar but data reduction can be performed on the Dell workstations, simply mount /DATA/KAPUTAR_3 via the automount facility e.g. "cd /DATA/KAPUTAR_3". Your home directory is accessible from the workstations so jobs like editing & latex can be done locally. The workstations usually have a substantial data disk of their own.
Note that some miriad programs (xmtv) expect an 8 bit display and won't work on a 24 bit display. You can switch between these two options by setting either OpenWin8 or OpenWin24 in your .login file as follows:
setenv WINDOWS OpenWin24
setenv WINDOWS OpenWin8
and logging out & back in.
An account is generally setup for you, a visitor, before your arrival. On arrival, you can collect your password from Robin Wark, or, in her absence, from the Duty Astronomer. You should then change the password to something else. We do not encourage sharing of accounts, unless collaboration on the same data set makes this the only sensible course of action.
There is no booking system for these workstations and their usage is is regulated largely by the visiting astronomers amongst themselves. It is rare that the load is too great for us to handle in some suitable way with the available resources.
When you leave Narrabri, please ensure that you delete all your data files, and also return your home directory to its bare minimum. If you do not make prior arrangements, any old files left on the system will be deleted without notice if need be.
If you wish, you can fiddle about with the .login and .cshrc files and use your favourite procedures. However, every institution seems to install windowing software and all the support libraries differently, and you might spend all your time trying to get your scripts to run.
Having logged in for the first time, please change your password by entering the Unix command
and then follow the instructions.
The Narrabri computer network is discussed in a separate chapter of this document. Here we just mention a few useful commands or utilities that are availabe for your use in accessing other computers connected to Narrabri by the net.
Accessing Remote ComputersTo login to a remote another computer, use the ssh command. For example, to login to, say, Kaputar, from somewhere else, you would enter
% ssh kaputar
You will be prompted for your password.
If the computer you are trying to access is not in our local network, you may need to provide the full internet address. For Kaputar this would be
% ssh kaputar.atnf.csiro.au
Note that if you want to forward the X server output back to your terminal you must invoke ssh with the -X option For Kaputar this would be
% ssh -X kaputar.atnf.csiro.au
Exchanging Data with Remote ComputersTo retrieve or send files to another computer use a command such as
% sftp kaputar.atnf.csiro.au
to connect to the remote host. You then log in as prompted. Use the usual Unix command cd to change directories on the remote computer. Use the commands
ftp> get filenames
ftp> put filenames
to retrieve and send files respectively. If you are transmitting many files whose names you can wild card, try
ftp> prompt off
ftp> mget *.txt
to get all files with suffix .txt, for example. Terminate the session with the command quit
One common error with ftp is to forget to set the stream mode appropriately. By default, ftp thinks that it is transmitting ascii files. If you are transmitting a binary file, such as an executable, or a FITS file, or an RPFITS file, you must use the command
first, before retrieving or sending files. If you neglect to do this, the file will be irretrievably corrupted. To reset ascii mode, use the command
It is common to want to open an X-window display on a remote computer. Let us say that your are sitting at Turrawan-cj, but you have done an rlogin to Kaputar and wish to display something computed on Kaputar on Boggabri-cj screen. You must do two things. On Boggabri-cj, you must enter the command
% xhost +Kaputar
to tell Boggabri-cj to accept a connection from Kaputar. Then on Kaputar, you should set the environment variable DISPLAY (note case) with
% setenv DISPLAY Boggabri-cj:0
to tell Kaputar that it should send its X-display to Boggabri-cj. Then you are ready to do whatever it is you are doing!
Browsing the World Wide Web
To browse the World Wide Web, we offer the X-window based browser called Firefox. You start it like this:
% firefox &
To access the Web from a non-windows based terminal, use the command
The basic Unix help utility is called man and is accessed with a command such as
% man grep
to learn all about the search utility grep. This means you need to know the name of what you want help on before you can find out about it, so it's a bit annoying if you are in the dark to start with. Thus, you can use the command
% apropos searching
which hunts through the man pages for references to searching and returns them to you. Then you can use man more specifically.
Printing from the Unix workstations is documented here
By default, your working directory is your home directory where you can put a small (please try and keep this to less than 20Kbytes) amount of files. For visitors the default account setup has your home directory in Epping, acessed across the network. If your are planning on doing local work in your home directory, it's best to request a local home directory to speed things up. The main directories available for data reduction are on Kaputar and the workstations and are called /DATA/KAPUTAR_3, /DATA/KAPUTAR_4, /DATA/MACHINE_1, where MACHINE is the name of the workstation you're sitting at. For AIPS reduction access to this is automatic, for miriad reduction see the miriad section in the Application Software chapter on how to create your own area.
You can access RPFITS data still present on the CACCC disk directly by looking in the directory /DATA/CACCC_1 on Kaputar or the workstations. From miriad, you can directly access this in atlod by specifying e.g., atlod in=/DATA/CACCC_1/96-12-12_1520.C999. From AIPS, the CACCC disk is accessible from ATLOD by specifying INFILE='RPFITS:96-12-12_1520.C999'.
Mail is handled by the exchange system, so you need an IMAP capable mail program to access your mail.
Available mail handlers are:
- pine (keyboard driven)
- netscape (X-window based, select from window menu in browser)
If you are a new Unix user, the easiest Unix mail utility that works from any terminal is called pine. It has built-in help to get you going and has its own simple text editor.