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Hydra - Getting Started To use the cluster, you should log in to the front end, called hydra.sapac.edu.au, which has dual 2.4 GHz Intel Xeon processors running Linux (Redhat Enterprise Linux AS3). The front end should be used for compiling, debugging and testing your program code, and for submitting production jobs to the cluster. You should never need to log on to a node of the cluster, only to the front end. Please read all of this User's Guide before you try to run any jobs on the cluster, particularly the sections on compiling programs and running jobs. You must use ssh (secure shell) to log in to Hydra, and sftp (secure FTP) to transfer data. If you have not used ssh before, see the primer below for a brief guide on how to use it. Using ssh and sftp to access Hydra. ssh stands for Secure SHell, and is a secure replacement for telnet, rlogin and rsh, i.e. it is for logging in to a remote machine. The standard ssh packages also provide sftp and scp, which are secure replacements for ftp and rcp, i.e. for transferring data to and from a remote machine. If ssh is not available on your local machine, you can ask your systems administrator to install it, or install it yourself. You can download a ssh client for Unix from http://www.openssh.com/. You can download a ssh client for MS Windows from http://www.chiark.greenend.org.uk/~sgtatham/putty. On Hydra we are using openssh version 3.6.1p2. Older versions of ssh may not be compatible with this one, so you may need to upgrade. Using ssh and sftp is simple. To connect to Hydra from the SAPAC domain: For a Unix based computer, use, ssh hydra sftp hydra If you are outside the sapac.edu.au domain, you will of course need to specify the complete hostname: ssh hydra.sapac.edu.au sftp hydra.sapac.edu.au If your username on Hydra is different to your username on the machine you are logging in from, you will need to specify your username on Hydra: ssh username@hydra.sapac.edu.au sftp username@hydra.sapac.edu.au The process for a MS Windows based computer using the Putty ssh client is similar but slightly different in that the connection is done through a GUI. Please read the accompanying documentation or consult your systems administrator. The first time you connect, ssh may tell you that you have not connected to this host before, and ask if it should go ahead and connect. ssh username@hydra.sapac.edu.au
Host key not found from the list of known hosts.
Are you sure you want to continue connecting (yes/no)? yes
Host 'hydra' added to the list of known hosts.
username@hydra's password:
Last login: Tue Sep 26 10:16:48 2000 on tty1
NOTE - make sure you type "yes" not just "y": Using SCP to transfer data to and from Hydra. Another utility ssh provides is scp, which works exactly the same way as rcp for remotely copying files. To copy a file from your local machine to your home directory on Hydra, use: scp myfile.dat username@hydra: Note the ':' at the end. You can also specify a directory where you want the file to go: scp myfile.dat username@hydra:/home/username/mydir or a new name for the file, as with the standard cp file copying command: scp myfile.dat username@hydra:/home/username/mydir/mynewfile.dat There is a GUI based scp client for MS Windows based computers that has a "drag and drop" facility and an inbuilt file editor. It can be obtained from http://winscp.net/eng/index.php Using XWindows applications with Hydra. If you wish to run an xterm or another XWindows application such as pgprof from a Unix based computer, you will need to enable X forwarding. This is done from a Unix based machine by passing the -X option (you may find that you will need to use the -Y option instead in some cases). ssh -X username@hydra.sapac.edu.au For MS Windows based computers you will also need a Windows XServer running. For advice, contact the SAPAC helpdesk. Login files (.cshrc) and environment variables Every time you login to Hydra a default .cshrc system file is run. This file establishes some of your basic environment, setting your prompt and ensuring your $PATH variable gives access to basic system commands. In addition you have a file in your home directory, .cshrc.hydra, that is invoked by this global .cshrc login file and can be easily configured to allow access to the various application software packages you wish to run. The global default .cshrc file can be found in your home directory You should take the time to read the comments in this file as they provide details of changes you may wish to make to your environment. NOTE: Do not attempt to change the default .cshrc file in your home directory. Any changes you make will be overwritten by the system the next time you login. Any changes you wish to make to your operating environment should be made in the .cshrc.hydra file in your home directory. Below is an example of a typical .cshrc.hydra file:
This file make the following additions to your environment:
NOTE: You should avoid putting commands in your .cshrc.hydra file that write output to the screen, since this may affect some non-interactive jobs. SAPAC's system administrators already supply a basic .cshrc.hydra file when your account is created. You will only need to alter it if you need access to certain other installed software. If you are unsure as to how to effect changes, contact the SAPAC helpdesk Modules SAPAC will be changing the way access to software packages is acquired in the near future. This will involve the use of the modules mechanism. Researchers who have used APAC's SGI cluster will have already had some exposure to this more dynamic mechanism for gaining access to software.
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