To communicate with the cluster head node, you will need 2 programs installed. Both of these protocols are native to the Linux operating system, so in most cases they will be installed on your system already. If you are using Windows however, you will need to download and install the following two pieces of software:
• SSH Client. SSH stands for Secure SHell. The cluster operates on a Linux operating system called CentOS. You will log in to this operating system using the SSH protocol. The SSH protocol was developed mainly for UNIX/Linux use, so it is not included in the basic installation of Windows. In order to connect to a SSH server you need to install a SSH client. You can use any SSH Client, but I use and recommend PuTTY, which is a small free SSH client that supports many SSH encryption algorithms, and other communication protocols. Download and install PuTTY from here.
• SFTP Client. SFTP stands for Secure File Transfer Protocol. It is a subsystem of SSH, and allows users to upload and download files to and from a server securely. As with SSH clients, there are also many SFTP Clients to choose from, but I use and recommend FileZilla. Click here to download FileZilla Client. Make sure that you download the client program and not the server program (FileZilla Server).
Connecting to the Cluster
The first thing we want to do is connect to the server (AKA cluster head node). Open up PuTTY (or whatever other SSH client you have, if you have none, refer back to section 1). If connecting to bc247 (not avalible from outside Monash University), the name of the computer we are connecting to is “bc247.eng.monash.edu.au”. If you are following this tutorial for another cluster, type the cluster address here. The protocol we want to use is “SSH”. Once you have these settings, then click Open. If you want, you can enter a name in the “Saved Sessions” box and Save the session so next time you will not need to retype the server address.
If this is the first time you have logged in from your computer, your computer will not have a hash of bc247 stored, and will ask you if you still trust the identity of the computer. The hash is like a fingerprint, and your computer does not already know this fingerprint, so it cannot be sure that the computer your connecting to is really bc247. Because we trust that the connection is to the right computer, we will accept the connection anyway.
Once connected, you will be prompted with “login as:” Enter the username you were given from bc247admin and hit Enter. You will then be prompted with “username’s password:”. Again, type in the password given from bc247admin and hit Enter. Note that UNIX systems are case-sensitive, so FooBar is not the same as foobar which is not the same as FOOBAR. Also your password will not come up on the screen, even as hidden characters, you can still use backspace to correct any errors though.
You should now get a whole bunch of information show up on the screen. This information includes some of the conditions of using bc247, so please read it now. At the end of all this is the shell prompt [00:00:00-username@bc247 ~]$ This is the bash prompt, and how you will be talking to bc247. username is your username, bc247is the node (computer) that you have logged onto, ~ is the folder which you are in, where ~ stands for your home directory. $ is the prompt indicating that you are logged in as a user (not an administrator).
Transferring Files to the Cluster
Open up FileZilla (or whatever other SFTP client you have, if you have none, refer back to section 1) and type “bc247.eng.monash.edu.au” for the Host; then type your username and password, and finally the port for SSH connections which is 22. Then click Quickconnect. You will then have the files on your computer displayed on the left hand side of the screen, and the files on bc247 displayed on the right side of the screen.
Note the different structure, in UNIX systems, all files, folders, devices, inputs and outputs are listed under /, known as “root”. For a good overview on the filesystem structure, click here.
Once logged on, you should automatically be taken to your home directory, which we saw abbreviated before as ~. This is your private directory that other users cannot access. The path to your home is /home/username. Note that there is a maximum quota of 1000 MB per user, and a limit of 1200 MB per user for storing in your home directory. To check your usage, open up an SSH shell (using PuTTy) and type quota –v The information next to home username is the relevant quota.