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Getting Started with Linux

This is a page to help you get started with logging on to the bcni server, and creating and using desktops via VNC.

The assumption is that the average user who wants to use this page will be starting from Windows... If they are not already installed on your machine, you need to download PuTTY and a VNC viewer, NOT a VNC server - which has led to us being hacked into before...


 

Logging on to Linux

Run putty.exe. This enables you to connect to the Linux box, and log on.

In the host name section of the dialog, type bcni.psychol.cam.ac.uk, and make sure that SSH & port 22 are selected.

note you can give the session a name in the saved sessions box, and click save. This will reduce the typing you have to do every time.

Click Open to connect. If no-one has logged onto bcni from your machine or profile before, you will be asked whether to 'trust' the machine. Click yes.

You will now be given a login prompt. The first time you log in, you should change your password with the yppasswd command.

Note: this will not change your password for logging onto the Windows machines in the bcni computer / seminar rooms. For this you should log onto the workstations, and press ctrl-alt-delete. Your windows and linux passwords will initially be the same, but they need not be, and must be changed independently...

Logging onto other Linux machines

Once you are logged on as above, you can start a desktop. This allows you to run graphical programs that need the mouse, such as Matlab/SPM.

When you first log on, you will be connected to iron (see Computing Resources). iron is the real name of the machine that appears on the internet as bcni.psychol.cam.ac.uk.

Because iron functions as a gateway machine to the BCNI network, and runs a number of essential services, it's not used as a compute server for data analysis. For this reason, it's not possible to create a VNC session on iron. Instead, you must log onto one of the other machines (bcni11, bcni12, bcni13, bcni14, bcni15, or bcni16) and start your VNC desktop there.

To do this, type e.g.

ssh bcni12

You will be prompted for your password again (the same Linux password works for all the Linux machines). You may also be asked if you trust the machine, as with PuTTY. Type yes.

Once you have logged on, your commands are going to the machine you have ssh-ed to (bcni12 in the example above).

If you are logging on from *inside* the bcni firewall

You can log on to one of the bcni* machines by just typing this name into the hostname in putty. This cannot be done from outside the firewall, as these machines are not on the 'public' internet.

Starting your Linux Desktop

To create a new desktop type:

vncserver -depth 24 -geometry 1280x1024

This will give you a desktop with 24-bit (i.e. good) colour, and a resolution of 1280 by 1024. If you use a larger or smaller screen resolution on your workstation, I suggest you alter the above to match this resolution.

the first time you run the vncserver, it will ask you for a password. This is a password used to use this virtual desktop, and does not have to be the same as your Linux password

This command will create a new 'virtual desktop', and tell you the number of the desktop you have created.

Example output for user abc123:

[abc123@bcni12 abc123]$ vncserver -depth 24 -geometry 1280x1024

You will require a password to access your desktops.

Password:
Verify:
xauth:  creating new authority file /home/abc123/.Xauthority

New 'bcni12:6 (abc123)' desktop is bcni12:6

Starting applications specified in /home/abc123/.vnc/xstartup
Log file is /home/abc123/.vnc/bcni12:6.log

[abc123@bcni12 abc123]$

Write down bcni12:6 on a bit of paper so you don't forget what desktop number you have just created.

You can now log out of the server(s) you are logged into, and connect to the desktop you created using VNCviewer.

Please note - you only really need ONE desktop at a time. Once you have created this desktop, you do not need to do it again, unless the desktop is killed for some reason (e.g. the server is restarted)

Problems with VNC sessions crashing

Make sure the screensaver is not activated, otherwise your VNC session may crash overnight.

Connecting to your Linux Desktop

If you are within the firewall, this is easy. Run the VNCviewer, and type the name of the desktop into the dialog.

If you are outside the firewall (e.g. at Addenbrooke's or HSB), it is a bit more complicated. You need to add an ssh tunnel to the Putty session, which is in the connections-ssh-tunnels section of putty.

Help on how to set up an ssh tunnel can be found here.

Configuring a tunnel in PuTTY

Run putty.exe again to connect to the Linux server, and log on.

In the 'host name' section of the dialog box, type bcni.psychol.cam.ac.uk, and make sure that SSH & port 22 are selected.

In the Saved Sessions section type in something like: 'BCNI-VNC' and press “save”. Now go to the Tunnels in the Catergory (left panel, SSH)

In Source Port type in: 5901, In Destination type: bcni12:5906 (06 because (bcni12:6) in this case it's the 6th desktop, it will start at 5900; a new number for each 'new' desktop)

Then press 'add' you will see something like this

L5901 bcni12:5906

Go back to session and make sure you save the tunnel by pressing 'save' and that you've saved it in the 'BCNI-VNC' and click OK to create the tunnel connection.

After you've done this go to your VNC-viewer. It will ask for a Server. Type in localhost:01 (01 because you set it at 5901) Then it will ask for your password, use the password you've also used in putty.

For further information on managing VNC sessions, see FrequentlyAskedQuestions/AboutVncSessions