Connecting to server

In the course, you will be working on a Linux server. You can connect to this server via ssh, using the same username and password as for AIS2. In the computer classroom at the faculty, we recommend connecting to the server from Linux.

Connection through ssh

If connecting from a Linux computer, open a console (command-line window) and run:

ssh your_username@vyuka.compbio.fmph.uniba.sk -XC

The server will prompt you for password, but it will not display anything while you type. Just type your password and press Enter.

If connecting from a Windows 10 or Windows 11 computer, open command-line window in Ubuntu subsystem for Windows or Powershell or cmd.exe Command Prompt and run

ssh your_username@vyuka.compbio.fmph.uniba.sk

When prompted, type your password and press Enter, as for Linux. See also more detailed instructions here [1] or here [2].

For Windows, this command allows text-only connection, which is sufficient for most of the course. To enable support for graphics applications, follow the instructions in the next section.

Installation of X server on Windows

This is not needed for Linux, just use -XC option in ssh.

To use applications with GUIs, you need to tunnel X-server commands from the server to your local machine (this is accomplished by your ssh client), and you need a program that can interpret these commands on you local machine (this is called X server).

• Install putty client which you will use instead of ssh.
• Install X server, such as xming
• Make sure that X server is running (you should have "X" icon in your app control bar)
• Run putty, connect using ssh connection type and in your settings choose Connection->SSH->X11 and check "Enable X11 forwarding" box
• Login to the vyuka.compbio.fmph.uniba.sk server in putty
• echo $DISPLAY command on the server should show a non-empty string (e.g. localhost:11.0)
• Try running xeyes &: this simple testing application should display a pair of eyes tracking your mouse cursor

Copying files to/from the server via scp

• You can copy files using scp command on the command line, both in Windows and Linux.
• Alternatively use the graphical WinSCP program for Windows.

Examples of using scp command

# copies file protocol.txt to /submit/perl/username on server
scp protocol.txt username@vyuka.compbio.fmph.uniba.sk:/submit/perl/username/

# copies file protocol.txt to the home folder of the user on the server
scp protocol.txt username@vyuka.compbio.fmph.uniba.sk:

# copies file protocol.txt from home directory at the server to the current folder on the local computer
scp username@vyuka.compbio.fmph.uniba.sk:protocol.txt .

# copies folder /tasks/perl from the server to the current folder on the local computer
# notice -r option for copying whole directories
scp -r username@vyuka.compbio.fmph.uniba.sk:/tasks/perl .

Mounting files from Linux server to your Linux computer via sshfs

• On Linux, you can mount the filesystem from the server as a directory on your machine using sshfs tool, and then work with it as with local folders, using both command-line and graphical file managers and editors.

An example of using sshfs command for mounting a folder from a remote server:

mkdir vyuka  # create an empty folder with an arbitrary name
sshfs username@vyuka.compbio.fmph.uniba.sk: vyuka   # mounting the remote folder to the empty folder
# From now on, folder vyuka will contain your home folder on vyuka server.
# You can copy files to and from the server and even open them in editors as if they were on your computer,
# however with network-related slowdown.

MacOS

• Command ssh in text mode should work on MacOS.
• For GUIs you need an X server, try installing XQuartz.
• Alternatively, you can install sshfs from macFUSE and mount vyuka as shown above.