Connecting to the HPC infrastructure¶

This text will help you to start using the HPC infrastructure at UGent.

Before you can really start using the HPC clusters, there are several things you need to do or know:

To work on the HPC infrastructure you need some basic knowledge of the Linux operating system, using a terminal and the shell (bash). Make sure you understand these concepts before continuing.
To protect you, your data and the HPC infrastructure, access is limited, and connections must be encrypted (by using ssh and https)
You need to log on to the HPC cluster with your VSC credentials.
The connection is done by using an SSH client or the HPC web portal. If you do not have VSC credentials yet, fix this now.
Before you can do some work, you'll have to transfer your files that you need from your own computer to the HPC cluster. At the end of a job, you might want to transfer some files back.
Optionally, if you wish to use programs with a graphical user interface, you will need an X-server on your client system and log in to the login nodes with X-forwarding enabled.
Often several versions of software packages and libraries are installed, so you need to select the ones you need. To manage different versions efficiently, the VSC clusters use so-called modules, so you will need to select and load the modules that you need.

Connection restrictions¶

For security reasons restrictions are in place that limit from where you can connect to the VSC HPC infrastructure.

VSC login nodes are only directly accessible from within university networks, and from (most) Belgian commercial internet providers. FIXME ook eduroam?

All other IP domains are blocked by default. If you are connecting from an IP address that is not allowed direct access, you have the following options to get access to VSC login nodes:

Use a VPN connection to connect to the UGent network (recommended). See https://helpdesk.ugent.be/vpn/en/ for more information.
Add your IP address automatically to the list of trusted IP addresses. Go to the VSC firewall and log in with your UGent account.
- While this web connection is active new SSH sessions can be started.
- Active SSH sessions will remain active even when this web page is closed.
Contact your HPC support team (via hpc@ugent.be) and ask them to add your IP range (e.g., for industry access, automated processes) to the list of trusted IP addresses.

Trying to establish an SSH connection from an unknown IP address will give an error message like this one:

ssh_exchange_identification: read: Connection reset by peer

First Time connection to the HPC infrastructure¶

The remaining content in this text is primarily focused for people using a terminal with SSH.

If you want to use the web portal, read following page: Using the HPC web portal.

If you have any issues connecting to the HPC after you've followed these steps, see Issues connecting to login node to troubleshoot. steps, see Issues connecting to login node to troubleshoot.

Connect¶

Open up a terminal and enter the following command to connect to the HPC.

ssh vsc40000@login.hpc.ugent.be

Here, user vsc40000 wants to make a connection to the "hpcugent" cluster at UGent via the login node "login.hpc.ugent.be", so replace vsc40000 with your own VSC id in the above command.

The first time you make a connection to the login node, you will be asked to verify the authenticity of the login node.

The authenticity of host 'login.hpc.ugent.be (157.193.252.74)' can't be established.
ED25519 key fingerprint is SHA256:8AJg3lPN27y6i+um7rFx3xoy42U8ZgqNe4LsEycHILA.
This key is not known by any other names.
Are you sure you want to continue connecting (yes/no/[fingerprint])?

Please check "Warning message when first connecting to new host" on how to handle this.

FIXME dit hoort in troubleshooting doc A possible error message you can get if you previously saved your private key somewhere else than the default location ($HOME/.ssh/id_rsa):

Permission denied (publickey,gssapi-keyex,gssapi-with-mic).

In this case, use the -i option for the ssh command to specify the location of your private key. For example:

ssh -i /home/example/my_keys

Congratulations, you're on the HPC infrastructure now¶

To find out where you have landed you can print the current working directory:

$ pwd
/user/home/gent/vsc400/vsc40000

Your new private home directory is "/user/home/gent/vsc400/vsc40000". Here you can create your own subdirectory structure, copy and prepare your applications, compile and test them and submit your jobs on the HPC.

$ cd /apps/gent/tutorials
$ ls
Intro-HPC/

This directory currently contains all training material for the Introduction to the HPC. More relevant training material to work with the HPC can always be added later in this directory.

You can now explore the content of this directory with the "ls -l" (lists long) and the "cd" (change directory) commands:

As we are interested in the use of the HPC, move further to Intro-HPC and explore the contents up to 2 levels deep (-L 2):

$ cd Intro-HPC
$ tree -L 2
.
'-- examples
    |-- Compiling-and-testing-your-software-on-the-HPC
    |-- Fine-tuning-Job-Specifications
    |-- Multi-core-jobs-Parallel-Computing
    |-- Multi-job-submission
    |-- Program-examples
    |-- Running-batch-jobs
    |-- Running-jobs-with-input
    |-- Running-jobs-with-input-output-data
    |-- example.pbs
    '-- example.sh
9 directories, 5 files

This directory contains:

This HPC Tutorial
An examples subdirectory, containing all the examples that you need in this Tutorial, as well as examples that might be useful for your specific applications.

$ cd examples

Tip

Typing cd ex followed by Tab (the Tab-key) will generate the cd examples command. Command-line completion (also tab completion) is a common feature of the bash command line interpreter, in which the program automatically fills in partially typed commands.

Tip

For more exhaustive tutorials about Linux usage, see Appendix Useful Linux Commands

The first action is to copy the contents of the HPC examples directory to your home directory, so that you have your own personal copy and that you can start using the examples. The "-r" option of the copy command will also copy the contents of the sub-directories "recursively".

cp -r /apps/gent/tutorials/Intro-HPC/examples ~/

Go to your home directory, check your own private examples directory, ... and start working.

cd
ls -l

Upon connecting you will see a login message containing your last login time stamp and a basic overview of the current cluster utilisation.

Last login: Thu Mar 18 13:15:09 2026 from gligarha02.gastly.os

 STEVIN HPC-UGent infrastructure status on Mon, 19 Apr 2026 10:00:01
      cluster         - full - free -  part - total - running - queued
                        nodes  nodes   free   nodes   jobs      jobs
 -------------------------------------------------------------------------
           joltik           6      0      1      10        29       18
            doduo          22      0     75     128      1397    11933
         accelgor           4      3      2       9        18        1
          donphan           0      0     16      16        16       13
          gallade           2      0      5      16        19      136


For a full view of the current loads and queues see:
https://hpc.ugent.be/clusterstate/
Updates on current system status and planned maintenance can be found on
https://www.ugent.be/hpc/en/infrastructure/status

You can exit the connection at anytime by entering:

$ exit
logout
Connection to login.hpc.ugent.be closed.

Transfer Files to/from the HPC¶

Before you can do some work, you'll have to transfer the files you need from your desktop or department to the cluster. At the end of a job, you might want to transfer some files back.

The preferred way to transfer files is by using an scp or sftp via the secure OpenSSH protocol. All operating systems ship with an implementation of OpenSSH, so you don't need to install any third-party software to use it. Just open a terminal window and jump in!

Using a GUI¶

If you want a graphical user interface (GUI) please consider using the web portal.

If you prefer a graphical user interface (GUI) to transfer files back and forth to the HPC, you can use a file manager. Open your file manager and press Ctrl+l if you are on Linux or Cmd+k if you are using MacOS.

This should open up a address bar where you can enter a URL. Alternatively, look for the "connect to server" option in your file managers menu.

Enter: sftp://vsc40000@login.hpc.ugent.be/ and press enter.

You should now be able to browse files on the HPC in your file browser.

Using scp¶

Secure copy or SCP is a tool (command) for securely transferring files between a local host (= your computer) and a remote host (the HPC). It is based on the Secure Shell (SSH) protocol. The scp command is the equivalent of the cp (i.e., copy) command, but can copy files to or from remote machines.

It's easier to copy files directly to $VSC_DATA and $VSC_SCRATCH if you have symlinks to them in your home directory.
See symlinks on how to create symlinks.

Open an additional terminal window and check that you're working on your local machine. The command hostname should give you the name of your pc.

$ hostname
<local-machine-name>

If you're still using the terminal that is connected to the HPC, close the connection by typing "exit" in the terminal window.

Example: copy a file to the hpc cluster¶

We will copy the (local) file "localfile.txt" from your pc to your home directory on the (remote) HPC cluster.

Note the #-signs are used to indicate comments, you do not need to type the comments.

First we generate a small dummy file "localfile.txt", which contains the word "Hello". To create this file we use the tool "echo", which shows some text on the screen. We can redirect the output of a command to a file with the >-symbol.

$ echo "Hello"  # show the word Hello on the screen
Hello
$ echo "Hello" > localfile.txt # create the file
$ ls -l                        # verify if the file exists
...
-rw-r--r-- 1 user  staff   6 Sep 18 09:37 localfile.txt
$ cat localfile.txt # verify the contents of the file
Hello

Use your own VSC account, which is something like "vsc40000".

Don't forget the colon (:) at the end. If you forget it, it will just create a file named vsc40000@login.hpc.ugent.be on your local filesystem. You can even specify where to save the file on the remote filesystem by putting a path after the colon.

$ scp localfile.txt vsc40000@login.hpc.ugent.be:
localfile.txt     100%   6     0.0KB/s     00:00

Connect to the HPC via another terminal, print the working directory (to make sure you're in the home directory) and check whether the file has arrived:

$ pwd
/user/home/gent/vsc400/vsc40000
$ ls -l 
total 1536
drwxrwxr-x 2
drwxrwxr-x 2
drwxrwxr-x 10
-rw-r--r-- 1
$ cat localfile.txt
Hello

The scp command can also be used to copy files from the cluster to your local machine. Let us copy the remote file "intro-HPC.pdf" from your "docs" subdirectory on the cluster to your local computer.

First, we will confirm that the file is indeed in the "docs" subdirectory. In the terminal on the login node, enter:

$ cd ~/docs
$ ls -l
total 1536
-rw-r--r-- 1 vsc40000 Sep 11 09:53 intro-HPC.pdf

Now we will copy the file to the local machine. On the terminal on your own local computer, enter:

$ scp vsc40000@login.hpc.ugent.be:./docs/intro-HPC.pdf .
intro-HPC.pdf 100% 725KB 724.6KB/s 00:01
$ ls -l
total 899
-rw-r--r-- 1 user staff 741995 Sep 18 09:53
-rw-r--r-- 1 user staff      6 Sep 18 09:37 localfile.txt

The file has been copied from the HPC to your local computer.

It's also possible to copy entire directories (and their contents) with the -r flag. For example, if we want to copy the local directory dataset to $VSC_SCRATCH, we can use the following command (assuming you've created the scratch symlink):

scp -r dataset vsc40000@login.hpc.ugent.be:scratch

If you don't use the -r option to copy a directory, you will run into the following error:

$ scp dataset vsc40000@login.hpc.ugent.be:scratch
dataset: not a regular file

Using sftp¶

The SSH File Transfer Protocol (also Secure File Transfer Protocol, or SFTP) is a network protocol that provides file access, file transfer and file management functionalities over any reliable data stream. Compared to scp the sftp tool provides a more interactive way of doing file transfers.

One easy way of starting a sftp session is

sftp vsc40000@login.hpc.ugent.be

After the sftp program is started you get a prompt and you can issue commands.

Typical and popular commands inside an sftp session are:

Command	What the command does
?	Show a list of commands
bye	Quit the sftp session
ls	Get a list of the files in the current directory on the HPC.
lls	Get local directory listing (i.e. on your computer).
cd ~/exmples/fibo	Move to the examples/fibo subdirectory on the remote machine (i.e., the HPC)
get fibo.py	Copy the file "fibo.py" from the HPC to your computer
get tutorial/HPC.pdf	Copy the file "HPC.pdf" from the HPC, which is in the "tutorial" subdirectory.
lcd test	Move to the "test" subdirectory on your local machine.
lcd ..	Move up one level in the local directory.
put test.py	Copy the local file test.py to the HPC.
put test1.py test2.py	Copy the local file test1.py to the and rename it to test2.py.
*mget .cc**	Copy all the remote files with extension ".cc" to the local directory.
*mput .h**	Copy all the local files with extension ".h" to the HPC.

Fast file transfer for large datasets¶

$$$ rsync can resume jobs $$$ filesender?? See the section on rsync in the Linux intro.

It can be useful to have control over which login node you are on.

However, when you connect to the HPC (High-Performance Computing) system, you are directed to a random login node, which might not be the one where you already have an active session. To address this, there is a way to manually switch your active login node.

For instance, if you want to switch to the login node named gligar09.gastly.os, you can use the following command while you are connected to the gligar10.gastly.os login node on the HPC:

ssh gligar09.gastly.os

This is also possible the other way around.

If you want to find out which login host you are connected to, you can use the hostname command.

$ hostname
gligar09.gastly.os
$ ssh gligar10.gastly.os

$ hostname
gligar10.gastly.os

Rather than always starting a new session on the HPC, you can also use a terminal multiplexer like screen or tmux. These can make sessions that 'survives' across disconnects.

You can find more information on how to use these tools here (or on other online sources):

screen
tmux