Introduction to Bioinformatics NGS
  • Server Accounts
  • Server Access
  • Data
  • Quality Control
  • Mapping

On this page

  • Access server via the Terminal
  • Server access: on demand

Connect to the course server

Author

Amrei Binzer-Panchal


For this course, we will be working on a remote server, HPC2N. You should already have applied for a user account there. If you haven’t, do it now.

Here, you will access the server for the first time.

You will need:

  • a terminal,
  • your HPC2N user name and
  • the temporary password you will have gotten from HPC2N.
Important

If you have forgotten your password, or it’s no longer valid, you can re-set it using the Password reset service.

NoteIF NEEDED: Get a working Linux terminal on Windows

For the sake of simplicity we will teach you the way to use tools on Linux subsystems only. Hence, if you have a Windows PC or laptop you need to set up a way to access a Linux terminal. You can find plenty of tutorials online to do this, but here are some steps that should be easy enough to follow:

  • type in the bottom left search bar “powershell”, right-click on the result and select “run as administrator”
  • copy-paste in the window you opened the following command:
wsl --install
  • reboot your system
  • open the Microsoft store and search for Ubuntu
  • install Ubuntu 22.04.3 LTS
  • launch it, set a username and a password

Access server via the Terminal

  • Open the Terminal on your computer.
  • Type ssh username@kebnekaise.hpc2n.umu.se, where you substitute “username” with your HPC2N user name.
  • type in your temporary password.
CautionAfter the first log-in: reset password

In the welcome mail you got when your HPC2N account was created there was a link to create a first, temporary password. When you have logged in using that, you need to change your password.

From the HPC2N documentation:

This is done using the passwd command:

passwd

Use a good password that combines letters of different case. Do not use dictionary words. Avoid using the same password that you also use in other places.

  • It will first ask for your current password. The first time you login, that will be the temporary password you created with the HPC2N password reset service.
  • Type in that and press enter.
  • Then type in the new password you want, enter, and repeat.
  • You have changed the password.

You are now on connected to the login node of the cluster.

ImportantTo do for you

Read here more about HPC cluster architecture. Read until the header MPI.

This location is the home folder of your account.

Tip

You can check the path to your working directory with:

pwd

and the content with:

ls

Server access: on demand

HPC2N offers a on demand log-in, where you can start a visual interface to interact with the server.

You can access the on-demand log-in here.

ImportantTo do for you
  • Click on “Login to HPC2N OnDemand”.
  • Sign in to your account with your HPC2N user name and password.
  • On the top, select “Interactive Apps” and “VScode”.

Now you can set up the interactive session.

ImportantTo do for you
  • Select our compute project in the drop-down menu under “Compute Project”.
  • Select the appropriate number of hours.
  • Type in the path to the course directory in “Working Directory” (replace XXX with the actual project ID - you can find that when you log in to SUPR/NAISS):
/proj/nobackup/hpc2nstor2025-XXX
  • Click Launch.

Your session will start, once it is running you can click the blue “Connect to VS Code” button in the bottom. The VS Code interface will open up in your browser.

ImportantTo do for you
  • Look around the storage project:
ls
  • Create a directory with your name (replace <your-name> below with your actual name):
mkdir <your-name>
  • Check that the directory was created successfully:
ls
Source Code
---
title: Connect to the course server
authors:
  - name: Amrei Binzer-Panchal
---


<br>
For this course, we will be working on a remote server, HPC2N. You should already have applied for a user account there. If you haven't, [do it now](server_accounts.qmd).

Here, you will access the server for the first time. 

**You will need:**

- **a terminal,**
- **your HPC2N user name and** 
- **the temporary password you will have gotten from HPC2N.**

::: {.callout-important}
If you have forgotten your password, or it's no longer valid, you can re-set it using the [Password reset service](https://docs.hpc2n.umu.se/documentation/password/). 
:::

::: {.callout-note}
## IF NEEDED: Get a working Linux terminal on Windows 

For the sake of simplicity we will teach you the way to use tools on Linux subsystems only. Hence, **if you have a Windows PC or laptop** you need to set up a way to access a Linux terminal. You can find plenty of [tutorials](https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/#:~:text=Assuming%20you%20have%2064%2Dbit,t%20work%20until%20you%20reboot.) online to do this, but here are some steps that should be easy enough to follow:

- type in the bottom left search bar "powershell", right-click on the result and select "run as administrator"
- copy-paste in the window you opened the following command:

```{.bash}
wsl --install
```

- reboot your system
- open the Microsoft store and search for Ubuntu
- install Ubuntu 22.04.3 LTS
- launch it, set a username and a password

:::

## Access server via the Terminal

- Open the Terminal on your computer.
- Type `ssh username@kebnekaise.hpc2n.umu.se`, where you substitute "username" with your HPC2N user name. 
- type in your temporary password.

::: {.callout-caution}
## After the first log-in: reset password

In the welcome mail you got when your HPC2N account was created there was a link to create a first, temporary password. When you have logged in using that, you need to change your password.

From the [HPC2N documentation](https://docs.hpc2n.umu.se/documentation/access/#first__time__login__password__change): 

This is done using the passwd command:

```{.bash}
passwd
```

Use a good password that combines letters of different case. Do not use dictionary words. Avoid using the same password that you also use in other places.

- It will first ask for your current password. The first time you login, that will be the temporary password you created with the HPC2N password reset service.
- Type in that and press enter.
- Then type in the new password you want, enter, and repeat.
- You have changed the password.
:::


You are now on connected to the login node of the cluster. 

::: {.callout-important}
## To do for you

Read [here](https://docs.hpc2n.umu.se/tutorials/clusterguide/#beginners__intro__to__clusters) more about HPC cluster architecture. Read until the header `MPI`. 
:::

This location is the home folder of your account. 

::: {.callout-tip}
You can check the path to your working directory with: 

```{.bash}
pwd
````

and the content with: 

```{.bash}
ls
```
:::


## Server access: on demand

HPC2N offers a on demand log-in, where you can start a visual interface to interact with the server. 

You can access the on-demand log-in [here](https://portal.hpc2n.umu.se/public/landing_page.html). 

::: {.callout-important}
## To do for you

- Click on "Login to HPC2N OnDemand".
- Sign in to your account with your HPC2N user name and password. 
- On the top, select "Interactive Apps" and "VScode". 
:::

Now you can set up the interactive session.

::: {.callout-important}
## To do for you

- Select our compute project in the drop-down menu under "Compute Project".
- Select the appropriate number of hours. 
- Type in the path to the course directory in "Working Directory" (replace XXX with the actual project ID - you can find that when you log in to SUPR/NAISS):
```{.bash}
/proj/nobackup/hpc2nstor2025-XXX
```
- Click Launch.  
:::

Your session will start, once it is running you can click the blue "Connect to VS Code" button in the bottom. The VS Code interface will open up in your browser. 

::: {.callout-important}
## To do for you

- Look around the storage project: 
```{.bash}
ls
```

- Create a directory with your name (replace `<your-name>` below with your actual name): 
```{.bash}
mkdir <your-name>
```

- Check that the directory was created successfully: 
```{.bash}
ls
```

:::