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+ + + + + + + + + + + + + + + + + + +SSH (Secure Shell) is a widely used protocol for securely gaining access to a shell (or terminal) on remote Linux machines and is the primary way to access the BioCloud servers. This page provides instructions on how to access the BioCloud through SSH using a few different SSH clients and platforms. There are many other SSH clients available, it is entirely up to you which you prefer, but regardless of the client everything will run over the same SSH protocol (port 22) in the exact same way. You authenticate using your AAU email and password (possibly also a second factor) and you must be on the AAU network unless you are connected to the AAU network from the outside using either VPN or by using the AAU SSH gateway, both are described later under external access.
+If you need to run GUI apps like CLC, Arb, RStudio, VS Code, etc, you can instead use the interactive web portal described on the next page. For everything else, you need to learn how to submit SLURM jobs through one of the login-nodes bio-ospikachu01.srv.aau.dk
, bio-ospikachu02.srv.aau.dk
, or bio-ospikachu03.srv.aau.dk
. After successfully logging in please consult the SLURM guide. You can then start developing code, write scripts, install software and browse around etc, but you are NOT ALLOWED to run anything on a SLURM login node, everything must be submitted through SLURM jobs.
It's rarely enough with just a terminal because you more often than not need to edit some scripts in order to do anything, which is not very convenient to do in a terminal, so below are some instructions on how to connect using a few popular code editors, or IDEs (integrated development environments), with built-in SSH support, but also just a terminal.
+Visual Studio Code (VS Code) is a popular free cross-platform code editor with a myriad of extensions available for anything and everything including syntax highlighting for any programming language, integrated git support, GitHub copilot for AI autocompletion of code, and the list goes on. If you want one editor for everything, there isn't currently anything better out there. If you need an interactive VS Code session and actually run things from there, please follow this guide to connect VS Code directly to a SLURM job instead. Alternatively, you can also start a Code Server (an open source alternative to VS Code) in a SLURM job from the interactive web portal described on the next page.
+Download and install using the instructions on the official website.
+@
and then the server's hostname, for example: abc@bio.aau.dk@bio-ospikachu01.srv.aau.dk
, orA more old-school and Windows-only client is MobaXterm. It's not as full-featured as VS Code, but is more lightweight.
+Download and install MobaXterm Home Edition from the official website.
+ssh
command to connect to a server by entering AAU email followed by @
and then the server's hostname, for example: ssh abc@bio.aau.dk@bio-ospikachu01.srv.aau.dk
.If you add the servers to your SSH config file the server hostnames should auto-complete.
+For a simple terminal you can on Windows use for example PuTTY or msys2, and the integrated terminal and the ssh
command itself directly if on Linux or macOS (also Windows). Type ssh email@hostname
like above to connect immediately or just the hostname if you've added them to the SSH config file.
Both VS Code and MobaXterm support file transfers, but you can also use other GUI apps like FileZilla or WinSCP. When just using a terminal there are several tools like scp
, rsync
, rclone
, or sftp
, all of which connect through the SSH protocol. You can also browse and transfer files through the interactive web portal described on the next page.
To access the servers while not directly connected to any AAU or eduroam network there are two options. Either you connect through VPN, which will route all your traffic through AAU, or you can use the SSH gateway through sshgw.aau.dk
for SSH connections only. If you need virtual desktop access only VPN will work (for now).
The simplest way is to connect to the AAU VPN using the guide provided by ITS here. After you connect everything should work as though you were at AAU.
+The SSH gateway is simply a server hosted at AAU whose only purpose is to bridge SSH connections from the outside (open port 22 ingress) to something else on the internal AAU network. Setting up 2-factor authentication is required in order to connect. To enable the "proxy jumping" you need to adjust the SSH config file by uncommenting the ProxyJump sshgw.aau.dk
line under the *.srv.aau.dk
host, see the SSH config template file. Keep in mind that as long as it's enabled it will always connect through sshgw.aau.dk
regardless of which network you are connected to, including the AAU network.
To avoid typing hostnames and user names constantly here's a template SSH config file that includes all current servers. The file must be saved at certain locations depending on your OS. On Windows it's here, and on macOS and Linux it's usually under ~/.ssh/config
. Hostnames in the file will then be auto-completed and if you've set up SSH public key authentication you won't need to type anything else than for example ssh bio-oscloud02.srv.aau.dk
and you're in.
# nice-to-have global options that apply to all servers,
+# prevents disconnects on network glitches and wifi reconnects,
+# allows forwarding GUI apps to client
+Host *
+ ServerAliveInterval 60
+ ServerAliveCountMax 2
+ ExitOnForwardFailure yes
+ ForwardX11 yes
+ ForwardX11Trusted yes
+
+# this is only used for external access
+Host sshgw.aau.dk
+ HostName sshgw.aau.dk
+ User abc@bio.aau.dk
+ Port 22
+ ForwardAgent yes
+
+# use the same user name (and optional SSH key) for all bioservers
+# uncomment the ProxyJump line for external access without VPN
+Host *.srv.aau.dk bio-os*
+ User abc@bio.aau.dk
+ Port 22
+ IdentityFile ~/.ssh/keys/bioservers
+# ProxyJump sshgw.aau.dk
+
+Host bio-ospikachu01.srv.aau.dk
+Host bio-ospikachu02.srv.aau.dk
+Host bio-ospikachu03.srv.aau.dk
+
SSH public key authentication offers a more secure way to connect to a server, and is also more convenient, since you don't have to type in your password every single time you log in or transfer a file. An SSH private key is essentially just a very long password that is used to authenticate with a server holding the cryptographically linked public key for your user (think of it as the lock for the private key). You can even add an additional layer of security by encrypting the private key itself using a password when generating the pair. Any SSH client that you choose to use will connect through the SSH program on your computer under the hood, so public key authentication will also apply to them if set up like below.
+This must be done locally for security reasons, so that the private key never leaves your computer. If you use a password manager (please do) like 1Password or bitwarden you can usually both generate and safely store and use SSH keys directly from the vault without it lying around in a file. It's important that the key is not generated using the default (usually) RSA type algorithm, because it's outdated and can be brute-forced easily with modern hardware, so please use for example the ed25519
algorithm instead.
win+r
and type cmd
)ssh-keygen -t ed25519
~/.ssh/
in your home folder)Copy your public key to the server using ssh-copy-id -i ~/.ssh/biocloud.pub username@hostname
, or manually add the contents of the public key file into the ~/.ssh/authorized_keys
file on any of the servers (the home folder is shared across them all). SSH requires that your user is the only one able to read the contents before you are allowed to login, so ensure the correct permissions are set using chmod 700 ~/.ssh && chmod 600 ~/.ssh/authorized_keys
.
You should now be able to login securely without typing a password - have fun!
+ + + + + + + + + + + + + +Another way to access the BioCloud compute resources is to use the interactive web portal based on Open Ondemand developed by Ohio Supercomputer Center. The main purpose of the web portal is to greatly simplify running interactive and graphical apps such as virtual desktops and IDEs, which are served directly from isolated SLURM jobs running on the compute nodes, but you can also easily browse around and transfer files, obtain a shell, check the job queue, or compose job batch scripts based on templates, and more - all from your browser without having to learn a multitude of terminal commands.
+This page only describes briefly how to connect to the web portal. Guides detailing how to use all of its features are available under the Guides section. It is also absolutely essential to read and understand how SLURM and resource management works (described on the next page), before using any of the apps, because interactive apps are often terribly inefficient (i.e. CPUs do nothing when you are just typing or clicking around)!
+In order to access the web portal you must first be connected to the local AAU campus network, or through VPN. Then go to https://biocloud.bio.aau.dk and log in using your usual AAU credentials if you aren't already (for example if you've already signed in to your AAU webmail, etc). For security reasons the website is NOT exposed to the public internet, hence your browser will likely warn you that the site is insecure because the SSL certificate can't be validated by an authority because it can't access it:
+ +But don't worry, traffic is still encrypted. To solve this, depending on your browser, just click Advanced and then proceed to biocloud.bio.aau.dk (unsafe):
+ +If this is the first time you ever log in to any of the BioCloud resources, your home directory does not yet exist on the network storage and you will likely see an error. To create your home directory you must log in just once either through SSH as described on the previous page or using the web portal shell, which is available here. You can also just contact an admin. Now you should be greeted by the front page:
+ +Now, please read through the SLURM guide on the following pages before using any of the apps. Afterwards you can go through the guides for the individual apps under the Guides section.
+ + + + + + + + + + + + + +{"use strict";/*!
+ * escape-html
+ * Copyright(c) 2012-2013 TJ Holowaychuk
+ * Copyright(c) 2015 Andreas Lubbe
+ * Copyright(c) 2015 Tiancheng "Timothy" Gu
+ * MIT Licensed
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