6 How to connect to servers?
6.1 How will we work?
In this workshop, we will use our computers, and we will connect to high performance computing (HPC) systems. Therefore, you will need to bring your laptops with you.
You should be comfortable using the Unix/Linux command line to take this course. In this page, you will find recommendations on how to connect to high performance computers depending on your laptop’s operating system.
N.B. During this course, we will use the terms server, cluster and high performance computers interchangeably.
6.1.1 Linux systems
If you have a Linux system (e.g. Ubuntu), you’re all set! Most of the command line tools (like the necessary ssh) will be already installed on your system.
6.1.2 Mac systems
Mac systems also have a default support on the command line. The terminal application on your Mac system is enough. But you can also install iTerm2 as a terminal replacement for your Mac, if you’d like something fancier.
6.1.3 Windows systems
If you have a Windows system, the easiest choice to connect to a remote server is Mobaxterm.
6.2 High performance computers
In this workshop, we have two different cluster systems at our disposal. The first system TRUBA (Turkish National Scientific Cluster) is funded by the TUBİTAK (The Scientific and Technological Research Council of Türkiye). The second system is located at Middle East Technical University.
6.2.1 TRUBA Cluster system
This cluster system accepts connections from a Turkish university network only. Therefore, you should be in a university network in order to access TRUBA computers. We will provide a username and a password for your connection.
You can connect to TRUBA by writing this command in your terminal:
ssh your_username@levrek1.ulakbim.gov.trN.B. There is a trick to connect to the TRUBA system outside of the university network described at the end of this document.
6.2.2 Middle East Technical University computing systems
This computer system is located at Middle East Technical University. It consists of two subclusters: baggins and NEOGENE.
Since the NEOGENE cluster does not accept connections from outside the university networks, we will first connect to baggins via ssh. Then we can connect to NEOGENE from within this system.
Your username and password will be provided on the first day of the workshop.
Connect to the baggins server with your username like this:
ssh -p 2275 your_username@144.122.38.49Afterwards, you can connect to NEOGENE from withing baggins this way:
ssh your_username@144.122.38.506.2.3 Connecting to the TRUBA system from outside the university network
We can connect to the TRUBA system from outside the university network with a small trick. First, we connect to the baggins cluster as described above, so to be using the Middle East Technical University network. Then we can connect to TRUBA from within that terminal.
ssh -p 2275 your_username@144.122.38.49
# Enter your password when prompted
ssh your_username@levrek1.ulakbim.gov.tr6.3 Configuration
All the tools are installed on these server systems. Before using the tools, we need to set the PATH variable and show the system where these tools are installed, in case we want to run commands from the terminal. The PATH variable will already be set for you in the bash scripts in TRUBA.
6.3.1 Configuration of the TRUBA system
To use all the tools for aMeta, please set your PATH variable like this:
export PATH=${PATH}:/truba/home/egitim/miniconda3/envs/aMeta/bin/6.3.2 Configuration on the Ankara computers
To use all the tools for aMeta, please set your PATH variable like this:
export PATH=${PATH}:/usr/local/sw/anaconda3/envs/aMeta/The workshop folder on the Ankara computer will be here:
cd /mnt/NEOGENE4/projects/microbe_2023/