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server_setup.md

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Setup server

The instructions provided in this tutorial are aimed at establishing a standard SSH connection to a server within the user's network. This setup assumes that you have access to a remote computing server with SSH enabled, allowing you to securely connect and run the necessary software.

On your local machine

Install ssh

SSH is required to access the remote server resource. If you haven't installed ssh, follow one of these instructions to install ssh:

Linux
  • Open the Terminal
  • Type command: sudo apt-get install openssh-server
  • Enable the ssh service: sudo systemctl enable ssh
  • Start the ssh service: sudo systemctl start ssh
MacOS Download and install ***macFUSE*** here: https://osxfuse.github.io/
Windows

  1. Open Settings, select Apps, then select Optional Features.

  2. Scan the list to see if the OpenSSH is already installed. If not, at the top of the page, select Add a feature, then:

    • Find OpenSSH Client, then select Install
    • Find OpenSSH Server, then select Install

  3. Once setup completes, return to Apps and Optional Features and confirm OpenSSH is listed.

  4. Open the Services desktop app. (Select Start, type services.msc in the search box, and then select the Service app or press ENTER).

  5. In the details pane, double-click OpenSSH SSH Server.

  6. On the General tab, from the Startup type drop-down menu, select Automatic.

  7. To start the service, select Start.

Adapted from: https://learn.microsoft.com/en-us/windows-server/administration/openssh/openssh_install_firstuse?tabs=gui

Setup ssh keygen

This step create the key for server access that does require password.

Linux and MacOS
  1. Open Terminal
  2. mkdir -p /.ssh && chmod 700 ~/.ssh && cd ~/.ssh
  3. Paste the text below, replacing the email used in the example with your email: ssh-keygen -t rsa -b 4096 -C "[email protected]". Click ENTER until finishing.
  4. Check if successful by ls ~\.ssh. The results should contain these two files: id_rsa and id_rsa.pub.
Windows
  1. Open Terminal as Administrator following this instruction: https://learn.microsoft.com/en-us/windows/terminal/faq
  2. mkdir -p /.ssh && chmod 700 ~/.ssh && cd ~/.ssh
  3. Paste the text below, replacing the email used in the example with your email: ssh-keygen -t rsa -b 4096 -C "[email protected]". Click ENTER until finishing.
  4. Check if successful by ls ~/.ssh. The results should contain these two files: id_rsa and id_rsa.pub.

Setup ssh configuration

This step allows you to alias the server address for easy access.

  1. Open Terminal (On Windows, follow this instruction to run the Terminal as Administrator: https://learn.microsoft.com/en-us/windows/terminal/faq)

  2. cd ~/.ssh

  3. touch config & chmod 600 ~/.ssh/config

  4. nano config then enter these contents in the file config:

    GSSAPIAuthentication no
ServerAliveInterval 120
TCPKeepAlive no

Host <hostname>
    HostName <host_address>
    User <your_username>
    ForwardAgent yes
    ProxyCommand none
    IdentityFile ~/.ssh/id_rsa

    Replace the contend inside <> with your own information.

  5. Ctrl + x → y

On server

Add local ssh keygen to authorized list

  1. Copy the content in ~/.ssh/id_rsa.pub
  2. SSH to your server: ssh <hostname>, enter the required password.
  3. nano ~/.ssh/authorized_keys → paste the content of id_rsa.pub as new line
  4. Ctrl + x → y

After this step, you can access to the server without entering password.

Install the mousechd package

  1. SSH to your server: ssh <hostname>, enter the password (if required).
  2. Download the MouseCHD Apptainer: wget https://zenodo.org/records/13928753/files/mousechd.sif

Locate the shared folder

On the remote server, locate the shared folder at $HOME/DATA.

  • If the shared folder is remote, mount your shared folder at $HOME/DATA
  • If your shared folder is on the server, use mkdir <shared_folder_name> && ln -sf <path/to/shared/folder>/* ~/DATA/<shared_folder_name>

Congratulations! You've successfully completed the setup to run the plugin on the remote server. Here are some key parameters that require your attention during plugin input:

Servername: it is the hostname you placed in your config file.
Apptainer execution command: the command to run apptainer. Default: apptainer exec -B /pasteur --nv mousechd.sif mousechd. -B to mount volume if necessary, --nv to run with GPU.
Slurm: your server uses Slurm Workload Manager " to request the resource or not. If yes, what is the command? Default: srun -J 'mousechd' -p gpu --qos=gpu --gres=gpu:1
Load modules: Do you need to load some modules to run the program? If yes, specify. Default: module load apptainer

These paremeters will automatically saved for future use