How to connect to a remote cluster

The protocol used to connect to remote machines is called SSH — Secure Shell.
It allows you to log into remote servers and clusters securely from your computer.

Step 1: create a private/public key pair

SSH authentication is typically based on a pair of cryptographic keys: a private key and a public key. The public key is mathematically derived from the private key. You keep the private key on your machine and never share it. The public key, on the other hand, can safely be sent to the administrator of a remote server.

These files live in the hidden directory ~/.ssh, usually under the names id_rsa (private key) and id_rsa.pub (public key).

You can check whether these files already exist:

cd ~/.ssh
ls

If they are not present, generate them with:

ssh-keygen -t rsa

You can inspect their contents using:

cat id_rsa
cat id_rsa.pub

Step 2: send your public key to the server administrator

To access a remote server, your public key must be installed on that server.

Typically, you simply send the content of id_rsa.pub to the administrators managing the cluster at your institution.

Step 3: connect to the remote server

Once your public key has been registered, you can connect using:

ssh username@remoteserver.com

The first time you connect, SSH will ask whether you trust the host. Type yes. Behind the scenes, two things happen:

The server verifies your identity by checking that your machine possesses the private key corresponding to the public key it received.
Your computer verifies the server’s identity and stores its fingerprint in the file known_hosts inside ~/.ssh.

Step 4: simplify the connection

Typing

ssh username@remoteserver.com

can become tedious. Sometimes it is even more complicated: you may need to first connect to a gateway server at your institution before accessing the cluster.

SSH allows you to simplify this using a configuration file called config, stored in the ~/.ssh directory.

For example, suppose your username is ochehab and you want to connect to a computing cluster called dragon at Harvard, which is accessed through a gateway server. Your configuration file could look like this:

Host *
  UseKeychain yes
  AddKeysToAgent yes
  IdentityFile ~/.ssh/id_rsa

##################################################
# Harvard gateway

Host harvard
  HostName ssh.harvard.edu
  User ochehab

##################################################
# Dragon cluster

Host dragon
  HostName dragon.harvard.edu
  User ochehab
  CheckHostIP no
  ProxyCommand ssh harvard /usr/bin/nc %h %p

##################################################
# General rule for Harvard machines

Host *.harvard.edu
  ProxyCommand ssh -q harvard /usr/bin/nc -w 1 %h 22
  IdentityFile ~/.ssh/id_rsa
  User ochehab
  ForwardAgent yes
  ForwardX11 no

With this configuration in place, connecting to the cluster becomes as simple as:

ssh dragon

instead of typing:

ssh ochehab@ssh.harvard.edu
ssh ochehab@dragon.harvard.edu