Arun Seetharam

Arun Seetharam

My main interests are in the fields of Bioinformatics and evolutionary Genomics. Currently, I am working on various projects involving next-generation sequencing, including the first *de novo* assembly of a teosinte genome. I am also developing pipelines to streamline the assembly and annotation process for newly sequenced organisms. My long-term goal is to study genome organization and the evolution of grass species.

DataScience Workbook / 06: High-Performance Computing (HPC) / 2. Remote Access to HPC resources / 2.2. Secure Shell Connection (SSH) / 2.2.1. SSH shortcuts and password-less login

Setup password-less login for HPC

Most HPC resources should now require double authentication which will make this type of password-less login not possible. For those that don’t have double authentication, this will work.

To login automatically from your machine to the remote host, you can save the private/public key pair in both machines. This way, you don’t have to enter password each time you login.

Step 1: Create public and private keys (local computer)

ssh-keygen

Step 2: Copy the public key to remote-host

ssh-copy-id -i ~/.ssh/id_rsa.pub userid@MACHINENAME

Step 3: Login

ssh userid@MACHINENAME
# Ensure file permissions for ~/.ssh/.id_rsa (local) and ~/.ssh/authorized_keys (remote) are such that it is only readable by you!

Shortcuts for SSH hosts

Are you tired of typing full length host-names while connecting via SSH?
Do you frequently scp files from one server to another and have to lookup what the host-names are? Do you want to rsync between local and remote host easily with a simple command? Then, read-on!

The hard-way approach (requires typing anew each time):

# connect
ssh username@login.scinet.science
# scp
scp yourfile usename@login.scinet.science:/path/to/destination/
# rsync
rsync -e 'ssh -c aes128-ctr' -rts your_folder username@login.scinet.science:/path/to/destination/

As you can see, if you have a bunch of hosts, it gets really hairy to retype them every time you want to do any of these things.

The Solution

Create a config file under the ~/.ssh directory, with the short name for these host-names. Then you can simply connect to the server by using the short name instead of the full host-name!

  1. First, edit the config file: 
      vi ~/.ssh/config
  2. And, add the details: 
    Host ceres
  Hostname login.scinet.science
  User username
  ForwardX11 yes
  ServerAliveInterval 300
Host condo
  Hostname condo2017.its.iastate.edu
  User username
  ForwardX11 yes
  3. Set permissions straight: 
      chmod 600 ~/.ssh/config

Now, have fun!
The above commands can now be done using:

# connect
ssh ceres
# scp
scp yourfile ceres:/path/to/destination/
# rsync
rsync -e 'ssh -c aes128-ctr' -rts your_folder ceres:/path/to/destination/

You can read more about the config by opening the man page: man ssh-config

Now, combine this with password-less login and work smart!