Linux Shell FAQs
Once you have accessed Polaris through SSH, you will be in a Linux Bash shell. This will not be a comprehensive guide, but instead will give a general overview of our most frequently asked questions.
Linux File Permissions
A good overview of Linux file permissions can be found here, but a brief overview is that permissions are tiered into User, Group, and Other. Each tier has three permissions that can be enabled or disabled; Read (r), Write (w), and Execute (x).
To find a file's permissions, use the ls -l command.
[picardjl@polaris:~]$ ls -l prime-directive.txt
-rw-rw----. 1 picardjl picardjl 0 Dec 9 10:47 prime-directive.txt
In this case, the file prime-directive.txt has Read and Write permissions for the User picardjl, Read and Write for the Group picardjl, and no permissions for anyone else.
In order to change permissions, we need to use the chmod command. Let's say we want everyone to be able to read this file. We would nead to add the 'Read' bit to 'Other' in the file's permissions.
[picardjl@polaris:~]$ chmod o+r prime-directive.txt
[picardjl@polaris:~]$ ls -l prime-directive.txt
-rw-rw-r--. 1 picardjl picardjl 0 Dec 9 10:47 prime-directive.txt
Our file now has the Read (r) bit set.
Another method would be to use o= and supply our mask. Let's say we want to remove all ability to edit this document from Group (g) and Other (o).
[picardjl@polaris:~]$ chmod g=r,o=r prime-directive.txt
[picardjl@polaris:~]$ ls -l prime-directive.txt
-rw-r--r--. 1 picardjl picardjl 0 Dec 9 10:47 prime-directive.txt
Let's move this document into a folder of other public documents we also want everyone to have access to. One quirk of the Linux file structure is that, in order to move through a directory, you don't use Read (r) permissions, you use Execute (x). Therefore, if we want people to have access to this directory (Execute) AND list all the files inside (Read), we need to grant them Read (r) and Execute (x) permissions. ls -ld will show the permissions of a directory.
[picardjl@polaris:~]$ mkdir federation_docs
[picardjl@polaris:~]$ mv prime-directive.txt federation_docs/
[picardjl@polaris:~]$ ls -ld federation_docs/
drwxrwx---. 2 picardjl picardjl 33 Dec 9 10:59 federation_docs/
[picardjl@polaris:~]$ chmod o+rx federation_docs/
[picardjl@polaris:~]$ ls -ld federation_docs/
drwxrwxr-x. 2 picardjl picardjl 33 Dec 9 10:59 federation_docs/
For a more comprehensive guide to the chmod command, please see this HowToGeek article.
Host Key Authentication Failure
Over the summer of 2025 Polaris went through a change that caused the ED25519 SSH Host key to be renewed. Some clients did not like this, and now throw errors when attempting to log in, similar to the message below.
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
@ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY!
Someone could be eavesdropping on you right now (man-in-the-middle attack)!
It is also possible that a host key has just been changed.
The fingerprint for the ED25519 key sent by the remote host is
SHA256: 2eKINs5IxQFwm/22wQJE7KKHLbsGrCNtQsrl0L644pI.
Please contact your system administrator.
Add correct host key in /home/picardjl/.ssh/known_hosts to get rid of this message.
Offending RSA key in /home/picardjl/.ssh/known_hosts:1
Host key for polaris.clarkson.edu has changed and you have requested strict checking.
Host key verification failed.
To clear the message, you will need to remove the offending host key from your known hosts file. That file is mentioned in your error message; in the example above, that file is /home/picardjl/.ssh/known_hosts. Substitute your file name in for the one in the command below.
# Substitute the path to the file for the one provided by your error message
ssh-keygen -f /home/picardjl/.ssh/known_hosts -R 'polaris.clarkson.edu'
Windows Terminal/PowerShell Users
Windows adds escape characters to their paths by default. For example;
# Message provided by Windows OpenSSH
---
Add correct host key in C:\\Users\\picardjl/.ssh/known_hosts to get rid of this message.
---
# 'Real' path: C:\Users\picardjl\.ssh\known_hosts
ssh-keygen -f 'C:\Users\picardjl\.ssh\known_hosts' -R polaris.clarkson.edu
# OR (Without escape quotes)
ssh-keygen -f C:\\Users\\picardjl/.ssh/known_hosts -R polaris.clarkson.edu
After this, the incorrect host keys will be removed. If you want to be technically correct, proceed to the next section on verifying host keys.
Verify SSH Host Keys
If you are connecting to Polaris for the first time, and you want to make sure there's nothing strange happening, Polaris has published SSHFP records. SSHFP is a way of verifying SSH Host heys using DNS records. For more information on SSHFP and how it is used in security, read this APNIC article. In short, the valid fingerprints for the SSH keys are published through DNS records.
Manually
Polaris's SSH Host keys can be found using ssh-keyscan polaris.clarkson.edu. Polaris's public keys are below, so you can compare what your client sees to what Polaris actually has.
polaris.clarkson.edu ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBCzpD5RGis9WRUQTyzhHpVL4gbG8x+bKLNYonfdBrYmT04DUUgwzhpSWAvAI3EC0KKRPZvDWybjGeVccH6j2hwc=
polaris.clarkson.edu ssh-rsa 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
polaris.clarkson.edu ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIHnN0+TDiQaMGeHChcuzw9dokEvnEUqVaMCwQervM5NQ
In a Shell
Validating SSH in a shell can be done as part of the SSH command.
ssh polaris.clarkson.edu -o VerifyHostKeyDNS=yes
You can also add these options to an SSH config file.
#~/.ssh/config
Host polaris.clarkson.edu
VerifyHostKeyDNS=yes