NMRhub_SSH_Troubleshooting

SSH Troubleshooting

NMRhub now requires an SSH key pair to connect. Use SSH / SFTP / rsync and tools like FileZilla to connect to NMRhub virtual machines (VMs).

Where is my private key?

After following the instructions at NMRbox User Dashboard SSH Key Setup, your private key should be at:

I have the private key in place, but I can’t connect.

  1. Try connecting to more than one VM to make sure it’s not just an issue with that specific VM. (Please let us know if you can SSH to one VM but not another via support@nmrbox.org).
  2. Use ssh -vvv to verify if SSH is attempting to use your private key.

It’s trying to use the key, but it still doesn’t work.

If you can’t connect after uploading your SSH key, verify the following commands give the same result. Windows users should run these commands from PowerShell:

ssh-keygen -lf $HOME/.ssh/id_ed25519
ssh-keygen -lf $HOME/.ssh/id_ed25519.pub

Ensure the key listed at NMRbox User Dashboard SSH Key matches your $HOME/.ssh/id_ed25519.pub.

Date key set

Home Directory Permissions

If your home directory is writable by anyone other than you, SSH will not work. Connect via VNC and run:

ls -l ~

If w appears after the first group of permissions (e.g., drwx), use the following command to correct it:

chmod go-w ~

How do I use a private key with rsync?

Add the following option to your rsync command:

-e "ssh -i /path/to/your/private_key"

How do I use a private key with sftp?

Add the following option to your sftp command:

-i /path/to/your/private_key

How do I use a private key with FileZilla?

Go to FileZilla’s Site Manager and make the following settings in the General tab. You can leave the port blank, as it defaults to the correct value (22).

How do I use a private key with WinSCP?

See The Authentication Page.

SSH Key Setup for Multi-User Shared Account

This guide covers setting up individual SSH keys for multiple users who share a single system account, with password-protected keys and convenient SSH config entries.

Overview

When multiple people share one account on a machine, each person should have their own SSH key pair for security and accountability. This setup allows:

Part 1: Generate Individual SSH Keys

Each user should generate their own key pair on the shared machine.

Step 1: Create a key pair with a descriptive name

ssh-keygen -t ed25519 -C "your-email@example.com" -f ~/.ssh/id_ed25519_username

Options explained:

Alternative for older systems: If the server doesn’t support Ed25519, use RSA instead:

ssh-keygen -t rsa -b 4096 -C "your-email@example.com" -f ~/.ssh/id_rsa_username

Step 2: Set a strong passphrase

When prompted, enter a strong passphrase to protect the private key:

Enter passphrase (empty for no passphrase): [type your passphrase]
Enter same passphrase again: [type your passphrase again]

Important: Never leave the passphrase empty! On a multi-user machine where others have access to this key, doing this would let other users log in as you.

Step 3: Verify the keys were created

ls -la ~/.ssh/id_ed25519_username*

You should see two files:

Part 2: Install Public Keys on the Server

Step 1: Copy your public key to the server

View your key by running:

cat ~/.ssh/id_ed25519_username.pub

Then add your individual user key to your NMRbox account at https://nmrbox.nmrhub.org/user-dashboard/ssh-key.

Part 3: Configure SSH Client for Easy Access

On the shared user account, configure the local SSH client to know about the different keys available.

Step 1: Edit your SSH config file

On your local machine:

nano ~/.ssh/config

Step 2: Add a host entry

Add this configuration (adjust for your setup) - one record as shown below per user on the machine:

Host user1
    HostName krypton.nmrbox.org #or a different NMRbox host
    User user1
    IdentityFile ~/.ssh/id_ed25519_username1
    IdentitiesOnly yes

Host user2
    HostName krypton.nmrbox.org #or a different NMRbox host
    User user2
    IdentityFile ~/.ssh/id_ed25519_username2
    IdentitiesOnly yes

# etc ...

Options explained:

Step 3: Set proper permissions

chmod 600 ~/.ssh/config

Step 4: Test the connection

ssh user1

You’ll be prompted for your key’s passphrase (not the server password). After entering it once, the connection should establish.

Please note that in the SSH example directly above, you don’t need to specify a hostname or key - just the alias for the connection (in this case user1) as defined in your .ssh/config file.

As you’ll have one record for each user with a key on this system, each user can use their own alias to SSH into their own account using the proper key.

Troubleshooting

“Permission denied (publickey)”

“Bad permissions” errors

chmod 700 ~/.ssh
chmod 600 ~/.ssh/config
chmod 600 ~/.ssh/id_ed25519_*
chmod 644 ~/.ssh/*.pub

Can’t remember which key is which

# View public key fingerprint
ssh-keygen -lf ~/.ssh/id_ed25519_username.pub

# List all keys in SSH agent
ssh-add -l
This site is open source. Improve this page.