This document is for accessing an Arvados VM using SSH keys in Unix-like environments (Linux, macOS, Cygwin, Windows Subsystem for Linux). If you would like to access VM through your browser, please visit the Accessing an Arvados VM with Webshell page. If you are using a Windows environment, please visit the Accessing an Arvados VM with SSH – Windows Environments page.
Arvados requires a public SSH key in order to securely log in to an Arvados VM instance, or to access an Arvados Git repository. The three sections below help you get started:
Start by opening a terminal window. Check if you have an existing public key:
$ ls ~/.ssh/id_rsa.pub
If the file
id_rsa.pub exists, then you may use your existing key. Copy the contents of
~/.ssh/id_rsa.pub onto the clipboard (this is your public key). You can skip the rest of this section and proceed by adding your key to the Arvados Workbench.
If there is no file
~/.ssh/id_rsa.pub, you must generate a new key. Use
ssh-keygen to do this:
$ ssh-keygen -t rsa -C "email@example.com" Generating public/private rsa key pair. Enter file in which to save the key (/home/example/.ssh/id_rsa): Enter passphrase (empty for no passphrase): Enter same passphrase again:
-tspecifies the key type (must be “rsa”)
-Cspecifies a comment (to remember which account the key is associated with)
We strongly recommend that you protect your key with a passphrase. This means that when the key is used, you will be required to enter the passphrase. However, unlike logging into remote system using a password, the passphrase is never sent over the network, it is only used to decrypt your private key.
Display the contents of
~/.ssh/id_rsa.pub (this is your public key) using
cat and then copy it onto the clipboard:
$ cat ~/.ssh/id_rsa.pub ssh-rsa AAAAB3NzaC1ycEDoNotUseExampleKeyDoNotUseExampleKeyDoNotUseExampleKeyDoNotUse9lmzkpBq983bQradKGT3LuKda9QOGe8MatI6wzSrJLSGhHm3hk6D8OWWUG4SneuCtKIk2bH0pgBj1G29+uzDIez90WzfCTZKbz4RcVQmPkowSSUAQDwb0ffwvRDhCgcJ1loT1wQAJzqJmljQ7xEYaCOIMqnfYE0lX7B3MSvCV6Ie2rWL33YecLp48LVtqiCOZU4XRyO8RSDFRFLVW+mjkLirwtDHZCRtORScaIEN0jw51p+T+9X5iA9QH/Mn+xlgk7fCgH+JtpBj808N/Qds2Gpff+Kb6ulUrVVfMK6L firstname.lastname@example.org
Now you can set up
ssh-agent (next) or proceed with adding your key to the Arvados Workbench.
If you find you are entering your passphrase frequently, you can use
ssh-agent to manage your credentials. Use
ssh-add -l to test if you already have ssh-agent running:
$ ssh-add -l
If you get the error “Could not open a connection to your authentication agent” you will need to run
ssh-agent with the following command:
$ eval $(ssh-agent -s)
ssh-agent -s prints out values for environment variables SSH_AUTH_SOCK and SSH_AGENT_PID and then runs in the background. Using “eval” on the output as shown here causes those variables to be set in the current shell environment so that subsequent calls to SSH can discover how to access the agent process.
ssh-agent, or if
ssh-add -l prints “The agent has no identities”, add your key using the following command. The passphrase to decrypt the key is the same used to protect the key when it was created with
$ ssh-add Enter passphrase for /home/example/.ssh/id_rsa: Identity added: /home/example/.ssh/id_rsa (/home/example/.ssh/id_rsa)
When everything is set up,
ssh-add -l should yield output that looks something like this:
$ ssh-add -l 2048 eb:fa:15:f2:44:26:95:58:37:37:f4:aa:ff:ee:c2:85 email@example.com (RSA)
You may now proceed to adding your key to the Arvados Workbench.
In the Workbench top navigation menu, click on the dropdown menu icon to access the user settings menu and click on the menu item SSH keys to go to the SSH keys page. Click on the + Add new SSH key button in this page. This will open a popup as shown in this screenshot:
Paste your public key into the text area labeled Public Key, and click on the Submit button. You are now ready to log into an Arvados VM.
To see a list of virtual machines that you have access to, click on the dropdown menu icon in the upper right corner of the top navigation menu to access the user settings menu, then click on the menu item Virtual machines to go to the Virtual machines page.
This page lists the virtual machines you can access. The Host name column lists the name of each available VM. The Login name column lists your login name on that VM. The Command line column provides a sample
ssh command line.
At the bottom of the page there may be additional instructions for connecting your specific Arvados instance. If so, follow your site-specific instructions. If there are no site-specific instructions, you can probably connect directly with
The following are generic instructions. In the examples the login will be you and the hostname will be shell.ClusterID.example.com and . Replace these with your login name and hostname as appropriate.
If the VM is available on the public Internet (or you are on the same private network as the VM) you can connect directly with
ssh. You can probably copy-and-paste the text from Command line column directly into a terminal.
Use the following example command to connect as you to the shell.ClusterID.example.com VM instance. Replace
you@shell.ClusterID.example.com at the end of the following command with your login and hostname from Workbench.
$ ssh you@shell.ClusterID.example.com
Some Arvados installations use “switchyard” to isolate shell VMs from the public Internet.
Use the following example command to connect to the shell VM instance as you. Replace
you@shell at the end of the following command with your login and hostname from Workbench:
$ ssh -o "ProxyCommand ssh -p2222 turnout@switchyard.ClusterID.example.com -x -a shell" -x you@shell
This command does several things at once. You usually cannot log in directly to virtual machines over the public Internet. Instead, you log into a “switchyard” server and then tell the switchyard which virtual machine you want to connect to.
-o "ProxyCommand ..."configures SSH to run the specified command to create a proxy and route your connection through it.
-p2222specifies that the switchyard is running on non-standard port 2222.
firstname.lastname@example.org the user (
turnout) and hostname (
switchyard.qr1hi.arvadosapi.com) of the switchyard server that will proxy our connection to the VM.
-xtells SSH not to forward your X session to the switchyard.
-atells SSH not to forward your ssh-agent credentials to the switchyard.
shellis the name of the VM that we want to connect to. This is sent to the switchyard server as if it were an SSH command, and the switchyard server connects to the VM on our behalf.
-xto disable X session forwarding to the virtual machine.
you@shellspecifies your login name and repeats the hostname of the VM. The username can be found in the logins column in the VMs Workbench page, discussed in the previous section.
You should now be able to log into the Arvados VM and check your environment.
The command line above is cumbersome, but you can configure SSH to remember many of these settings. Add this text to the file
.ssh/config in your home directory (create a new file if
.ssh/config doesn’t exist):
Host *.qr1hi TCPKeepAlive yes ServerAliveInterval 60 ProxyCommand ssh -p2222 email@example.com -x -a $SSH_PROXY_FLAGS %h User you
This will recognize any host ending in “.qr1hi” and automatically apply the proxy, user and forwarding settings from the configuration file, allowing you to log in with a much simpler command:
$ ssh shell.qr1hi
You should now be able to log into the Arvados VM and check your environment.
The content of this documentation is licensed under the
Commons Attribution-Share Alike 3.0 United States licence.
Code samples in this documentation are licensed under the Apache License, Version 2.0.