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Accessing the BMRC cluster

Before following this step-by-step guide:

  1. You will need to have registered for and received a cluster account. This provides you with the username, password and two factor authentication token that you will need.
  2. For remote connections (away from the University), you will need to connect to the University of Oxford network via VPN. For instructions, please see  IT Services' VPN page or consult your local IT team.
  3. We also recommend that you read the introduction to our cluster computing guide in order to understand what a cluster is and why you might want to access it. NB You don’t need to read the whole cluster computing guide yet! - just glance through the introduction to get the basic concepts.

PLEASE NOTE: You will need to be connected to an Oxford University VPN before connecting via SSH. See step 2 above for further details.

Getting started

If you’ve read our introduction to cluster computing, you know that access to our cluster is via one of two login nodes, either cluster1.bmrc.ox.ac.uk or cluster2.bmrc.ox.ac.uk.

SSH - The Secure Shell

To access cluster1.bmrc.ox.ac.uk or cluster2.bmrc.ox.ac.uk you need to use a piece of software called an ssh clientssh is short for secure shell. The secure part of the name indicates that, when used correctly, your connection will be secure. The shell part of name indicates that you will interact with this software by typing things into a command line (the shell).

How you use the SSH software depends on which operating system your computer is running. See below for instructions specific to Windows, Mac and Linux.

However, the basic connection settings are the same for any SSH connection, including SSH connections from devices running other operating systems e.g. iOS (iPhone or iPad), Android (phones or tablets), ChromeBooks, etc.

Basic SSH Connection Information

First connect to an Oxford University VPN as described above.

If connecting from a terminal such as those provided under Linux, Mac OS Terminal app, or from Windows Subsystem for linux, then type:

ssh username@cluster1.bmrc.ox.ac.uk

Replace username with the username for your account.

For all other SSH clients, please refer to the following information:

  • SSH Address: cluster1.bmrc.ox.ac.uk or cluster2.bmrc.ox.ac.uk
  • SSH Port: 22 (i.e. This is the standard port for SSH so you will not normally need to change it)
  • SSH Username: The username for your BMRC account

First Login and Two Factor Authentication Tips

Login to BMRC requires two factor authentication (sometimes abbreviated to 2FA). This means that users will require a one-time code as well as their password to log in to BMRC services. BMRC require users to use an Authenticator app (such as Microsoft Authenticator, Google Authenticator, Authy, etc) on a smartphone to provide the second factor. This will be a 6 digit code which will be generated every 30 seconds. When logging in, users will be prompted for First factor which means your password and then Second Factor which means the six-digit code from your phone.

NB1 Two factor codes are single use i.e. they cannot be re-used even after a failed login attempt. If you wait 30 seconds, your 2FA app will generate a new six-digit code.

NB2 Two factor codes are generated based on a secret token stored by your phone and the current time. For this reason, your phone must be set to the correct time if it is to generate valid two factor codes. Please ensure that your phone is configured to set its time automatically via your mobile phone network. It does not matter which timezone your phone is set to use, only that your phone is set to the correct time within whatever timezone you are using.

When logging in for the first time, you will need to set a new password. Passwords must comprise at least sixteen characters with at least three character classes (uppercase, lowercase, numeral, symbol).

After making your SSH connection, proceed through the on-screen prompts as follows:

First factor: Enter the temporary password from your welcome email
Second Factor: Enter the six-digit code from 2FA app
Password expired: change your password now
First factor (Current password): Re-enter the temporary password from your welcome email
Second Factor: Wait for a new six-digit code from your 2FA app and enter
New password: Enter your new password
Retype new password: Re-enter your new password to confirm

NB3 When entering passwords or two factor codes, it is normal not to see anything on screen (your typing is not echoed). So you need to just type and press enter to proceed.

NB4 If you see the message "Old password not accepted", it's likely that you have entered your new password too soon. You should be able to retry from scratch.

NB5 If the server prompts you for Password rather than First factor/second factor, it's likely that your account has been temporarily blocked, so please wait 15 minutes and then retry. If problems persist, then please contact us.

After successfully logging and setting your new password, you will be shown a welcome messages from BMRC and then your prompt will indicate that you have successfully logged in to either rescomp1 or rescomp2. You can also confirm by running the hostname command which will report either rescomp1.hpc.in.bmrc.ox.ac.uk or rescomp2.hpc.in.bmrc.ox.ac.uk. If you do not see the welcome message or prompts, it's likely that your first login and password change has been unsuccessful, so you'll need to retry from the beginning.

Read on for further information about making SSH connections using different OSes and different SSH clients.

Connecting from Windows

There are numerous ways of using ssh from within Microsoft Windows.

  • If you already use the Windows Subsystem for Linux, then you effectively have a Linux environment available, so see our Linux ssh instructions below.
  • Alternatively, you will need some third-party ssh client software. We offer no official recommendation and users are encouraged to explore the options themselves. Some popular SSH clients include:

Given the range of available software, it is impossible to offer detailed instructions for all of them. In most cases, all you will need is the Basic SSH Information shown above. Purely by way of example, we show below how to use that information for the PuTTY SSH client software.

  1. Visit the PuTTY website (link above) and click the link “You can download PuTTY here”. This will take you to the download page.

  2. On the PuTTY download page, find the Package Files section and then click the link to download the MSI (Windows Installer) version of PuTTY for Windows 64-bit. For example, at the time of writing the latest version is putty-64bit-0.73-installer.msi, but this will update in future. Click to download the latest version for your version of Windows and CPU architecture (in almost all cases, you should choose the 64 Bit version).

  3. After clicking you may see a notification at the bottom of the screen asking you to Run or Save this file - please click Run. Alternatively, click Save and then locate the file in your Downloads folder and double click to run. This will run the PuTTY installer you can complete the installation with the default settings).

  4. When the installation has finished, click on the Windows Start button and you should see program PuTTY appear (alternatively, type PuTTY to search for it). You need to run the program which is called PuTTY (i.e. don’t run PuTTYgen or anything else).

  5. Enter the following connection settings into the PuTTY window (use your real username in place of 'username')and then click Open.

    PuTTY Config

Connecting from Mac

The Apple operating system Mac OS already includes everything you need to connect via SSH using the Terminal software.

  1. Open the Terminal (located in /Applications/Utilities/Terminal.app)

  2. At your terminal prompt, type ssh <username>@cluster1.bmrc.ox.ac.uk and press [Return]. You should substitute <username> with your BMRC username.

  3. When prompted, type your password

Connecting from Linux and MAC

  1. Linux users: If running in a graphical environment, start your preferred terminal program (e.g. Gnome Terminal or Konsole). Alternatively, if already running in console mode, simply proceed to step 2. Mac users: Start the Terminal program in Applications / Utilities / Terminal.app.

  2. At your terminal prompt, type ssh <username>@cluster1.bmrc.ox.ac.uk and press [Return]. You should substitute <username> with your BMRC username.

  3. When prompted, type your first factor (password) and second factor (two factor code).

Troubleshooting: Why can't I login via SSH?

If you cannot connect via ssh, look carefully at the error message received to help diagnose the issue and see what your options are.

Message Explanation & Resolution

ssh: Could not resolve hostname rescomp1.well.ox.ac.uk: Name or service not known (likewise for rescomp2.well.ox.ac.uk)

The login gateways for the BMRC have changed to cluster1.bmrc.ox.ac.uk and cluster2.bmrc.ox.ac.uk on Tuesday 23rd November 2021. Please update your SSH configuration and discontinue use of the old names. Once logged in, these hosts will continue to report their local hostname as rescomp1-2.

ssh: connect to host cluster1.bmrc.ox.ac.uk port 22: No route to host (Likewise for cluster2)

All connections to our systems must originate from within the Oxford University IT network. For local users, you can connect either via ethernet or via an Oxford University-hosted VPN. For remote users, you will need to connect via Oxford University-hosted VPN. NB A VPN provided by another university or institution will not work.

Further details are available on the University's VPN page.

ssh: connect to host cluster1.bmrc.ox.ac.uk port 22: Connection refused

(Likewise for cluster2)

Alternatively you may see:

ssh: connect to host cluster1.bmrc.ox.ac.uk port 22: Operation timed out

(Likewise for cluster2)

Your IP address has been temporarily blocked due to suspected malicious activity. This can happen e.g. if you or another user on the same IP address enter an incorrect password too many times. Please note that for blocking purposes, cluster1 and cluster2 are separate, so if you are blocked from one, you can still try the other.


In normal cases, your IP address will have been blocked for just 10 minutes. So you can either switch to logging in on the other node (i.e. switch to cluster2 if you have been blocked by cluster1) or you can wait ten minutes and see if you are automatically unblocked.

If the block remains after ten minutes and you still cannot login, please Google "what's my ip address" and then email bmrc-help@medsci.ox.ac.uk with the address that Google reports. It will be in the format of four numbers (0-127) separated by dots e.g. 110.82.10.03

Do you support login via SSH keys?

The BMRC cluster does not support login via SSH keys. UK research institutions are a target for hacking and in 2020 another UK research institution suffered a login breach that was due to SSH keys. As a result, many UK institutions no longer permit SSH keys. We are currently reviewing our login methods to ensure that they remain up to date with the latest security guidance.

Next Steps after your first login

Once you’ve successfully logged in, you will be presented with:

  • a login message (beginning Acknowledgements)
  • a terminal running on one of our login nodes, either cluster1.bmrc.ox.ac.uk or cluster2.bmrc.ox.ac.uk.

You can check which login node you are currently on by running the hostname command which will report either rescomp1.hpc.in.bmrc.ox.ac.uk or rescomp2.hpc.in.bmrc.ox.ac.uk.

From here you may wish to look at your home directory (i.e. your home folder) located at /users/<group>/<username>/ or your data directory/folder located at /well/<group>/users/<username>

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