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Information on compute facilities hosted by BioMedical Research Computing (BMRC)

BMRC Facilities

The WIN Centre recommends the use of the HPC facilities provided by the BioMedical Research Computing (BMRC) team. The BMRC facilities are located in the Big Data Institute and Wellcome Human Genetics building on the Old Road Campus. These pages form the basic information for researchers; BMRC's own documentation is available on their site.

Before you can use the BMRC equipment you and the project grant holder need to register with the BMRC team - see our BMRC account pages.

Data Governance Information

The BMRC cluster storage system utilises RAID technology to minimise risk to data as a result of disk hardware failure, however they DO NOT backup​ any data stored on this system and should be treated the same way as /vols/Scratch is on FMRIB's systems. Do not rely on this storage for your only copy of data you create, unless it is trivially regenerated. Please ensure you copy important results to storage hosted at FMRIB/OHBA or to another University approved secured storage location.

Raw MRI/MEG scan data is already protected at source so does not need additional protection and public datasets can be re-downloaded if required so may not need additional protection. You must document your proposed protection methodology in your data management plan and DPA/DPIA.

The BMRC storage is encrypted at rest (using AES256), but any project processing sensitive, identifiable human data will need to be separately assessed for suitability using the University's DPS/DPA/DPIA scheme. Until this approval is obtained from the Department/University you must not upload such data to their cluster.

Server Resources

In addition to the shared BMRC cluster the WIN Centre has exclusive and/or priority access to several machines. These are detailed on our BMRC Servers page.

Interactive/GUI Ac​​cess

In addition to the BMRC shared interactive nodes ( and, WIN have five dedicated interactive nodes accessible via the BMRC's Virtual Desktop Infrastructure service.

Initial setup of your account

Getting started​

​When you get your new account you should first take a look at the BMRC help pages​.

Access to their facilities is either via SSH to a pair of machines and or via WIN/BMRC's Virtual Desktop Infrastructure running on one of our dedicated servers.

The cluster1/cluster2 machines must not​ be used for any processing, they are purely for you to manipulate your files, upload/download data and submit tasks to the queues and to gain access to other resources. You may use the VDI hosts for any compute purpose.

On first connecting your SSH client will ask if you trust the remote server - check that the 'fingerprint' given matches these values - your version of SSH will decide whether you see the RSA, ECDSA or ED25519 fingerprint.

​Host ​Fingerprint 
​ ​2048 SHA256:zCwHn9ElYYevVCWIgKUmSDefdHrOqnXWUzzOnfowBRg (RSA)
256 SHA256:jbKUwq+x8n/zfNZZhvM+oQR5ip66od+RSYvmmlA2SZo (ECDSA)
256 SHA256:xNDl7NG8ovL99Su3kqTF9b9bmczxLlsXo+AGxoK4jeQ (ED25519)
​ ​2048 SHA256:zCwHn9ElYYevVCWIgKUmSDefdHrOqnXWUzzOnfowBRg (RSA)
256 SHA256:un7QAKQJR+HBwEsnGkLZYjQp2J7ZMPy5kYxCecJj2+I (ECDSA)
256 SHA256:LdZ54ymATu6YbgNLC0RUYCVBROmLkx1qqnFRCUSYpbw (ED25519)

Instuctions on getting started with your BMRC account, including WIN specific details are on our BMRC usage pages with instructions on using the BMRC cluster can be found on our BMRC cluster page​ along with details on the compute resources at BMRC​.

Setting up your account

​Once you have an account on their system you should add some WIN specific settings to your account​, you can do this with:


After running this command, please log out and back in. You will then have access to our WIN specific software modules - see Modules​. An important module is fsl_sub, use:

​module add fsl_sub

​to activate (you might want to put this line after the WIN Config section in your .bash_profile).

Storage locations

​User home folders (at /users/<groupname>/<username>...) are intentionally limited in size so do not store any project data in this location. Users have a dedicated folder within their group at /well/<groupname>/users/<username> - you should store all data and files there.

Graphical Programs

​WIN Centre users have access to a web-based Virtual Desktop Infrastructure that can be used to run graphical software on any of our cluster nodes. This is to be preferred over X11 forwarding over SSH, particularly when accessing from a non-University ethernet network and/or long running tasks.

Submitting to the Cluster​

For information on submitting jobs to the CPU or GPU cluster nodes see our BMRC cluster pages.

Introduction to the BMRC Cluster


​WIN@BMRC operate a compute cluster formed from rack-mounted multi-core computers. To ensure efficient use of the hardware, tasks are distributed amongst these computers using queuing software. Compute tasks are distributed amongst the cluster in the most optimum manner with available time shared out amongst all users. This means you usually have to wait a while for your jobs to complete, but there is the potential to utilise vastly more compute resources than you would have available to you on a single computer such as your laptop or a workstation.

The BMRC User guides are available at with some additional information, particularly about the fsl_sub submission program we provide detailed in this section.

​The BMRC Cluster

The BMRC cluster consists of main user-accessible computers (some times called Head Nodes) '' and '' and a farm of processing nodes which are not directly visible. The two cluster head nodes should only be used to submit tasks. To view results we recommend using the WIN Virtual Desktop Infrastructure (VDI) - the hosts accessible via this route can also be used to run simple tasks or interactive analysis tools. All other tasks must be run via the job submission system described below; in this way jobs get shared among the available processing nodes.
BMRC's documentation is available here:
Please remember, you must not run compute tasks of any form on the cluster1 and cluster2 computers. Any tasks found running there are liable to be killed as these kind of tasks have resulted in loss of service for all uses at times.

Submitting and monitoring tasks

For details on how to submit and the monitor the progress of you jobs see the BMRC cluster page.

Long Running Tasks

Unlike the Jalapeno cluster, BMRC's cluster does not offer 'infinite' queues (equivalent to verylong.q, bigmem.q and the cuda.q on the jalapeno cluster). You must break your task up into shorter components or regularly save state to allow restart and submit these parts (or resubmit the job continuing where it left off) using job holds to prevent tasks running before the previous one completes.​



Submitting jobs to the compute cluster

Submitting and monitoring tasks

For details on how to submit and the monitor the progress of you jobs see the BMRC cluster page. 

The UKBB data set is available on the BMRC facilities. To gain access you need to be added to one or more of the following groups:


  • win-ukb-imaging​ - this group gives access to the MRI imaging data​
  • win-ukb-genetics - this group gives access to the Genetics information
  • win-ukb-life - this group gives access to the lifestyle data


Approval for addition to these groups must come from Professor Smith or WIN IT. 

​Once you are in the appropriate groups the data is available in the following locations:

  • Imaging - /well/win-biobank/projects/imaging/data/data3
  • Genetics - /well/win-biobank/projects/genetics/data/v3/21k
  • Lifestyle - /well/win-biobank/projects/life/data/...​ (not currently available?)​

N.B. ​You must 'cd' directly to the appropriate final folder (e.g. data3 in the case of the imaging dataset) as the permissions on the parent folders will not allow you to view the contents of the 'data' folder only pass through it (so no tab-completion).

The BMRC website includes various user-guides, hints and tips. New users should start by reading the new users welcome page.

​If your problem relates to a WIN software package (e.g. FSL, fsl_sub error messages) then contact in the first instance. For issues with running tasks on the cluster (assuming fsl_sub managed to submit successfully) then contact

If you have a particular problem please use the following table to determine the most efficient route to obtaining support.

​Issue is with...​Who to contact
​Problems logging in ​
​fsl_sub gives an error ​
​fsl_sub submits job but it never runs ​ and then if they confirm fsl_sub has submitted incorrectly
​Unable to access a dataset ​ to request group membership
​Error/crash when running programs ​
​Issue with using VNC ​
​Run out of disk space ​Ask your PI to contact
​Problem with WIN maintained software (in /well/win/software) ​

BMRC Servers​ - WIN Priority Servers

​In addition to the shared servers the BMRC facilities provide, WIN owns several machines which are either for our exclusive use or can be given priority access, details of the resources appear here. N.B. Access to these machines is via - you cannot SSH directly to these devices.


Interactive Machines

To run interactive tasks, e.g. MATLAB or non-queued software WIN has five machines available for use as detailed in the table below.​ These machines should be accessed either by direct login, the Virtual Desktop Infrastructure or via srun -p win --pty bash as per the table entry. Please ONLY use win000 for large memory tasks.

Interactive Machines
HostnamePurpose​Access viaMemoryCPU cores/model
win000 High memory tasks (>128GB per job) ssh, VDI 3TB 112 Intel Xeon Platinum 8280 @ 2.7GHz
win001 ​small jobs ssh, VDI 1.5TB 56 ​Intel Xeon Gold 6258R @ 2.7GHz
win002-004 Medium memory tasks (<128GB) VDI, srun -p win --pty bash 1.5TB 56 Intel Xeon Gold 6258R @ 2.7GHz

GPU Machines​

These machines are notially shared with all users of the BMRC facilities (in return to access to the other GPU nodes). If you are experiencing difficulties in getting your jobs to be scheduled or you know you have a large number of jobs to run/have a deadline, then please contact WIN IT support as we can request exclusive access to one or more nodes.

GPU Machines
HostnameQueuesGPU Card and Quantity​Memory​CPU cores/model
​compg010-011 gpu_short, gpu_long ​P100 (16GB) x 4 ​384GB 24 ​Intel Xeon Gold 5118 @ 2.3GHz
​compg016 ​gpu_short, gpu_long ​V100 (32GB) x 2 ​768GB ​24 Intel Xeon Gold 6136 @ 3.0GHz
compg028-030 gpu_short, gpu_long Quadro RTX8000 (48GB) x4 768GB 32 Intel Xeon
compg031-033 gpu_short, gpu_long A100 (40GB) x 4 384GB 32 Intel Xeon


Research Group Dedicated Machines

​In addition to the shared resources some research groups have purchased their own hardware. These devices would typically be accessed via SSH from Access is by arrangement with the head of the research group.


Dedicated Machines
HostnameResearch GroupGPU Card and Quantity​Memory​CPU cores/model
​compg017 Mark Woolrich ​V100 (32GB) x 2 ​768GB ​24 Intel Xeon Gold 6136 @ 3.0GHz
  • Access to a queued job cluster of close to 10,000 x86_64 compute cores (16GB/core)
  • Ability to rent space on a 5PB + of high-performance cluster storage platform
  • ca 72 NVIDIA CUDA GPUs (36 of which have priority or dedicated access to WIN members), including the latest A100 cards
  • 4x 1.5TB, 56 core interactive Linux hosts dedicated to WIN users
  • 1x 3TB, 112 core interactive Linux host dedicated to WIN users