Storage

The following storage is available on the cluster:

Name Mount point Current capacity Mounts on Purpose
Home folders /users 39 TiB login, compute Software, code, configuration and other basic files, files not directly used in scheduled jobs; small amounts of data where I/O speed is not critical
Scratch /scratch 930 TiB login, compute Files used directly in or created by scheduled jobs, large amounts of data and/or where low latency and/or high bandwidth access is important

Attention

Please see the terms of use for guidance on the types of data it is or is not appropriate to store on the system.

Important

Please note, that although there is some degree of resilience provided at the hardware level, both /users and /scratch are not backed up. Make sure that you always have appropriate backups of the data stored within.

Home folders

Should be used to store data, such as software, code, configuration in situations, where I/O speed is not critical. By default only accessible by the owner, or the account holder. It is provisioned automatically when the account is created. Can be accessed via the /users/<user id> path, e.g. /users/k1234567.

Scratch

Fast storage utilising the Lustre parallel file system. Should be used to store the data actively produced, or being consumed by the simulations where low latency and/or high bandwidth access is required. Different types of scratch are listed below.

Personal scratch

Only accessible by the owner, or the account holder and provisioned automatically when the account is created. Can be accessed via the /scratch/users/<user id> path, e.g. /scratch/users/k1234567.

If the data contained within needs to be shared with other users, group scratch should be considered instead.

Group scratch

Accessible by the members of the group that owns the share. It will have its own quota allocation, that will not count towards the members own allocation. Can be accessed via the /scratch/groups/<group id> path, e.g. /scratch/groups/biocore.

Group scratch shares are not provisioned automatically and have to be explictly requested.

Info

When requesting group shares, please provide the following information:

  • Name of the share: This ideally should be the research group, or project name.
  • Data owner(s): Individuals that will be the primary point of contact for the data, and will be responsible for its management and access control.
  • List of members: List of individuals, or an existing group, that will have a read/write access to the share.
  • Lifetime: The amount of time after which the share can be expired.

Datasets

A special type of a group share designated to host datasets. By default it will be read-only, with a dataset owner(s) having write access and publicly accessible within the cluster. Can be accessed via the /scratch/datasets/<dataset id> path, e.g. /scratch/datasets/ukbiobank.

Dataset shares are not provisioned automatically and have to be explictly requested.

Info

When requesting dataset shares, please provide the following information:

  • Name of the dataset.
  • Use case and the relevant infrormation about the dataset (estimated size, external source, etc).
  • Data owner(s): Individuals that will be the primary point of contact for the data, and will be responsible for its management and access control. Data owner will automatically have write access.
  • Lifetime: The amount of time after which the share can be expired.

Quotas

The following quota allocations are currently in place on the cluster:

User class Home /users Personal scratch /scratch/users
Size Files1 Size Files1
Users from the GSTT2 and SLaM3 BRCs 40 GiB 400,000 500 GiB 2,000,000
NMS4 research staff and PhD students 40 GiB 400,000 100 GiB 1,000,000
All other King’s staff and PhD students 40 GiB 400,000 100 GiB 1,000,000
All taught students 40 GiB 400,000 20 GiB 500,000

Info

Group and dataset share quotas are set and adjusted on-demand.

Checking quota allocation

Home folders

To check your home directory quota allocation use

quota -s

you should see something similar to

[k1234567@login3(rosalind) ~]$ quota -s
Disk quotas for user k1234567 (uid 1234567):
     Filesystem   space   quota   limit   grace   files   quota   limit   grace
storage1:/export/users
                 10590M    40G     40G             187k   400k    500k

Lustre scratch space

To check your personal scratch space allocation use

lfs quota -h -p `id -u` /scratch

This will output the following:

[k1234567@login3(rosalind) ~]$ lfs quota -h -p `id -u` /scratch
Disk quotas for prj 123456789 (pid 123456789):
     Filesystem    used   quota   limit   grace   files   quota   limit   grace
   /scratch        4k     500G    510G       -        1  2000000 2100000     -

To check your group scratch space allocation use

lfs quota -h -g wg_test-group /scratch

This will output the following:

[k1234567@login3(rosalind) ~]$ lfs quota -h -g wg_test-group /scratch
Disk quotas for wg_test-group (gid 12345678):
     Filesystem    used   quota   limit   grace   files   quota   limit   grace
   /scratch        4k     1T      1.1T       -        1  2000000 2100000     -

Tip

When you go over the soft quota limit (defined by the quota value), it will be indicated by the * (asterisk) symbol next to the value in the used, or use column, e.g. 1.4T*. You still will be able to write to the storage until either the grace period expires, or you reach the hard limit (defined by the limit value).


  1. Technically, the limit on number of files is actually for number of inodes — each directory consumes one inode, in addition to one inode per file within. 

  2. NIHR Biomedical Research Centre at Guy’s & St Thomas′ NHS Foundation Trust and King’s College London 

  3. NIHR Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and the Institute of Psychiatry, Psychology & Neuroscience at King’s College London 

  4. Faculty of Natural & Mathematical Sciences, King’s College London