Filestores

Every HPC user has access to up to six different storage areas:

• Home directories: per-user backed-up, snapshotted storage

• Data directories: additional per-user snapshotted storage (not on Bessemer)

• Fastdata areas: high-performance shared filesystem for temporary data - optimised for reading/writing large files from multiple nodes and threads simultaneously

• Shared (project) directories: per-PI shared storage areas (snapshotted and backed-up) for project data - can be accessed from non-HPC machines too

• Scratch directories: per-node temporary storage - useful for reading/writing lots of small files within one job

• Community areas for software: cluster-wide storage areas to allow users to share software.

The storage areas differ in terms of:

• the amount of space available;

• whether they are available from multiple nodes;

• whether they are shared between clusters;

• whether the underlying storage system is performant if reading/writing large files;

• whether the underlying storage system is performant if reading/writing small files;

• frequency of storage snapshotting, whether storage is mirrored and the maximum duration data can be retained for;

• whether they handle permissions like a typical Linux filesystem.

At present none provide encryption at rest.

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Choosing the correct filestore

To make a quick assessment of what storage area is likely to best fulfil your needs, please take a look at the provided decision tree below:

Warning

This decision tree only provides a quick assessment, please check the full details of each filestore before committing to using them for your work.

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Home directories

All users have a home directory on each system, some of which are shared between systems:

System	Path	Type	Quota per user	Shared between system login and worker nodes?	Shared between systems?
Bessemer	/home/yourusername	NFS	100GB	Yes	No
ShARC	/home/yourusername	NFS	10GB	Yes	No

See also: How to check your quota usage and * If you exceed your filesystem quota.

Snapshotting and mirrored backups

Frequency of snapshotting	Snapshots retained
Every 4 hours	10 most recent
Every night	Last 7 days

Frequency of mirrored backups	Backups retained
Every 4 hours	6 most recent
Every night	28 most recent

See also: Recovering files from snapshots.

Data directories

Every user on ShARC (not Bessemer) has access to a larger data storage area:

System	Path	Type	Quota per user	Shared between system login and worker nodes?	Shared between systems?
Bessemer	N/A	NFS	N/A	N/A	N/A
ShARC	/data/yourusername	NFS	100GB	Yes	No

See also: How to check your quota usage and * If you exceed your filesystem quota.

Snapshotting and mirrored backups

Frequency of snapshotting	Snapshots retained
Every 4 hours	10 most recent
Every night	Last 7 days

Frequency of mirrored backups	Backups retained
Every 4 hours	6 most recent
Every night	28 most recent

See also: Recovering files from snapshots.

Automounting

Data directories are made available to you (mounted) on demand: if you list the contents of just /data after first logging on then your /data/te1st subdirectory (where te1st is your username) might not be shown. However, if you list the contents of /data/te1st itself or change into that directory then its contents will appear.

Later on if you list the contents of /data again you may find that /data/te1st has disappeared again, as it is automatically unmounted following a period of inactivity.

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Fastdata areas

Fastdata areas are optimised for large file operations. These areas are Lustre filesystems.

They are are faster than Home directories, Data directories and Shared (project) directories when dealing with larger files but are not performant when reading/writing lots of small files (Scratch directories are ideal for reading/writing lots of small temporary files within jobs). An example of how slow it can be for large numbers of small files is detailed here.

System	Path	Type	Quota per user	Filesystem capacity	Shared between systems?	Network bandwith per link
Bessemer	/fastdata	Lustre	No limits	460 TB	No	25Gb/s Ethernet
ShARC	/fastdata	Lustre	No limits	669 TB	No	100Gb/s (Omni-Path)

Snapshotting and mirrored backups

Snapshotting is not enabled for fastdata areas and these areas are not backed up.

Managing your files in fastdata areas

In order to avoid interference from other users’ files it is important that you store your files in a directory created and named the same as your username e.g. if your username is te1st then you can a fastdata area for yourself using:

mkdir /fastdata/te1st

By default the directory you create will have world-read access. If you want to restrict read access to just your account then run

chmod 700 /fastdata/te1st

after creating the directory. A more sophisticated sharing scheme would have private and public directories

mkdir /fastdata/te1st
mkdir /fastdata/te1st/public
mkdir /fastdata/te1st/private

chmod 755 /fastdata/te1st
chmod 755 /fastdata/te1st/public
chmod 700 /fastdata/te1st/private

Automatic file deletion

Warning

There are no quota controls in fastdata areas but older files are automatically deleted: a report of files older than 60 days is regularly generated, the owners of these files are then notified by email then a week after the email(s) are sent the identified files are deleted.

We reserve the right to change this policy without warning in order to ensure efficient running of the service.

It is important to therefore not use fastdata areas for long-term storage and copy important data from these areas to areas suitable for longer-term storage (Home directories, Data directories or Shared (project) directories).

You can use the lfs command to find out which files in a fastdata directory are older than a certain number of days and hence approaching the time of deletion. For example, if your username is te1st then you can find files 50 or more days old using:

lfs find -ctime +50 /fastdata/te1st

File locking

As of September 2020 POSIX file locking is enabled on all Lustre filesystems. Prior to this the lack of file locking support on the University’s Lustre filesystems caused problems for certain workflows/applications (e.g. for programs that create/use SQLite databases).

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Shared (project) directories

Each PI at the University is entitled to request a free 10 TB storage area for sharing data with their group and collaborators. The capacity per area can be extended and additional shared areas can be purchased (both at a cost).

After one of these project storage areas has been requested/purchased it can be accessed in two ways:

• as a Windows-style (SMB) file share on machines other than Bessemer/ShARC using \\uosfstore.shef.ac.uk\shared\;

• as a subdirectory of /shared on Bessemer/ShARC (you need to explicitly request HPC access when you order storage from IT Services).

Snapshotting and mirrored backups

Frequency of snapshotting	Snapshots retained	Backed up onto separate storage system
Every 4 hours	10 most recent	Yes
Every night	Last 7 days	Yes

See also: Recovering files from snapshots.

Automounting

Similar to Data directories, subdirectories beneath /shared are mounted on demand on the HPC systems: they may not be visible if you simply list the contents of the /shared directory but will be accessible if you cd (change directory) into a subdirectory e.g. cd /shared/my_group_file_share1.

Specifics for Bessemer

If you need to access a /shared area on Bessemer please contact research-it@sheffield.ac.uk to arrange this.

Warning

• If you access a /shared directory stored in Sheffield from Bessemer then you may experience slower performance, espeicially for small files.

• Network traffic between Bessemer and Sheffield Research Filestore is not encrypted when travelling between Sheffield and Leeds over JANET

• /shared areas can be created on Bessemer’s filestore system if you need faster access from Bessemer

Permissions behaviour

You may encounter strange permissions issues when running programs on HPC against the /shared areas e.g. chmod +x /shared/mygroup1/myprogram.sh fails. Here we try to explain why.

Behind the scenes, the file server that provides this shared storage manages permissions using Windows-style ACLs (which can be set by area owners via the Research Storage management web interface. However, the filesystem is mounted on a Linux cluster using NFSv4 so the file server therefore requires a means for mapping Windows-style permissions to Linux ones. An effect of this is that the Linux mode bits for files/directories under /shared on the HPC systems are not always to be believed: the output of ls -l somefile.sh may indicate that a file is readable/writable/executable when the ACLs are what really determine access permissions. Most applications have robust ways of checking for properties such as executability but some applications can cause problems when accessing files/directories on /shared by naively checking permissions just using Linux mode bits:

• which: a directory under /shared may be on your path and you may be able to run a contained executable without prefixing it with a absolute/relative directory but which may fail to find that executable.

• Perl: scripts that check for executability of files on /shared using -x may fail unless Perl is explicitly told to test for file permissions in a more thorough way (see the mention of use filetest 'access' here).

• git: may complain that permissions have changed if a repository is simply moved to /shared/someplace from elsewhere on Bessemer/ShARC. As a workaround you can tell git to not to track Linux permissions for a single repository using git config core.filemode false or for all repositories using git config --global core.filemode false.

Changing how attempts to change permissions are handled: each /shared area can be configured so that

1. Attempts to change file/directory mode bits fail (e.g. chmod +x /shared/mygroup1/myprogram.sh fails) (default configuration per area) or

2. Attempts to change file/directory mode bits appear to succeed (e.g. chmod +x /shared/mygroup1/myprogram.sh does not fail but also does not actually change any permissions on the underlying file server) (alternative configuration per area)

If you would like to switch to using the second way of handling permissions for a particular /shared/ area then the Owner of this area should make a request via the Helpdesk.

Further information

The documentation for the /shared storage service includes information on:

• how access/permissions are managed

• how to create folders with associated permissions within /shared storage areas

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Scratch directories

For jobs that need to read/write lots of small files the most performant storage will be the temporary storage on each node (under the /scratch directory).

This is because with Home directories, Data directories, Fastdata areas and Shared (project) directories, each time a file is accessed the filesystem needs to request ownership/permissions information from another server and for small files these overheads are proportionally high.

For the /scratch store, such ownership/permissions metadata is available on the local machine, thus it is faster when dealing with small files.

As the /scratch areas are node-local storage and files/folders are deleted when jobs end:

• any data used by the job must be copied to /scratch when the jobs starts.

• any output data stored in /scratch must also be copied off to another area before the job finishes. (e.g. to Home directories or Data directories).

Further conditions also apply:

• Anything in the /scratch area may be deleted periodically when the worker-node is idle.

• The /scratch area is not backed up.

• There are no quotas for /scratch storage.

• The /scratch area uses the ext4 filesystem.

Danger

/scratch areas are temporary and have no backups. If you forget to copy your output data out of the /scratch area before your job finishes, your data cannot be recovered!

Where to store data inside /scratch areas:

The schedulers automatically create a per-job directory for you under /scratch. The name of this directory is stored in the $TMPDIR environment variable e.g.

On ShARC:

[te1st@sharc-login1 ~]$ qrshx
[te1st@sharc-node003 ~]$ cd $TMPDIR
[te1st@sharc-node003 667443.1.all.q]$ pwd
/scratch/667443.1.all.q

On Bessemer:

[te1st@bessemer-login1 ~]$  srun -c 1 --mem=4G --pty bash -i
[te1st@bessemer-node001 ~]$ cd $TMPDIR
[te1st@bessemer-node001 2660172]$ pwd
/scratch/2660172

The scheduler will then clean up (delete) $TMPDIR at the end of your job, ensuring that the space can be used by other users.

Warning

If using qrsh on ShARC to start an interactive job then the TMPDIR environment variable will unfortunately be undefined so you will need to manually create a directory under /scratch (named using your username) and this will not be cleaned up when the job ends.

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Community areas for software

Most data that researchers want to share with their collaborators at the University should reside in Shared (project) directories. However, as mentioned in Permissions behaviour, these areas may not be ideal for storing executable software/scripts due to the way permissions are handled beneath /shared.

Also, users may want to install software on the clusters that they want to be accessible by all cluster users.

To address these two needs users can request the creation of a new directory beneath of the three directories listed below and if their request is granted they will be given write access to this area:

System	Path	Type	Software install guidelines	Public index of areas	Notes
Bessemer	/usr/local/community	NFS
ShARC	/usr/local/community	NFS	Community software	Software install guidelines	Also available at /usr/local/extras

Note that:

• Software installation should follow our installation guidelines where provided.

• Software installations must be maintained by a responsible owner.

• Software which is not actively maintained may be removed.

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How to check your quota usage

To find out your storage quota usage for your home directory and data directory (if not on Bessemer) you can use the quota command:

[foo11b@sharc-node004 binary]$ quota

Size  Used Avail Use%  Mounted on
10G    10G    0G 100%  /home/foo11b
100G     0  100G   0%  /data/foo11b

In the above, you can see that the quota was set to 10 gigabytes and all of this is in use which is likely to cause jobs to fail.

To determine usage in a particular Shared (project) directories you can use the df command like so:

[foo11b@sharc-node004 binary]$ df -h /shared/myproject1
Filesystem                        Size  Used Avail Use% Mounted on
172.X.X.X:/myproject1/myproject1   10T  9.1T  985G  91% /shared/myproject1

To assess what is using up your quota within a given directory, you can make use of the ncdu module on ShARC or the ncdu module on Bessemer. The ncdu utility will give you an interactive display of what files/folders are taking up storage in a given directory tree.

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If you exceed your filesystem quota

If you reach your quota for your home directory then many common programs/commands may cease to work as expected or at all and you may not be able to log in.

In addition, jobs may fail if you exceed your quota for your data directory or a Shared (project) directory.

In order to avoid this situation it is strongly recommended that you:

• Check your quota usage regularly.

• Copy files that do not need to be backed up to a Fastdata area or remove them from Bessemer/ShARC completely.

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Recovering files from snapshots

Home directories, Data directories and Shared (project) directories are regularly snapshotted. See above for details of the snapshot schedules per area. A subset of snapshots can be accessed by HPC users from the HPC systems themselves by explicitly browsing to hidden directories e.g.

Storage area	Parent directory of snapshots
Home directory	/home/$USER/.snapshot
Data directory	/data/$USER/.snapshot
A Shared (project) directory	/shared/myproject1/.snapshot

From within per-snapshot directories you can access (read-only) copies of files/directories. This allows you to attempt recover any files you might have accidentally modified or deleted recently.

Note that .snapshot directories are not visible when listing all hidden items within their parent directories (e.g. using ls -a /home/$USER): you need to explicitly cd into .snapshot directories to see/access them.