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QMUL ITS Research Systems Usage Policy

ITS Research reserve the right to make amendments to this usage policy without notice, as required to ensure availability, security and fair usage of the services provided.

1 User Accounts

There are two types of account available: HPC and GitHub only. HPC accounts allow access to the HPC, GitHub Enterprise (research version) and other research services. GitHub only accounts have no access to the HPC cluster.

1.1 Account Eligibility

  1. Accounts are available for QMUL Staff, Students and External collaborators sponsored by a member of QMUL Staff. Accounts may be requested via the forms on this website.

  2. All accounts are subject to approval by ITS Research; account requests may be rejected if ITS Research deem the request to be incomplete, invalid or inadequate.

  3. Accounts are limited to one per user; use of multiple accounts to avoid resource and storage quotas will result in suspension of all involved accounts.

  4. Students who move on to a postgraduate degrees and receive a new ITS username must request a replacement account with the new username by contacting us. The previous account will be suspended after a maximum 2 week transfer period.

  5. An existing GitHub only account (research version) may be upgraded to a full HPC account with the appropriate approval from relevant parties. Contact us for more information.

  6. Accounts for Undergraduate and Postgraduate taught students are subject to approval from their project supervisor; approval will be confirmed before account creation.

  7. External collaborator account requests are subject to approval by their QMUL sponsor. Approval status lasts for up to twelve months, after which the sponsor will be required to confirm their status.

1.2 Security

  1. Accounts, passwords and SSH keys must not be shared with anyone and must be kept secure. For SSH keys, this means that the private part must be protected by a passphrase.

  2. Users may change their account password using the ITS Research Password Change website, accessible only from a university network.

  3. Use of another person's account is a violation of this policy and will result in suspension of all accounts and users involved.

1.3 Suspension and Termination

1.3.1 Account Suspension

  1. Accounts held by staff and students leaving QMUL, or external collaborators ending their collaboration with QMUL will be suspended without prior warning.

  2. Users found to be in breach of any statute in this usage policy may be suspended at the discretion of ITS Research without prior notice.

  3. Suspended users may not access ITS Research Systems.

  4. Suspended users may be reinstated at the discretion of ITS Research; requests for reinstatement must come from the user's supervisor, line manager or sponsor.

1.3.2 Account Termination

  1. All student accounts will be terminated four years after the course start date unless an extension is requested and approved by their project supervisor.

  2. All data stored in the home and scratch directories of terminated accounts will be deleted.

  3. Project shares owned by a terminated account must be transferred to a suitable replacement data owner.

  4. External collaborator accounts will be terminated twelve months after creation, or on a specified date, whichever is earlier. Notice of impending termination will be sent to the sponsor, who may request another twelve months for the collaborator.

  5. Principal Investigators must notify ITS Research when their PhD student has completed their study at QMUL. Accounts of leaving PhD students will be suspended, then terminated after 90 days.

1.4 Personal Details

  1. ITS Research will hold a record of the details you submit on the account request forms in accordance to the Data Protection Act.

  2. Users may request a copy of the details ITS Research hold about their person, free of charge.

  3. Users must inform us of any changes to their personal details, including (but not limited to): first name, surname, email address, username, department or institution.

2 HPC Systems

The HPC system is used by a large number of users, although there are some enforced limits to ensure fair usage. ITS Research rely on individual users to practice good cluster etiquette, be aware of the potential impact of their own activities on other users and comply with the requirements in Legal Notices.

2.1 HPC Jobs

  1. All jobs must be run via the queuing system. It is permissible to log directly into the compute nodes only to check on the state of a job but actual compute work must not be started in this way.

  2. Intensive tasks must not be run on the head/login nodes; these should be reserved for editing code and job scripts, submitting jobs and managing the queuing system.

  3. Compilation should be done in a qlogin session to reduce load on head/login nodes.

  4. Any analysis work must be carried out on your desktop machine or one of the nodes via either a qlogin, qsub or OnDemand session, if more resources are required.

  5. Arrays should be used where appropriate when submitting a large number of jobs. Array jobs with high network or storage usage must use an appropriate Task Concurrency setting to ensure there is no performance impact on the cluster. For information on how to use arrays see the Array Jobs page.

  6. Job submissions must only request required resources, waste of cluster resources by poorly scheduled jobs will result in your jobs being held or deleted.

  7. Job submissions must only use their allocated resources, using additional resources not allocated by the scheduler will result in the job being automatically or manually deleted.

  8. Use of the cluster is granted for work and research purposes only and resources must not be consumed for personal use.

  9. Jobs or processes that are having an adverse effect on the cluster may be deleted / killed / held as required by ITS Research with no prior notification. All efforts will be made to inform users once initial issues have been resolved so amendments can be made.

  10. Licensed software is only available to QMUL staff and students but may be available to non-QMUL staff and students depending on license restrictions.

  11. Cryptocurrency mining and blockchain research must not be run on the cluster, except by prior arrangement and with approval by ITS Research.

2.2 Access to restricted nodes

  1. Access to restricted nodes will only be granted with permission from the node owner.

  2. Access to GPU nodes will only be granted after an examination of the code and job script. This is to ensure correct usage of the nodes and to avoid wasted resources or conflicted jobs. Misuse of the GPU nodes may result in access being revoked.

2.3 Storage

  1. All files / data stored must comply with the Legal Requirements.

  2. Sensitive and/or identifiable data must not be stored or processed on the HPC cluster. All data must be anonymised before uploading to the cluster for analysis.

  3. Access to Group / Project / Lab shares will only be granted with permission from the share owner.

  4. The "scratch" filesystem is not backed up and data may be deleted from it at any time without prior warning. Files stored in scratch will be automatically deleted 65 days after the last modification time.

  5. Temporary files stored in the "scratch" filesystem should be deleted as soon as possible (for example at the end of a HPC job).

  6. Frequent or regular use of the touch command to circumvent the 65 day automatic deletion policy in the "scratch" filesystem will be considered as misuse and may lead to account suspension or termination. Users must contact ITS Research if files stored in "scratch" need to remain longer than this period.

  7. The free 1TB storage can only be claimed once per Research Group.

2.4 Ephemeral Databases

  1. Databases must only exist for the lifetime of the job, persistent databases will be removed without prior warning.

  2. If space usage increases beyond initial estimates users must contact ITS Research so arrangements can be made to ensure conflict with other usage is avoided.

  3. Ephemeral databases are not backed up. Users should take regular backups of their databases.

3 Citing Apocrita in your research

Published research should reference this facility using:

This research utilised Queen Mary's Apocrita HPC facility, supported by QMUL Research-IT.

Alternatively, the following text may be used:

This research utilised Queen Mary's Apocrita HPC facility, supported by QMUL Research-IT. doi:10.5281/zenodo.438045

Please see the citing page for more detail.

4 GitHub Enterprise

This section applies to the following GitHub Enterprise servers:

4.1 Usage

  1. You must not store large binary files in repositories - large binaries may be removed without warning to ensure service availability.

  2. All files / data stored must comply with the Legal Requirements.

5.1 Access

Access to any data, program or other information on Queen Mary University of London (QMUL) systems must be authorised by QMUL. It is a criminal offence to obtain unauthorised access or make unauthorised modifications to this computer system. QMUL may refer any unauthorised access to appropriate authorities. Unauthorised users may be subject to criminal prosecution and/or civil action and/or QMUL disciplinary proceedings.

5.2 Use

All usage of the HPC systems is also subject to the QMUL IT Regulations.

Users Must NOT process, publish, create, store, download, distribute or transmit material or data that is:

  • Prohibited by UK Law
  • Discriminatory or defamatory
  • Harassing or threatening
  • Derogatory to any individual or group
  • Obscene or pornographic
  • Engaged in any purpose that is illegal or contrary to QMUL policy or business interests
  • Likely to bring QMUL into disrepute

5.3 Monitoring

Queen Mary University of London monitors its IT systems for the purposes of Operational Integrity, Policy Enforcement and Crime Prevention.

6 Maintenance

  1. Access to ITS Research services may be temporarily restricted to ensure stability and security of the service.

  2. ITS Research services may be restarted or temporarily shutdown in extenuating circumstances without prior notice.

  3. Users will be informed of planned service-affecting maintenance works via the relevant mailing list.

  4. In the event of service-affecting failures or emergencies outside of scheduled maintenance windows, ITS Research will inform users as soon as reasonably possible via the relevant mailing list.

  5. Scheduling of jobs to a node may be disabled for the purposes of testing or maintenance; existing jobs on a disabled node will not be affected and will run to completion.

6.1 Upgrades

  1. For the purposes of security, performance and stability, updates may be applied to ITS Research services. These updates may require temporary downtime which will be announced via the relevant mailing list, as a Slack message, as a post on the announcements page or any combination of the above.

  2. Updates affecting service will only be applied during a scheduled maintenance window.

  3. Updates affecting running jobs will only be applied on empty nodes.