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IT Services

Frequently Asked Questions

If you have any questions regarding High Performance Computing or how to access ITS Research services at QMUL, please see the Frequently Asked Questions below.

If you are unable to find the answer you are looking for, please email: its-research-consultants@qmul.ac.uk.

We welcome any suggestions you may have.

Apocrita

What is Apocrita?

Apocrita is a 290+ node heterogeneous HPC Cluster running Centos 7 Linux managed by ITS Research at Queen Mary University of London, located in the Jisc Shared data centre in Slough.

The Apocrita system has been specifically designed to meet the needs of a wide variety of research in the areas of our three faculties: Humanities and Social Sciences, Science and Engineering, and Medicine and Dentistry.

For more information, please see the Apocrita docs site: docs.hpc.qmul.ac.uk

What is High Performance Computing?

Using an HPC cluster can substantially reduce the time taken to compute problems by running analyses in parallel or breaking them up into pieces. Both strategies allow for the problem to be worked on by many separate compute cores (CPUs) at the same time.

For more information, please see the Apocrita docs site: docs.hpc.qmul.ac.uk

How do I get an account on Apocrita?

You need to request an account here: docs.hpc.qmul.ac.uk/intro/hpc-account/.

I have forgotten my password/locked myself out, how do I get it reset?

You can raise a ticket with ITS Research Support who will be able to reset it for you.

You can email them here: its-research-support@qmul.ac.uk

Where can I find other support material for Apocrita?

Documentation for Apocrita can be found here: docs.hpc.qmul.ac.uk/using/.

You can also visit our Guided Tutorials and Introduction to Linux pages: learn.hpc.qmul.ac.uk/

Please note: you will need your Apocrita username and password to access the Tutorials.

Is there a HPC Slack channel?

 Yes. If you have an @qmul.ac.uk or @se18.qmul.ac.uk email address, you can create an account.

The HPC Slack Channel can be found here: #hpc

What public datasets can I access on Apocrita?

To prevent duplication of data and to save valuable research time we provide a local copy of some widely used public datasets.

You can see the available datasets here: https://docs.hpc.qmul.ac.uk/storage/datasets/

If you require any datasets that are not currently available, please contact us: its-research-support@qmul.ac.uk

What nodes are available on Aprocrita?

Apocrita runs a variety of different job types, and the cluster is comprised of different node types and queues to accommodate this.

For more information on available node, please see the Apocrita docs site: docs.hpc.qmul.ac.uk/nodes/

Can I purchase my own node for Aprocrita?

First, check to see if we have a suitable node on Apocrita that meets your requirements. Try running various jobs on the node to see how the node performs for your particular analysis.

You can see the available node here: https://docs.hpc.qmul.ac.uk/nodes/

Use of Apocrita is free, but it is a shared service. If a research project is going to make intensive use of the cluster then we request that you add compute capacity as part of your grant application.

We can help you purchase a node for your research, please contact the ITS Research Consultants: its-research-consultants@qmul.ac.uk

Can I access any external HPC clusters?

We have access to several Tier 2 clusters which are among the TOP500 list of the world's most powerful computer systems. If you are running multi-node parallel jobs you may benefit from access to these. Tier 2 HPC facilities include:

  • Thomas - Hub in Materials and Molecular Modelling - Thomas is funded by EP/P020194/1 and is designed for materials and molecular modelling. QMUL receive 4 Million CPU hours for each 3 month accounting period.
  • Athena - HPC Midlands Plus - Athena is funded by EP/P020232/1. QMUL receive 7.4 Million CPU hours for each 6 month accounting period on Athena.
  • JADE - Joint Academic Data science Endeavour - JADE is a GPU cluster designed for machine learning and molecular dynamics applications. The Nvidia DGX-1 nodes run optimised versions of Caffe, Tensorflow, Theano and Torch for machine learning.

QMUL Academics may apply to use a cluster free of charge if they meet certain criteria.

For more information please see the Tier 2 pages: https://docs.hpc.qmul.ac.uk/tier2/

How do I cite Apocrita in my research?

Published research should reference this facility using the following text:

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

Can I request additional applications?

First check to see if we have the software you require, you can see the available applications here: docs.hpc.qmul.ac.uk/apps/.

If it is not available then you can request the software to be installed here: docs.hpc.qmul.ac.uk/apps/requesting/

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GitHub

What is GitHub?

GitHub is a web-based Git repository hosting service, which offers all of the distributed revision control and source code management (SCM) functionality of Git as well as adding its features. Unlike Git, which is strictly a command-line tool, GitHub provides an additional web-based graphical interface and desktop as well as mobile integration. It also provides access control and several collaboration features such as code reviews and integration with test suites.

Queen Mary University of London uses GitHub Enterprise. GitHub Enterprise offers the same functionality as the public GitHub.com offering but all data is hosted within QMUL, authenticating against QMUL servers. This allows for easy collaboration with other researchers while retaining full control over management and security of your data. All QMUL currently enrolled students, student-facing faculty, and anyone performing academic non-profit research can use it free of charge.

How do I request an account?

All QMUL users automatically receive a Github account with a HPC account. The log in details will be the same for both. You can create an account here: docs.hpc.qmul.ac.uk/intro/hpc-account/.

If you are a QMUL user and require a Github only account (not a HPC account), please click docs.hpc.qmul.ac.uk/intro/github-only-account/

I have forgotten my password/locked myself out, how do I get it reset?

You can raise a ticket with ITS Research Support who will be able to reset it for you. We will need your username and email address.

You can email them here: its-research-support@qmul.ac.uk

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Globus

What is Globus?

Globus is used for transferring, sharing, and discovering data via a web browser. It allows collaboration with other researchers, without requiring them to have accounts on QMUL systems. Globus uses widely-adopted industry standards for authentication and authorisation, as well as GridFTP and HTTPS protocols. Globus lets you share data with collaborators at other research institutions, whether your data exists on Apocrita, Tape archive, Scientific instrument or Laptop/PC.

How do I get access to Globus?

Visit app.globus.org and search for Queen Mary Univerity of London > click Continue and follow the log in process.

Is there a Globus Slack channel?

 Yes. If you have an @qmul.ac.uk or @se18.qmul.ac.uk email address, you can create an account.

The Globus Slack Channel can be found here: #globus

Can I get Globus Plus?

Yes. ITS Research can provide you access. Globus Plus users can create shared endpoints on their personal computers and transfer files between Globus Connect Personal endpoints.

To access this please contact the ITS Research Consultants: its-research-consultants@qmul.ac.uk

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Research Storage

What type of storage do you provide?

Apocrita has over a petabyte of IBM Spectrum Scale (formerly called GPFS) storage. This is a high-performance clustered file system which provides concurrent high-speed file access to your data. It is widely used in HPC both commercially and in academia. The storage system is connected to the QMUL Enterprise backup solution (TSM) to provide a high level of data resilience.

ITS Research can provide more information on how to gain access as well as discuss any additional requirements you may have, please contact the ITS Research Consultants: its-research-consultants@qmul.ac.uk

Can I store personal, sensitive or confidential data?

To ensure we meet strict data standards within the School of Medicine and Dentistry we can provide access to a Data Safe Haven (DSH) to allow research using personal, sensitive or confidential data.

ITS Research can provide more information on how to gain access as well as discuss any additional requirements you may have, please contact the ITS Research Consultants: its-research-consultants@qmul.ac.uk

How much storage can I have on Apocrita?

We provide storage for anonymised data up to 1TB free of charge.

If you require storage over 1TB, please contact the ITS Research Consultants:  its-research-consultants@qmul.ac.uk

Should I use Cloud storage?

This will depend on the type of research you are undertaking. Cloud storage providers may charge for:

  • Data storage
  • Network usage
  • Operations usage
  • Retrieval and early deletion

If you are using large volumes of data or conducting HPC analysis costs could add up quickly. You may also face compliance and regulatory issues depending on the Cloud provider.

To better understand your requirements, please contact the ITS Research Consultants: its-research-consultants@qmul.ac.uk

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REDCap

What is REDCap?

REDCap is an Electronic Data Capture (EDC) tool geared to support data capture and eCRF (Electronic Case Report Forms) development for clinical research studies.

REDCap is a mature, secure web application for building and managing online surveys and databases. REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. More information can be found on the Project REDCap website.

Queen Mary University of London is a member of the REDCap consortium.

 For more information, please click here: projectredcap.org/about/.

We are happy to provide a demonstration of REDCap to see if it meets your data capture requirements. Please email: its-research-consultants@qmul.ac.uk 

How do I cite REDCap in my research?

Published research should cite REDCap as follows:

Study data were collected and managed using REDCap electronic data capture tools hosted at Queen Mary University of London 1. REDCap (Research Electronic Data Capture) is a secure, web-based application designed to support data capture for research studies, providing 1) an intuitive interface for validated data entry; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for importing data from external sources.

1. Paul A. Harris, Robert Taylor, Robert Thielke, Jonathon Payne, Nathaniel Gonzalez, Jose G. Conde, Research electronic data capture (REDCap) - A metadata-driven methodology and workflow process for providing translational research informatics support, J Biomed Inform. 2009 Apr;42(2):377-81.

 Is there a REDCap Slack Channel?

 Yes. If you have an @qmul.ac.uk or @se18.qmul.ac.uk email address, you can create an account.

The REDCap Slack Channel can be found here: #redcap

Where can I find support material for REDCap?

Documentation for REDCap can be found here: docs.redcap.qmul.ac.uk

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Pre-Award and Data Management Plans

Do you provide any IT costings for research grants?

We provide an IT costing calculator for grant applications. Please note, due to currency fluctuations these prices are not guaranteed and are likely to change.

To access the calculator, please click here: Grant Costing Calculator

You will need your QMUL ID and password to access the calculator.

Are there any standard DMP templates?

DMPonline helps you to create, review, and share data management plans that meet institutional and funder requirements.

Some funders mandate the use of DMPonline, while others point to it as a useful resource.

Please follow the link for more information: https://dmponline.dcc.ac.uk/

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Miscellaneous

I need a simple website for a research project, how can I get one?

IT Services hosts various web sites on behalf of the University and generally, these are maintained by Marketing and Communications.

In the first instance, please contact the Web Support team for all web development related enquires: websupport@qmul.ac.uk

LAMP Containers are either provided "empty" for you to install or create a PHP web application, or the Drupal or Wordpress content management systems can be preinstalled. Typically they are used to host Wordpress blogs or similar sites, or small bespoke web applications.

For more information on LAMP Containers, please click here.

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