Contents

How can I acknowledge HECBioSim in publications?
Why was my application rejected based on a previous project containing unused resource allocation?
Why does the consortium have a list of supported codes?
How long can a project last?
What should go into the 2 page scientific case?
What are my options if my application is rejected?
Can people overseas be listed as a project user?
Can PhD's/PDRA's apply as a PI?
Can purely industrial users apply?
What is the GPU.hr and how many should I ask for?
When are the application deadlines?

 

How can I acknowledge HECBioSim in publications?

You should acknowledge both EPSRC and HECBioSim in any publications arising from your project, you should use the following test for this purpose:

This project made use of time on UK Tier 2 JADE granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (http://hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1)

 

Why was my application rejected based on a previous project containing unused resource allocation?

New project applications from applicants that have had previously successful applications and then subsequently went on to under use their allocation by 50% and upwards at the time the project closed, will be looked at. Project applications that fall into this category will likely be heavily penalised during the panel review.

 

Why does the consortium have a list of supported codes?

We maintain a list of supported codes that fit inline with our userbase and the expertise that we have within our community and the ability of these codes to effectively utilise the hardware of the machine. For supported codes we will perform benchmarking studies to obtain data for the performance behavior of these codes (scaling, job sizes and durations, etc.).The current list of software we support on JADE is:

  • Amber
  • GROMACS

Should you feel that you know of software that should appear on this list then please get in touch and explain why you think it should be on the list. It may arise that the consortium could utilise your knowledge/expertise with such software such that we can broaden our support for software.

 

How long can a project last?

A project can last no longer than 6 months.

 

What should go into the 2 page scientific case?

The scientific case should include the following:

  • A basic scientific background to the study area and project goals.
  • A description of the proposed calculations and any preliminary/related work.
  • A brief assessment of potential impact of the project work.
  • A statement as to why access to JADE is prefered over ARCHER.
  • References.

 

What are my options if my application is rejected?

Unfortunately due to the limited amount of JADE time at each HECBioSim panel and the high volume of applications for HECBioSim time on JADE, it is not always possible to accept every single application. If your application is rejected then your options include but are not limited to:

  • Submit another application to HECBioSim for the next decision panel (it will be subject to the same review process).
  • You can apply for various types of access to ARCHER either via our pages (check the guidance page for deadlines) or directly from the ARCHER website here.

 

Can people overseas be listed as a project user?

No, users can be of any nationality but must be working/studying at a UK institution.

 

Can PhD's/PDRA's apply as a PI?

In short, no. The PI must be a permanent member of academic staff affiliated to a UK institution. Proposals sent by PhD students or post doctoral researchers will be rejected.

 

Can purely industrial users apply?

We are unable to offer time directly to industrial users, nor can we sell access or act as a commercial service provider. We do however welcome applications from collaborative projects between academic and industrial parties, often such projects will be ranked highly due to having an industrial collaborator. These collaborations are highly encouraged, do not require financial contribution from the industrial partner and can be quite broad in scope (methods development, test applications, studentships, code development, to try out ideas, etc).

 

What is the GPU.hr and how many should I ask for?

 The GPU.hr is a unit of compute, where one GPU.hr corresponds to using 1 single GPU for 1 hour of walltime. If you use multiple GPU processing units either on a node or across nodes, each of these GPU's will contribute to the number of GPU.hr units used. To get a flavour of how many GPU.hr to ask for, you can use our benchmarks for the supported codes. or you can either ask us to benchmark other codes, or you can ask for pump-priming access to JADE to get a small amount of time to run your own benchmarks, to do this get in touch with us.

 

When are the application deadlines?

The deadlines for which you can apply for time on JADE can be found here.