HECToRNews 9, June 2010

Welcome to the HECToR newsletter.


For the previous issues please see here.

Training Course Timetable

Please note that to coincide with the HECToR Phase 2b upgrade the courses for Introduction to HECToR, Debugging, Profiling and Optimising and Multicore have all been updated to contain new material for Phase 2b. The current schedule is below:

These training courses run by NAG are provided free of charge to HECToR users and UK academics whose work is covered by the remit of one of the participating research councils (EPSRC, NERC and BBSRC).

For more information on HECToR training, including the most up to date schedule, please see here, or contact hector.training@nag.co.uk

HECToR Phase2b Upgrade

From Monday 14th June 2010 at 1200 hrs a 10-day availability trial will commence for all HECToR users to test the recently upgraded phase 2b hardware. During this period charging is suspended on the phase 2b system until such time that the availability trial has been successfully completed. The charging rate will be confirmed nearer the end of the trial.

A Cray XT6 will be operating alongside a reduction of the phase 2a XT4 system. The XT4 has been reduced to around half its original size, meaning that the maximum XT4 job size will be 8192 tasks. This will continue to be the main system until later in 2010 when the XT6 is fitted with a new network interconnect, code-named Gemini, and the combination of XT6 with Gemini becomes the main system. The XT6 will consist of 1856 24-core nodes, giving 44,544 cores in total, increasing the theoretical peak performance and memory footprint from around 200TF and 45TB in phase 2a to over 370TF and 59TB in phase 2b.

For a guide explaining the key differences in software and architecture which will impact the operation and performance of codes on the XT6 part of the HECToR service please see here.

If you would like to explore how to take advantage of the potential performance increase available in phase 2b, or would like dedicated help and advice on benchmarking, profiling or improving your code, please get in touch with the NAG CSE team by contacting hector-helpdesk@nag.co.uk or the HECToR helpdesk. Help and advice can then be given on how the code might be able to get full benefit from the hardware upgrade.

HECToR Direct Access

A reminder that the closing date for this year's final round for this mode of access is the 21st September. EPSRC are piloting a new access class for the HECToR service called 'Direct Access' (Class 1b) where users can request significant amounts ( i.e. greater than 1,000,000 AUs ) of computing resource only. However, for the September round the resources must be used from the 12th November and be consumed within a period of up to six months from this date. The Direct Access mechanism will provide successful applicants with discretionary access to the HECToR system in order to provide resource to cover activities such as:

  • Bridging access between grant applications,
  • Resource to trial application developments at scale,
  • Provide preliminary results in aid of grant applications via Responsive Mode or to a Call for Proposals;

The proposals are assessed by a Resource Allocation Panel (RAP) who will meet in October. Full details are available online here.


Domain decomposition library

As part of an ongoing dCSE project for the Incompact3d CFD application, a general-purpose 2D domain decomposition library has been implemented. This library is generally suitable for applications using 3D Cartesian data structures. It is particularly suitable for CFD applications that use spatially implicit numerical schemes but it may also be relevant to many other non CFD applications. It is also a framework on which higher level numerical libraries can be built. As an example, a distributed 3D FFT library has been implemented which scales very effeciently to tens of thousands of cores on HECToR. Descriptions of this dCSE project and the library can be found here.

If you think that your application may benefit from this work, please feel free to contact Dr Ning Li of the NAG HECToR CSE team (hector-helpdesk@nag.co.uk). Dr Li is the developer of the decomposition library, he will be able to assess your situation and give advice and discussion on further possiblities.

Cray User Group meeting in Edinburgh

The annual Cray User Group meeting was held 24th-27th May in Edinburgh and was hosted by EPCC. This international meeting was attended by personnel from several Cray sites including Oak Ridge National Laboratory (ORNL), the Arctic Region Supercomputing Center (ARSC), the National Institute for Computational Sciences (NICS), the National Energy Research Scientific Computing Center (NERSC) and the Swiss National Supercomputing Centre (CSCS).

Talks were given by several members of the HECToR partner sites. From the UK academic community of HECToR users a keynote address on materials chemistry simulations in HPC was presented by Professor Richard Catlow of University College London and an invited talk on Gait Reconstruction for Virtual Paleontology in HPC was presented by Dr Bill Sellers of Manchester University.

Distributed Support

This is also referred to as dCSE support and funding is available to provide extended help with improving the performance of existing HECToR codes and developing high-performance algorithmic improvements for them. Support is also available to port new codes from other systems to HECToR. Awards to support proposed projects are assessed via regular independent panel reviews.

There are twenty current projects that are underway and four new projects are scheduled to begin during 2010. The reports from the completed dCSE projects are available here along with examples of dCSE success stories arising from application codes whose performance has been dramatically improved through dCSE support. There will be several newly completed reports available over the coming months and you are recommended to refer to them if you are seeking to improve the performance of your code.

Further information on the dCSE support service can be found here. The next application deadline is the 21st June 2010. Applicants are advised to contact hector-helpdesk@nag.co.uk with a brief description of their proposed work before the application deadline. All applicants for the current round will be informed of the outcome of their proposals late July 2010. NAG staff are available to visit institutions to talk about this service. If you are interested in a visit please contact hector-helpdesk@nag.co.uk