N8 HPC Site Updates November 2015
Engagement with Business Development Managers / Industry
Durham
Nothing to report.
Lancaster
Nothing to report
Leeds
Early engagement with Transport BDM, following his attendance at the N8 BDM workshop on a prospective project.
Liverpool
There was an interesting signing of a Memorandum of Understanding between Liverpool and Hartree in September. The Virtual Engineering Centre showed off some of their impressive industrial collaborations. They are planning to push out some of their tools to make them more accessible. Liverpool is the first target, but N8 is a good secondary one. Gillian Murray is also on the N8 HPC Oversight / collaboration committee.
Manchester
- Met with Cisco to discuss the $1B investment in the UK.
- Exploring a digital hub working area with Manchester Science Parks.
- Initial contact with Alstom about industrial project with one of our PIs.
Newcastle
Nothing to report.
Sheffield
Nothing to report.
York
None
Training
Durham
Two Newcastle students in the IAPETUS DTP requested access to matlab course in Durham. Not exactly HPC but in the spirit of sharing resources although this raises some issues like local computer and swipe card access.
Lancaster
Nothing to report
Leeds
Worked with David Henty on 2016 ARCHER Training program within N8
- 2 x Software Carpentry workshops (1 x NERC; 1 x Leeds)
- 1 x Data Carpentry workshop (Leeds/ARCHER/SSI/PRACE)
- Introduction to HPC at Leeds
- Introduction to Unix for HPC
- Parallel programming with MPI and MPI/IO
Plus:
HPC workshops for Fluids DTC and Astbury Group
Upcoming:
Introduction to Unix for HPC
Introduction to HPC at Leeds
Installing and managing applications on the HPC service Computer architectures for HPC Introduction to OpenMP parallel programming Parallel programming with MPI and MPI/IO Version control with Git and Github Cloud Computing for Research High Performance Python
In development:
HPC Carpentry (with Sheffield and SSI)
Liverpool
Nothing to report
Manchester
-Intro to HPC
-Intro to Unix Shells and Programming
-Intro to Writing and Running Programmes
-Intro to Python
-Into to Optimisation
-Intro to Parallel Programming
-Extended Intro to CUDA
-Intro to Data Viz and Analysis
-Ran a tailored package of courses for the M4DE ( CDT
Newcastle
Running a guinea-pig experiment to get a motivated, non-linux using HPC newcomer up and running on the cluster, as a means to demonstrating the need for training at Newcastle, and the requirement for resources to deliver that training.
Sheffield
2x Introduction to HPC courses have been run
York
Training courses this term:
- University of York training resources
- Introduction to Research Computing
- Introduction to YARCC
- Introduction to the Linux Shell
- Introduction to Programming
- Programming with Python
- Introduction to NVivo
- Hosting and Archer OpenMP course
Promotion / publicity of N8 HPC
Durham
Reminded users about the facility and the improvements made that should give Durham a better throughput in the coming months.
Lancaster
Nothing to report
Leeds
Embedded into activities.
Liverpool
Gilberto Teobaldi provided Gillian and I some information on joint work with people in Leeds that led to Nature publications and that used the N8 HPC compute facilities
Manchester
N8 HPC part of our new Trusted Partner Platforms, on our new website, in our new Research IT brochure, advertised via new Twitter account, soon to have roadshows, presented at Sheffield Network Event.
Newcastle
Writing a paper for the university’s HPC steering group evaluating the benefits , both realised and potential, of our membership of the N8 HPC consortium.
Sheffield
Promotion through training, engagement with research computing advisory group and through recent multiscale simulation networking event
York
We have produced a research computing brochure. This includes a number of N8-HPC case studies. We will send you a copy when it is back from the printers. We are going to tie its launch with an N8-HPC promotion.
Services / Projects
Durham
Nothing to report.
Lancaster
New project starting up looking to use CASTEP on Polaris. I’ve had better success building this using Intel compiler v16 rather than earlier versions. Can we get Intel 16 and a recent OpenMPI installed on Polaris?
Leeds
Medical bioinformatics facility now in service.
Next tranche of HPC investment underway.
Liverpool
George Barakos moved to Glasgow at the end of August. His people and data have largely transitioned off Polaris. His was one of the larger user groups on Polaris, so there may be a drop in Liverpool utilisation for a couple of months. That fits nicely with boosting priority for York and Durham.
Mats Persson has started a new project and there have been a couple of new users on the system from the Surface Science area.
Manchester
New users on Herc1 and licensing issues being resolved (Stata/MP)
Newcastle
Co-writing the business case for an institutional HPC.
Sheffield
Nothing to report.
York
Nothing to report.
Issues Identified by Users
Lancaster
One user reports intermittent failure of large MPI jobs. One failure was identified as caused by an IB hw/swfault, I think the latest failure is still being investigated?
Liverpool
I’ve been seeing a roughly 33% performance improvement using Intel MPI with their collectives over OpenMPI (trying to use tuned collectives) on 32 cores with VASP. (e.g. OpenMPI – alltoall – 16.4% of 3572s = 585.8s vs. Intel MPI – alltoall – 11.8% of 3356s = 396s). That is a big difference. Anyone seen similar?
New Intel-16 MKL / MPI binaries are a pain to compile correctly. They have changed the way MKL and MPI interact dynamically.
For future systems: Based on what we have experienced on the executables (VASP/ONETEP) we have been using recently.
Keeping at least 2.4 GB/core (as on Archer) would be very much appreciated.
No big advantage in using GPU and/or XeonPhi architectures. Things may/should get better with the new releases of these two technologies (especially XeonPhi). Some large memory SMP node may be handy for quantum-chemical applications.
Sheffield
The new stochastic modelling project sponsored by the department of maths raised an interesting issue. ( N8HPC_SHE_JO_CALSTOCHMO). There was a delay in processing the application highlighting process issues here, which should be resolved. Also of interest is the fact that none of the project membersare from the University of Sheffield! To facilitate this access we have had to register external HPC users from sheffield.