HPC research

Forthcoming computational biomolecular research events

Author: Adam Carter
Posted: 9 Aug 2016 | 17:18

BioExcel is a newly launched Centre of Excellence that helps academic and industrial researchers to use high-performance computing and high-throughput computing in biomolecular research. 

We are running a number of events in September and October and I would be very grateful to anybody who circulates these to people or groups that may be interested (and bonus points if you are willing to share with me details of where/to whom you publicise so that we can reduce cross-posting).

 

Early experiences with KNL

Author: Adrian Jackson
Posted: 29 Jul 2016 | 16:45

Initial experiences on early KNL

Updated 1st August 2016 to add a sentence describing the MPI configurations of the benchmarks run.
Updated 30th August 2016 to add CASTEP performance numbers on Broadwell with some discussion

EPCC was lucky enough to be allowed access to Intel's early KNL (Knights Landing, Intel's new Xeon Phi processor) cluster, through our IPCC project.  KNL Processor Die

KNL is a many-core processor, successor to the KNC, that has up to 72 cores, each of which can run 4 threads, and 16 GB of high bandwidth memory stacked directly on to the chip.

Bringing art and science together

Author: Nick Brown
Posted: 1 Jul 2016 | 10:58

This week I have been at the FEAT (Future Emerging Art and Technology) workshop in Vienna, which aims to promote collaboration between scientists and artists. As I am sure many people will be aware, the EU-funded Future and Emerging Technology (FET) programme consists of scientific projects looking to push the boundaries of research in specific fields.

Collaboration, collaboration, collaboration

Author: Adrian Jackson
Posted: 15 Jun 2016 | 13:35

This week sees our annual collaboration workshop with Tsukuba University, Japan (more details are available here).  This is a great chance to get a flavour of the kind of research another HPC centre is undertaking, how they work, and what platforms they are investing in.

The Centre for Computational Sciences (CCS) at Tsukuba is a department very like EPCC, in that it is responsible for high performance and parallel computing at the university, runs and supports large-scale computers for researchers, and undertakes parallel computing research.

Investigating power use in parallel computing

Author: Mirren White
Posted: 3 Jun 2016 | 16:09

The Adept project has been working hard for over two years to further understanding of how power is used in parallel software and hardware, and we are now on the finishing straight. 

It's a good time to take stock of our achievements and reflect on how to focus our efforts in the final phase. Also to consider life after the project ends: how do we want to exploit the technologies we have developed and the knowledge we have gained? How do we ensure a lasting legacy for Adept?

NEXTGenIO: a step towards Exascale

Author: Mirren White
Posted: 27 May 2016 | 10:15

 

The NEXTGenIO project represents a step along the Exascale pathway.

We are developing a prototype platform that utilises the latest developments in memory technology, and that will offer vastly improved I/O performance compared to current HPC machines. The system will be developed end-to-end by the project partners – from inception through to delivery, with a full suite of systemware that can make use of the new technologies.

Better programming languages for HPC

Author: Stephen Booth
Posted: 5 May 2016 | 16:43

Recently I seem to have had many conversations about programming languages for HPC. In some ways this is not a new subject - I have been having similar conversations for the last 20 years. However as HPC hardware evolves, machines become more complex and the issues that need to be addressed by programmers also become more complex. So it is not surprising that we are wondering if there is more the compiler could be doing to help us.

HPC hardware in 2016 and beyond

Author: Adrian Jackson
Posted: 19 Apr 2016 | 23:14

Anyone taking more than a passing interest in HPC hardware recently will have noticed that there are a number of reasonably significant trends coming to fruition in 2016. Of particular interest to me are on-package memory, integrated functionality, and new processor competitors.  Intel Xeon Phi (KNL) Die

On-package memory, memory that is directly attached to the processor, has been promised for a number of years now. The first product of this type I can remember was Micron's Hybrid Memory Cube around 2010/2011, but it's taken a few years for the hardware to become mature enough (or technically feasible and cheap enough) to make it to mass market chips. We now have it in the form of MCDRAM for Intel's upcoming Xeon Phi processor (Knights Landing), and as HBM2 on Nvidia's recently announced P100 GPU.

Array index order matters, right?

Author: Adrian Jackson
Posted: 30 Mar 2016 | 17:46

Does array index order affect performance?

A couple of weeks ago I was teaching an ARCHER Modern Fortran course, and one of the things we discuss during the course is index ordering for multi-dimension arrays.  This course is an introduction to modern Fortran (primarily F90/F95), so we don't go into lots of details about parallel or performance programming, but as attendees are likely to be using Fortran for computational simulation it is important they understand which array dimensions are contiguous in memory so that they don't accidentally write code that is much slower than it should be.

GNU compiler performance

Figure 1: Performance using the GNU compiler

During one of the practical sessions on the course, one of the students wrote a little program to investigate the performance impact of iterating through array elements in a non-contiguous order.  They also included some code to investigate if there is a performance impact when using allocatable array rather than static arrays (I'd mentioned it shouldn't impact performance but I obviously wasn't convincing enough...).

HPC Community Survey

Author: Guest blogger
Posted: 30 Mar 2016 | 17:23

This blog article comes from one of our current Phd students: Athina Frantzana, who is researching the obstacles facing women in the HPC community, and how equality can be improved.

The under-representation of women in STEM workforces has been a widely discussed subject in recent years. However, the recording and analysis of data regarding the gender balance of HPC remains rare.

Our study is a preliminary analysis of workforce and research participation in HPC, and aims to quantify the current level of representation of women in HPC and to provide a baseline for evaluating possible reasons and suggesting ways for future changes to the demographics.

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