Computing Services

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24th October 2014: Seminar on a performance portable finite element framework

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📥  High Performance Computing (HPC), Research

Dear HPC users,

I would like to advertise a talk in the Math's Departments Numerical Analysis seminar tomorrow (Fri, 24th Oct): David Ham (Imperial College) will speak about

"Firedrake: automating the finite element method by composing abstractions"

An abstract can be found below. I think the topic is of wider interest for anyone working in HPC and thinking about writing good performance-portable code (a problem which will only get more challenging in the future), so please come along if you want.

As usual the seminar takes place at 12:15h in the Wolfson Lecture Theatre (4West 1.7) and we go for lunch with the speaker in the Claverton Rooms afterwards.

See you tomorrow,

Eike

*** Abstract ***

The creation of simulation software confronts an explosion of complexity: demands to simulate more complex systems require more complex numerics, and the effective use of ever-more complex hardware. Facing this challenge means effectively combining skills from across numerical analysis, computer science, and the scientific fields to which the simulation is to be applied. However the complexity of these fields means that it is not feasible for individual scientists to simultaneously be masters of them all. Progress requires that systems are developed which create sufficiently robust separations of concerns that experts in each field can make advances in their own research agendas while working on code which can be immediately employed by those in the other fields.

A solution to this problem is to employ mathematical abstractions not just in the derivation of numerical schemes, but also in their implementation. In this talk I will present Firedrake, a toolchain for the solution of partial differential equations by the finite element method. It's user interface is based on the Unified Form Language, a domain specific language for PDEs in weak form. These PDEs are translated into another abstract language, PyOP2, whose primitives are parallel operations over the computational mesh. Finally this representation is used to automatically generate high performance parallel implementations of PDE assemblers and calls to the PETSc linear and non-linear solver system. Firedrake effectively enables mathematicians and computer scientists to collaborate to produce simulations which are both high productivity and fast.

 

PhD studentships in High Performance Computing

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📥  High Performance Computing (HPC), Research

The University's new High Performance Computing (HPC) service (Balena) is being installed and will be available to users in the near future. Some information about the Balena HPC Service is available here: http://www.bath.ac.uk/bucs/services/hpc/facilities

HPC and ServersAssociated with the new facility, we are pleased to announce that two PhD studentships will be created, partly funded by ClusterVision. These studentships will fund a home or EU student for 3.5 years, starting in October 2015. Although the funding is not yet absolutely certain, we want to advertise the studentships fairly soon, so that academics have sufficient time to recruit to them.

Academic staff from across the University who are HPC users or potential HPC users are invited to put forward projects for these studentships. There will be a competitive process, overseen by the HPC management group (chaired by Prof David Bird). Priority will be given to projects that involve the development of new codes and applications rather than using existing codes. The management group would like to support academics who are new to HPC and cross-departmental collaborations if suitable projects come forward. We would welcome projects that involve a supervisor new to HPC teaming up with a more HPC-experienced co-supervisor.

Bids for these studentships should be sent to Emma Perry (E.Perry@bath.ac.uk) by 5pm on Wednesday 5 November.
Bids should include a title, names and departments of supervisors, and a 300 (strict maximum) word case that outlines the project and describes how it fits the above criteria. Dr Steven Chapman (s.a.chapman@bath.ac.uk) will be able to answer technical questions and to help people understand the capabilities of the new facility.

 

Installation of the Balena HPC cluster

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📥  High Performance Computing (HPC)

The last few weeks have been quite hectic with build of our new HPC system from ClusterVision.  We've had 14 pallets of computer equipment arrive and all of this needs to be assembled and racked ready so that ClusterVision can begin to configure the cluster.

Prior to any equipment arriving on site the Data Centre, where Balena would be housed, needed additional power and the cooling capacity need to be increased so that it could cope with the additional load.  The additional chillers and coolers needed to be craned into place.

The new rack cabinets were positioned and plumbed into the cooling system.

On Monday 15th September, our Data Centre and Operations Team took delivery of 8 pallets of Dell compute nodes and chassis. Then on Tuesday another 4 pallets arrived with the remainder of the equipment: management nodes, storage units, switches, an assortment of cables and even more compute nodes.  The team from ClusterVision began work in unboxing all the equipment ready to start racking the systems.

Below are some photos of the Intel Xeon Phi 5110p cards and the NVIDIA TESLA K20x cards.

Racking of all of the equipment was the quick part, the time consuming tasks were installing the Infiniband PCI cards in all of the nodes and the cabling, lots of cabling, which ClusterVision have kept nice and neat.  The black cables running in between the racks connect up the core Infiniband switches.   From the front the racks the cluster started to take shape, and we can see the Dell C8220 nodes with the blue ethernet and black infiniband cables linking these nodes to the rest of the cluster.

In the second week ClusterVision started to connect the power supplies to all the Dell C8000 chassis, ready for the nodes to be powered on for the first time.  We only experienced a few issues with the nodes once they had power, but ClusterVision were at hand to quickly resolve these issues.  At the end of this week ClusterVision had completed the physical build of the Balena HPC and had begun the configuring the networks, management tools and storage arrays.

 

We're now at the end of the third week, the majority of the cluster configuration is complete, burn-in tests have completed on the nodes. ClusterVision have just started run some Linpack (HPL) benchmark jobs, these will put a heavy load on Balena to help test the overall stability of the cluster. There is plently more work to be done before Balena is ready for general use; more updates will appear here.

To find out more about what the Balena HPC cluster will consist of visit: http://www.bath.ac.uk/bucs/services/hpc/facilities.

 

HPC undergrad to postgrad at the University

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📥  High Performance Computing (HPC), Research

HPC undergrad to postgrad at the University, September 2014

The power of parallel computing was illustrated by William Saunders, MSc student of Modern Applications of Mathematics at this year's High Performance Computing (HPC) symposium 2014. He received an iPod Nano for his presentation, A multi-GPU solver for the non-linear shallow water equations.

William Saunders receives prize at HPC symposium 2014

William Saunders receives prize at HPC symposium 2014

William's career with HPC began during his undergraduate studies when he took, Scientific Computing (MA40177). The module covers a high level computer language (FORTRAN) and asks students to get their head around the concept of parallel computing.

Academia or industry - the choice is yours

Industry and academia are both keen to employ the skills of graduates that have an understanding of HPC. Computational research increasingly benefits from the power that is only possible using parallelism. Graduates who can show they have the skills will be in demand.

William illustrates the progression of learning from undergraduate to postgraduate. He taught himself C and C++ and began using the University's previous HPC facility, Aquila. Having access to a local service allows graduates to build their knowledge and confidence in a supported environment before applying to national facilities. William made this step up during his MSc and completed his research using the national facility, Emerald.

William's next problem is one of choice - where next after his MSc? Great skills tend to come with lots of choices. We wish him lots of luck.

 

Using HPC to help find conditions for making sustainable materials

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📥  High Performance Computing (HPC), Research

Adam Jackson won best talk at this year's High Performance Computing (HPC) symposium with his presentation: Earth-abundant photovoltaics "from the beginning". Adam brought three areas together in his talk: computational chemistry, HPC and a ready recognition of the need to make academic research applicable as well as sustainable in the world.Adam Jackson receives prize at HPC symposium 2014

Adam's research focuses on earth-abundant and non-toxic elements: Copper, Zinc, Tin and Sulphur. The desire is to identify sources of terawatt scale renewable energy which does not rely on more expensive, rare elements and complex, extreme processing conditions.

Abundant...maybe. Easy...not yet.

Cu 2ZnSnS 4 (CZTS) is a promising candidate for using in thin film solar cells, however the downside is it is extremely hard to make. Finding the perfect spot that will result in CZTS, where the conditions (mainly temperature and pressure) are right, requires a lot of trial and error. It would be extremely time consuming to run all these trials in a lab. Instead, Adam uses computational chemistry and the power of HPC for his atomic-scale analysis to build a theoretical model to find the right conditions for CZTS (see Jackson, A.J. and Walsh, A., 2014. Ab initio thermodynamic model of Cu2ZnSnS4. Journal of Materials Chemistry A, 2 (21), pp. 7829-7836.)

HPC supports scientific research at the University of Bath

Adam's early research and familiarisation to HPC took place on the local Aquila HPC cluster here at the University of Bath and he is now using the ARCHER UK National Supercomputing Service. The University of Bath has invested £1.15 million in a new University of Bath facility which will be available to researchers in academic year 2014/2015. The new facility is called Balena and will offer a standard core count over 2,048 cores.

More information on sustainable chemistry and HPC at the University of Bath

 

ANSYS engineering software event, Friday 25 July 2014

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📥  High Performance Computing (HPC)

Beginners and experts are welcome to the ANSYS engineering software event taking place at the University of Bath, Friday 25 July 2014.  The event includes presentations from ANSYS experts and a hands-on tutorial workshop.

  • Audience:  Staff and postgraduates at the University of Bath who use ANSYS for their research and teaching (all levels of knowledge welcome)
  • Time: Friday 25 July 2014, 10am to 2.30pm - you can print out a pdf of the ANSYS event timetable
  • Locations: the talks will be held in 4 East 2.16 and the workshop will be held in 4 East 2.32a

 

For more details visit: http://www.bath.ac.uk/bucs/news/news_0003.html

 

 

What connects supercomputers and clever mammals

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📥  High Performance Computing (HPC), Research

Thank you to Professor Martyn Guest from Cardiff University, for his insightful keynote presentation, Application Performance in Materials Science, Chemistry and Nanoscience - Perspective, Performance and Challenges at the University of Bath's third High Performance Computing (HPC) symposium, 5 June 2014.

Balena - it's big and it's clever

HPC facility will be called Balena

Following the news that the University recently awarded funding in excess of £1 million for a resource to replace the aging Aquila system, Prof Kevin Edge, Deputy Vice-Chancellor, revealed that the name of the new successor system will be Balena.

Congratulations to Federico Brivio from the Department of Chemistry who suggested the name in keeping with the tradition of using Italian animal names. Balena translates to "whale".  The HPC facility will share several characteristics with the mammal: both are large, intelligent and never fully sleep.

Congratulations

The symposium brought academics from various disciplines at the University of Bath and from partner GW4 universities together to share knowledge and give presentations.

  • Congratulations to Adam Jackson from the Department of Chemistry for winning best talk, Earth-abundant photovoltaics "from the beginning".
  • Congratulations to Will Saunders from the Department of Mathematical Sciences for his winning presentation, A multi-GPU solver for the non-linear shallow water equations.

Feedback and keeping in touch

Find out campus HPC news and explore the High Performance Computing @ Bath blog .

Follow the University of Bath Computing Services (BUCS) on twitter at BUCSNews and get our latest news straight to your computer or mobile phone.

 

1st Balena HPC User Group Meeting

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📥  High Performance Computing (HPC)

On  Tuesday 10th June 15:00-16:30 in 3W 4.7 we will be holding the 1st Balena HPC User Group Meeting.

At this meeting we will be revealing more details about the Balena HPC system, what it will consist of and when it is expected to be fully operational.

This is also a good time to raise any other HPC matters which concern you. If you would like anything added to the agenda that you would like brought up at this meeting please email (hpc-support@bath.ac.uk).

Thanks - HPC Team

 

Aquila's successor will be Balena

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📥  High Performance Computing (HPC)

Yesterday at the University of Bath's 3rd Symposium on HPC, Prof Kevin Edge, Deputy Vice-Chancellor, revealed the name of the successor to the current Aquila HPC system. The new system will be named Balena.

The name was suggested by Federico Brivio from the Department of Chemistry. In order to continue the tradition of Italian-animal naming, Federico has suggested Balena. Balena means Whale: a big, clever mammal that never sleeps completely and represents a big, clever computer. There is an additional joke, since "balena" also means hurtle and flash, which is is a good description for the new supercomputer.

Well done Federico! We're all looking forward to when we can start using the Balena HPC in the near future.

 

Prof Kevin Edge presenting prize to Federico Brivio for suggesting the name Balena as Aquila successor

Prof Kevin Edge presenting prize to Federico Brivio, Dept Chemistry, for suggesting the name Balena as Aquila successor