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Posts Tagged ‘CSCS’

Interview with Robert Techentin, Mayo Foundation on the usage of Cray XMT for Clinical Research

Wednesday, November 30th, 2011

Robert (Bob) Techentin is Principal Software Engineer in the Special Purpose Processor Development Group at Mayo Foundation (Rochester, Minnesota). Robert is one of the first users of the new Cray XMT supercomputer specially designed to analyze large amounts of data.

The Mayo Clinic is a large clinical practice for medicine and is specialized on medical research and medical education. The new Cray XMT is being used to tackle different kinds of biomedical and bioinformatic problems that have been very challenging using traditional computer architectures.

In one research project Bob is going to work with the electronic medical records on a million of patients with millions of events. The researchers assume that there are secrets buried in the information that is very challenging to extract using traditional data mining techniques. One example is the discovery that weight loss drug Fen-phen can lead to heart valve damage. The relationship has accidentally been discovered by a Mayo clinic data analyst. A supercomputer could have helped researcher find earlier such a relationship.

There are other interesting and very valuable insights in the medical data that can not be mined out using a traditional relational data base management system. The Cray XMT is very good at graph analytics and can be used to find patterns that are very difficult to discover otherwise. The algorithms and the necessary data structures are being developed together with Cray and the Pacific Northwest National Laboratory. The first results of this common effort are expected in about one year from now.

At Mayo the Cray XMT is also being used to look at different ways to assemble the genomic sequences from the sequence data and to analyze the differences between individuals and the species references. Another possible application is free form text analysis. The clinic has a lot of free form text that is recorded as part of medical records that can be analyzed using the XMT to draw new conclusions.

CSCS is also deploying one of the first Cray XMT worldwide that is made available to research from different scientific fields.

hpc-ch Forum on GPU – Video on Cray XK6 Overview

Wednesday, November 23rd, 2011

Nicola Bianchi (CSCS) presents the last supercomputer arrival at CSCS: The Cray XK6 supercomputer which is a trifecta of scalar, network and many-core innovation. It combines Cray´s proven Gemini interconnect, AMD’s leading multi-core scalar processors and NVIDIA´s powerful many-core GPU processors to create a true, productive hybrid supercomputer.

Download the slides of the presentation (PDF) »

hpc-ch Forum on GPU – Video on Scheduling GRES resources With SLURM

Wednesday, November 23rd, 2011

Stephen Trofinoff (CSCS) presents how to schedule GRES resources with SLURM.

Download the slides of the presentation (PDF) »

hpc-ch Forum on GPU – Video on Installation and Operational Needs of Multi-purpose GPU Clusters

Tuesday, November 22nd, 2011

CSCS has experience of operating multi-purpose GPU clusters for a diverse project and service portfolio.

Vincenzo Annaloro (CSCS) presents details on system installation and operation for two clusters: a production and experimental testbed that serves as HP2C prototype system and a multi-purpose visualization and GPU development cluster.

Download the slides of the presentation (PDF) »

Lake Water to Cool Supercomputers at CSCS

Tuesday, November 15th, 2011

High-performance computing centres use a great deal of electricity. In order to run its new computer centre in Lugano-Cornaredo as energy-efficiently and cost-effectively as possible, CSCS is using the natural resource of Lake Lugano to cool its supercomputers and the new building.

A high-performance computing centre like the CSCS (Swiss National Supercomputing Centre) uses as much electricity every day as a small town. About a third of this electricity is used for cooling. If supercomputers are not constantly cooled, they overheat and, in the worst case scenario, may be damaged.

Three pumps move up to 760 litres of water per second
In conventional computing centres, compressors generate cold water to cool the computers. To save energy, CSCS will make use of a natural cooling resource: water extracted from Lake Lugano at 45 meters depth at a temperature of 6 degrees Celsius. This will greatly reduce the amount of electricity used by CSCS for cooling.

To operate the cooling system, a pumping station has been built on the lake shore in Parco Ciani, in the centre of Lugano. This is connected by a pipe to the 13 tonne, six metre high suction baskets which have been immersed at a depth of over forty metres. Through this pipe, three pumps in the pumping station will pump up to 760 litres of water per second. 460 litres will go to CSCS for cooling purposes, while up to 300 litres will be available to AIL for its water reservoir, which has yet to be built. On its way to CSCS, the water will climb 30 metres and cover a distance of 2.8 kilometres.

n the labyrinth of the pumping station: five metres beneath the lawns of Parco Ciani, over 700 litres of water per second are pumped out of Lake Lugano. (Picture: CSCS)

High-tech underground control centre
A steel ladder leads down to the high-tech underground control centre of the pumping station. The electrical infrastructure has been installed on steel mesh platforms about 2.5 metres above the ground, underneath this – covering a surface area of about 200 square metres –are the three pumps, a further backup pump, and two shock absorbing containers which will protect the pipeline from damage in the event of a sudden pressure surge.

On two sides of the pumping station, two massive pipes pierce the metre-thick walls. The pipeline connecting CSCS to the pumping station is 80 centimetres in diameter. On its way to CSCS, the water´s temperature will increase by up to 0.5°C. At the arrival point at CSCS, the lake water circuit and the internal cooling water circuit meet in man-sized heat exchangers. The internal water cooling circuit delivers the water, which has now reached 8 -9°C, to the supercomputers for cooling.

The suction strainers for the lake water pipe, just before they were lowered 45 metres into Lake Lugano. (Picture: CSCS)

One pumping operation for double the cooling effect
Once the water has passed through this first cooling circuit, it has been heated up by eight degrees. The now 16 to 17 °C is sent through a further heat exchanger, connected to a second cooling circuit. This mid-temperature circuit cools the air in the housings for the computers and hard drives of lesser energy density, that can therefore be cooled with water that is less cold. This means that with one pumping operation, two cooling is supplied to two circuits to cool two types of system.

The cold water pipe is designed to cool supercomputers of up to 14 megawatts on the first cooling circuit. The second circuit can cool  a further seven megawatts of computers. The more the second circuit is used, the higher the waste heat absorbed by the water and so the more useful it is to the local industrial works who will be able to use it.

Before the lake water returns to the lake, it passes through a stilling basin which can hold 120 cubic metres. The basin collects the water and makes sure that it flows freely down the return pipe back to the lake at a constant pressure and with no need for further power to be used. On the contrary, the plan is to use the energy generated as it falls to produce electricity. That is why connections for a microturbine have been provided in the pumping station.

So as not to affect the ecological balance of the lake, the water going back into the lake must never exceed 25 degrees Celsius. To ensure that this is always the case, a back-mixing funnel has been fitted which will add cold water if necessary.

(Article by Simone Ulmer, CSCS)

Additional reading: CSCS Media Release »