ct-grid June 2010

ct-grid@nikhef.nl

5 participants
5 discussions

[Ct-grid] In graphics: Supercomputing superpowers
by Driel, Ronald van 28 Jun '10

28 Jun '10

Dear All, Some nice presentation by the BBC of the Top500 list. It's not news that Linux powers most of the world's fastest supercomputers, but have you ever actually seen the list? I was not aware that there was an organization set up to track all those supercomputers and publish the details, but today I found Top500 Supercomputer sites<http://www.top500.org/> and its latest Top500 list for June 2010<http://top500.org/list/2010/06/100>. BBC News has a very cool graphical representation of the list<http://news.bbc.co.uk/2/hi/technology/10187248.stm>. http://news.bbc.co.uk/2/hi/technology/10187248.stm Regards, --- Ronald van Driel Senior Technologist Philips Research MiPlaza - e-Science Support High Tech Campus 37 -- Room 5.003 5656 AE Eindhoven, The Netherlands Phone: +31-40-27-97958 (Office), +31-6-23447726 (Mobile) Email: Ronald.van.Driel(a)philips.com<mailto:Ronald.van.Driel@philips.com> "In theory, practice is the same as theory. In practice, it isn't." ________________________________ The information contained in this message may be confidential and legally protected under applicable law. The message is intended solely for the addressee(s). If you are not the intended recipient, you are hereby notified that any use, forwarding, dissemination, or reproduction of this message is strictly prohibited and may be unlawful. If you are not the intended recipient, please contact the sender by return e-mail and destroy all copies of the original message.

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[Ct-grid] Demonstrators
by Jeff Templon 23 Jun '10

23 Jun '10

Hi *, I promised some links. The Jamboree Workshop : http://indico.cern.ch/conferenceDisplay.py?ovw=True&confId=92416 take a good look around, there is a lot of information there, for example under "Contributed docs". To see the talks, you have to switch to "detailed view" in the timetable, kind of annoying, sorry. Five year operational review, nice summary: http://www.usenix.org/events/nsdi10/tech/full_papers/freedman.pdf JT

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[Ct-grid] Next BiG Grid Meeting: Monday 7 June at 13.30h in room H3.31
by Dennis van Dok 21 Jun '10

21 Jun '10

The Next BiG Grid meeting will be held on Monday 7 June from 13.30-14.30h in room H3.31. Agenda: - Operations summary - Middleware - Applications - AOB - Presentation By Jan Bot: *Logic Networks on the Grid: handling 15 million jobs* (abstract below) This meeting may be joined by teleconferencing[1] in the Big Grid room. The appointed volunteer to take minutes is Ronald. See also the minutes of the previous meetings[2] and the schedule for taking minutes[3] for upcoming meetings. 1. http://www.nikhef.nl/pub/projects/grid/gridwiki/index.php/SurfVideoConf 2. http://www.nikhef.nl/pub/departments/ct/grid/2010/ 3. http://www.nikhef.nl/pub/departments/ct/grid/2010/minutes.html Enjoy the weekend, Dennis van Dok *Logic Networks on the Grid: handling 15 million jobs* Jan Bot, Jeroen de Ridder, Marcel Reinders In the Delft Bioinformatics Lab, logic networks, i.e. combinations of a few Boolean logic gates, are being employed to model gene regulation in cancer. To this end, a dataset containing cancerous mutations in combination with gene activity measurements is used. A good model is defined as the combination of mutations that best predict the gene activity. To find these models, a smart optimization strategy is employed that evaluates a large collection of candidate network topologies as well as a large number of input combinations. To evaluate the significance of these networks it is vital to determine the likelihood that these models will be found by chance. To this end the same optimization strategy has to be applied to a permuted version of the dataset. This results in a large amount (15 million) of small jobs which each generate a small amount of output data. Due to the large variance in running time (anywhere between two seconds and several hours) and the associated risk of violating the maximum wall-clock timer, collecting all outputs simultaneously may not be efficient or result in data loss of successful jobs. Moreover, the grid middleware cannot cope with this amount of small files. Therefore, we have implemented a solution based on ToPoS (for the inputs) and an XML-RPC server with a database back-end to store the outputs. In a real-life application this solution has proven to be able to handle all life science grid nodes running at once and also cope with the 600 additional nodes provided by our desktop cluster. Since it is expected that many more bioinformatics applications will suffer from this or similar problems, our solutions should prove useful in many more permutation or cross-validation procedures carried out on the Grid.

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[Ct-grid] Next BiG Grid Meeting: Monday 21 June at 13.30h in room H3.31
by Dennis van Dok 18 Jun '10

18 Jun '10

The Next BiG Grid meeting will be held on Monday 21 June from 13.30-14.30h in room H3.31. Agenda: - Operations summary - Middleware - Applications - AOB This meeting may be joined by teleconferencing[1] in the Big Grid room. The appointed volunteer to take minutes is Ronald. See also the minutes of the previous meetings[2] and the schedule for taking minutes[3] for upcoming meetings. 1. http://www.nikhef.nl/pub/projects/grid/gridwiki/index.php/SurfVideoConf 2. http://www.nikhef.nl/pub/departments/ct/grid/2010/ 3. http://www.nikhef.nl/pub/departments/ct/grid/2010/minutes.html Enjoy the weekend, Dennis van Dok

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[Ct-grid] EGI SSO username
by Ron Trompert 18 Jun '10

18 Jun '10

Hallo, Voor het EGI papierwerk wil ik aan de onderstaande lieden vragen, hun EGI SSO username aan mij te mailen. Als jullie geen EGI SSO account hebben, kun je hem aanmaken op: https://www.egi.eu/sso/email Ronald Starink Jeff Templon David Groep Tristan Suerink Paco Bernabe Sven Gabriel Dennis van Dok Jan Just Keijser Oscar Koeroo Arjen van Rijn Paul Kuipers Maurice Bouwhuis Tom Visser Coen Schrijvers Evert Lammerts Mvg., Ron

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ct-grid June 2010