published on Friday, January 31, 2003

Newsletter

A look back at SARA’s 19th supercomputer user meeting 2002
On 12 December 2002 SARA organized the 19th annual supercomputer user meeting. About eighty people visited the meeting: users, representatives of vendors, SARA personnel and other interested people. After a word of welcome by SARA director Dr. ir. Anwar Osseyran, regular program items were presented, such as the vision of the future of National Computer Facilities Foundation (NCF) by its director Dr. Patrick Aerts, and of SARA by Dr. Axel Berg, head of the HPC department.

Dr. Ron Trompert (SARA) talked about the practical use of the grid by scientists. Key note speaker Prof. Ed Seidel (MPI, Berlin) spoke in an animated manner about simulations of colliding black holes, that require a lot of computing resources. Using the grid one can employ the joint power of palmtops to supercomputers worldwide for those simulations and for the detection of very weak gravitational waves.

In two “back-to-back” lectures users and parallelization experts jointly presented parallelization, which were executed using NCF Grants. Dr. Albert Ballast (MARIN) and Dr. Willem Vermin (SARA) talked about parallelization of a program for the simulation of free surface waves. Prof. Dr. Henk van der Vorst and Dr. Fons van Hees (both from Utrecht) discussed the parallelization of the Jacobi-Davidson method.

Prof. Dr. Gert Vriend (Nijmegen) talked about the rapid growth in bio-informatics in recent years. This led to the start of BioASP, a foundation that – among other things – offers scientists access to genome databases using the web. Drs. Tim Hulsen (CMBI/Organon) presented a recent project on TERAS – the national supercomputer –, in which the amino acid sequences of 700,000 proteins were compared to divide them into (sub)families. In this way one aims to find a connection between genes and the functionality of proteins.

In the last part of the program Drs. Kirsten ten Tusscher (Utrecht) discussed how she uses TERAS for the simulation of electric currents that make our hearts work, and to examine what happens in the case of disturbances in those currents. After this Anders Tranberg (Amsterdam) told the audience how he uses the Beowulf cluster at SARA to explain why the amounts of matter and anti-matter in the universe differ. Finally, Dr. Jan Harm Koolstra (ACTA, Amsterdam) talked about using TERAS to model the human jaw joint.

SC2002
From 16 up to 22 November 2002, SARA took part in the SC2002 conference in Baltimore (USA) a global annual event in Supercomputing and Communication. For this event the National Computer Facilities Foundation (NCF) has initiated the idea of DISCO (Dutch Information technology, Supercomputing and Communications Overview). In a stand of 10 by 10 meters a number of Dutch institutes, including SARA Computing and Networking Services, presented themselves.

The contribution of SARA naturally attracted attention. On a huge screen, using passive stereo projection, SARA demonstrated the so-called Augmented Virtuality Technology. Together with colleagues from Chicago and Ottawa, SARA won a prize – the Supercomputing '02 High Performance Bandwidth Challenge Award.

In collaboration with SURFnet, SARA has been investigating the possibilities of doing teleconferencing in a VR environment. This collaboration has resulted in a system that is capable of putting live video feeds into an immersive virtual world. This involved live video streams from a local SC2002 location, as well as live video from Amsterdam over the Internet.

e-BOAT conference in Almere
On November 28, the Bestuurscommissie Openbaar Onderwijs (BCOO) and the Municipality of Almere organized the conference "The student in the knowledge society” in the Alnovum in Almere-Stad. The central issue of the conference was: “what will be the significance of Information and Communication Technology (ICT) in the daily practice of primary education”.
During the conference, SARA consultant drs. Harold van Aalderen demonstrated the technical infrastructure that is used in the e-BOAT project.

5th anniversary of ISOC.nl
On November 26, 2002 the Internet Society Nederland celebrated her 5th anniversary. ISOC is an association that focuses on Internet developments. During the festivities on November 26, the invitees also visited SARA’s advanced virtual reality the CAVE™ for a demonstration of virtual reality.

Visdagen
On November 28 and 29, Platform HPCN organized the annual visualization days (Visdagen). This time the Visdagen werd held at the University of Groningen. On November 28, one of SARA’s VR specialist Dr. Anton Koning gave a lecture on a virtual reality application that SARA has developed in a joint research project with the Bioinformatics group at Johnson & Johnson Pharmaceutical Research & Development. This VR application woffers state of the art data mining capabilities for drug discovery. 3D views in the CAVE™ show hierarchical relationships within gene families, and many to many relationship networks of gene expression data.

New (emergency) power supply ready on 1st of December
In week 48 a new (emergency) power supply with a total capacity of 1,030 kW has been installed at SARA Computing and Networking Services. During this huge operation the entire electrical installation was fed by three mobile power units with a total capacity of more than 3 MWatt.

The old main distribution board has been replaced by a new panel, including two UPS systems and a diesel unit. The basic principles for this huge project were: (1) the power supply of the AMS-IX should not be interrupted and (2) the work had to be finished in a very short period of time. SARA’s (emergency) power supply is now fully in accordance with the latest demands.

Genomics Momentum 2002
On December 4, 2002 the National Regie-Orgaan Genomics organized the Genomics Momentum 2002 in the Netherlands Congress Center in The Hague. In order to inform the audience of the Genomics Momentum 2002 about SARA’s activities in “life sciences", SARA had a stand at the Exhibition. SARA also took part in the poster presentations.
In collaboration with the BioASP, CMBI and UvA, a large-scale infrastructure concerning computing, data storage and related services will be realized for BioASP services for the Dutch Genomics society.

Visit of Prime Minister Balkenende en Minister De Geus
On December 4, 2002 mr. dr. J.P. Balkenende and mr. A.J. de Geus, Minister of Social Affairs and Employment, have paid a working visit to Science park Amsterdam (formerly Science and Technology Center Watergraafsmeer – WTCW). Within the scope of this visit, the Prime Minister and Minister De Geus have also visited SARA and attended several virtual reality demonstrations in the CAVE™, SARA’s virtual reality facility.

New agreement NCF-SARA for the availability of VR facilities
During the 19th Dutch National Supercomputing User Meeting, held on December 12, 2002 at SARA in Amsterdam, NCF (Foundation National Computing Facilities) and SARA Computing and Networking Services, signed a new agreement covering Virtual Reality and Visualization. Under this agreement, Dutch researchers from Universities, NWO and KNAW institutes are able to use the CAVE™ at SARA during the next years, without additional costs involved for them.

New is the possibility to request support from VR and Visualization experts at SARA to optimally visualize the scientific data, using existing and possibly new applications.

CIAO demonstrations at SARA
On January 15-17, Foundation CIAO (Computers in het Amsterdamse Onderwijs) and SARA organized three days with demonstrations for the primary schools in Amsterdam that are participating in the so-called CIAO project. About forty schools took this opportunity to explore the newly – by CIAO and SARA – developed TWIN+-concept. TWIN+ is a hybrid concept in which two environments, UNIX and Windows2000 work stations, are integrated.

Minister Van der Hoeven visits Science park Amsterdam and SARA
On Tuesday, January 21, Mrs M.J.A. van der Hoeven, Minister of Education, Culture and Science, has paid a working visit to Science park Amsterdam. During this visit, Minister Van der Hoeven has also visited SARA Computing and Networking Services, and attended several demonstrations in the CAVE™ – SARA’s virtual reality facility.

Reception for AMS-IX members
In colloboration with NIKHEF, SARA organizes a reception for, amongst others, members of the Amsterdam Internet Exchange (AMS-IX) on January, 31. One of the reasons for this event is the new (emergency) power supply that came into operation at SARA and NIKHEF in December 2002. During the reception SARA’s computer floors and technical rooms can be visited.

The reception at the Turingzaal.


Opening of the Superdag by SARA director Dr. ir. Anwar Osseyran.


Dr. Patrick Aerts, director NCF.


Dr. Axel Berg, head of HPC Department, SARA.







DISC -stand at SC2002 in Baltimore (USA).


A demonstration of virtual reality by SARA with passive stereo projection during SC2002.







SARA consultant Drs. Harold van Aalderen presents the technical infrastructuur of the e-BOAT project in Almere.


SARA staff members during the e-BOAT conference in Almere.







Diesel generator of SARA's new (emergency) power supply.







Visit of Prime Minister J.P. Balkenende. The group in the CAVE during a demonstration of the 3D visualization of the protein molecule Thrombin.







SARA director Dr. ir. A. Osseyran (left) and NCF director Dr. P.J.C. Aerts sign the new agreement for the availability of VR facilities and visualization support.





The teachers of the primary schools during the CIAO demonstrations.




Mrs M.J.A. van der Hoeven, Minister van Education, Culture and Science, in SARA's CAVE during a volume visualization of a MRI scan of a liver.