IBM Supercomputer undertakes complex simulations into cancer research

Heidelberg 09 July 2003An IBM supercomputer is deployed for complex biocomputing applications at the data centre of the German Cancer Research Center in Heidelberg for analysing the structures of human genomes and proteins within the worldwide "Human Genome Project". The recently expanded supercomputing system consists of IBM supercomputers including IBM eServer p690 systems with a total of 96 POWER processors.


The German Cancer Research Center, known as DKFZ, the Deutsches Krebsforschungszentrum, investigates the mechanisms for the development of cancer and identifies risk factors, which cause malignancy. Scientists of the Centre develop scientifically founded approaches for new concepts in diagnosis and therapy.

Furthermore, DKFZ is also doing research in the area of virology and immunology of tumours. The IBM supercomputer is used for various biocomputing applications from DKFZ's high capacity data centre. The partly internally developed applications are used for example for the analysis of human genomes and the simulation of the effectiveness of drugs against cancer. The IBM system now includes two eServer pSeries 690 with a total of 64 POWER 4 processors supported by IBM POWER 3 processors with a computing capacity of 330 GFLOPS. This is equivalent to 330 billion operations per second.

The first IBM supercomputer was already installed at the DKFZ in 1994 and has continually been expanded within the framework of four-year lease contracts. The DKFZ scientists depend on the ongoing increase of computing capacity to support their ever more complex simulations, which often require several weeks to complete even when using these efficient systems.

The scientists use applications such as Gaussian, TurboMol, Molpro and Amber, which simulate for example the structure of molecules and molecular movement. The results of the structure analysis of human genomes and proteins are saved in different DNA- and protein sequences databases and are exchanged regularly in the framework of international collaboration. Therewith the DKFZ is part of the worldwide "Human Genome Project".

For the cancer research institute, 64-bit-computing and the associated large address space is a pre-condition for the realisation of the needed performance. When selecting a suitable system one of the decisive factors for DKFZ are the price/performance ratio and the low heat dissipation.

Dr. Kurt Boehm, head of the central data processing unit at the DKFZ, summarised his experiences with the IBM supercomputer: "Permanent processor improvement is a crucial factor when aiming to achieve new results in cancer research by means of ever more complex simulations. We are totally satisfied with the capacity of the IBM supercomputer. Besides of price/performance ratio and the size, the low heat dissipation in comparison to other high performance systems is a factor of central importance."

The German Cancer Research Center was established as a foundation under public law of the state Baden-Württemberg in 1964 in Heidelberg. The DKFZ is a national research institute and has been a member of the Hermann von Helmholtz-Gemeinschaft deutscher Forschungszentren (HGF) and a member of the Deutschen Forschungsgemeinschaft (DFG) since 1977. The DKFZ is mainly funded by the State Ministry for Education and Research for 90 percent and by the Baden-Württemberg Ministry for Science, Research and Art for the remaining 10 percent.

The aim of the foundation is to make fundamental contributions to understanding the mechanisms of cancer development and to determining cancer risk factors. The results of its fundamental research are intended to lead to new approaches to cancer prevention, diagnosis and therapy.

Leslie Versweyveld

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