Mario (Cray C90)

The PSC’s CRAY C90 (or, more correctly, C916/512), nicknamed Mario, ran UNICOS, based on AT&T UNIX System V, with Berkeley extensions and Cray Research, Inc. enhancements.  Compared to the Y-MP, its predecessor at PSC, the C90 processor had a dual vector pipeline and a faster 4.1 ns clock cycle (244 MHz), which together gave three times the performance of the Y-MP processor. The maximum number of processors in a system was also doubled from eight to 16. The C90 series used the same Model E IOS (Input/Output Subsystem) and UNICOS operating system as the earlier Y-MP Model E.

PSC researchers made good use of the C90 from its installation in the fall of 1992 through May 1999.

Research

Some of the important research enabled by the C90 is highlighted here. To see more, check the Projects in Scientific Computing archive.

Modeling Cardiac Fluid Dynamics

Charles Peskin and David M. McQueen, New York University, Courant Institute of Mathematical Sciences

The main objective of the computation was to improve flow through the aortic valve. The result was a breakthrough: a more realistic match between the detail of the computation and actual heart anatomy. Every part of the model, each chamber and valve, did its job in synchrony through a complete cycle — a full computational heartbeat. This fully functioning 3-D computational model of the heart, its valves and nearby major vessels, may one day be used to pose important “what if” questions about the heart, many of which are difficult to address in animal research and clinical studies.
Read the full article: https://www.psc.edu/science/Peskin/Peskin.html

Shifty Biomolecules: Macromolecular Structures via NMR Experiments

Thomas L.James, University of California, San Francisco

The structure of a 13-basepair sequence of DNA from the HIV virus was determined using NMR methods and computational experiments on the C90.  The spiral staircase-like double-helix structure forms form base pairs that link the two DNA “backbones”.  Aligning DNA sequences from several HIV strains showed that this sequence, from the “long terminal repeat region” of the HIV-1 genome, is “highly conserved”.  This suggests that the sequence plays a role in HIV’s ability to reproduce itself in human cells, and the structure is a potential target for antiviral drugs.
Read the full article: https://www.psc.edu/science/James/James.html

Breathing Lessons: Computational Analysis of Small Airway Fluid Dynamics

Jeffrey Hammersley, Medical College of Ohio, Toledo, Ohio

Hammersley, a lung specialist at the Medical College of Ohio, combines his medical knowledge with engineering training in fluid dynamics to create a computational model of airflow in the lungs. Inhalation is an efficient way to deliver medication, requiring less total medication and less frequent doses, reducing side effects and cost. Looking to expand the drugs that can be administered this way, Hammersley and colleagues in engineering and computer science at the University of Arkansas, the NSF Engineering Research Center at Mississippi State and the University of Toledo, have converted computational fluid dynamics techniques used in the design of cars, airplanes and aerospace vehicles for use in the complex branching geometry of the lung’s small airways.
Read the full article: https://www.psc.edu/science/Hammersley/Hammer.html

Quantum Chemistry: Swimming Ions & Jumpy Electrons

Gregory A. Voth, University of Pennsylvania

Voth and his colleagues mounted the first major foray of computer simulation into the field of quantum chemistry.  Using the CRAY C90 at Pittsburgh, they completed a massive computation that, for the first time, simulates a typical electro-chemical reaction–an electron transferring from a platinum electrode to an iron ion immersed in water.  His surprising, interesting results lead to the conclusion that quantum methods are required to accurately simulate the electron transfer process in water.
Read the full article: https://www.psc.edu/science/Voth/Voth.html