BlueGene/L Facts

1. BlueGene/L Facts BlueGene/L compute ASIC 512-node prototype

2. BlueGene Molecular Dynamics Demo: The Blue Matter molecular dynamics framework is running on a 32-node BlueGene/L system. The IBM T221 display is updated in real-time by the simulation. Blue Matter is a modular system developed for the BlueGene science program. The simulations are running at constant particle number, volume, and energy (NVE). The first simulation is a small patch of lipid bi-layer in water representing a cell membrane. A large number of potential drug targets are membrane-bound proteins, making lipid bi-layers and proteins in lipid bi-layers important subjects of molecular dynamics research. Scientific simulations of membrane systems can involve tens to hundreds of thousands of atoms, making them ideal candidates for a BlueGene/L scale supercomputer. The second simulation is of a small peptide in water, a beta-hairpin with 16 amino acid residues taken from the C-terminus of Protein G. The folding of this hairpin shares many characteristics of folding in larger proteins and has been studied extensively. The folded system is at 500K and unfolds as the simulation proceeds. Each molecular dynamics time-step represents femtosecond (10-15 sec), while the folding time of the peptide chain at room temperature is measured in microseconds (10-6 sec). Billions of time-steps are required to simulate folding even in this small system. The Prototype Protein Viewer (PPV; http://alphaworks.ibm.com/) component of Blue Matter, is fed atom coordinates as they are generated by the molecular dynamics code. The viewer shows hydrogen bonds within the peptide and lipid and also displays derived information. Since hydrogen bonds are essential in determining the shape and function of proteins, seeing the bonds form and break provides a microscopic view of the folding process in action. The BlueGene/L Supercomputer: IBM, collaborating with Lawrence Livermore National Laboratory, other DOE/NNSA labs, and other partners, has developed a 512-node prototype of BlueGene/L at IBM Research in Yorktown. This prototype is ranked number 73 in the world with a peak speed of 2 TF/s, and sustains 1.4 TF/s on the LINPACK benchmark. The full BlueGene/L Supercomputer, to be completed in early 2005, will have 65,536 compute nodes and 1,024 I/O nodes. Each I/O node, running Linux, will manage a group of 64 compute nodes. BlueGene/L is expected to top the list of the world’s supercomputers with a peak processing speed of 180/360 TF/s and 16/32 TB of memory. It will process data at a rate of one terabit per second. Each BlueGene/L node has dual processors, each with two floating point pipes, and is capable of a peak speed of 2.8/5.6 GF/s. Two nodes are mounted onto a module; 16 modules fit into a chassis and 32 chassis to a rack. A total of 64 racks will be installed at the Lawrence Livermore National Laboratory by early 2005. In contrast to the ASCI White Computer, which has a footprint of 10,000 square feet, BlueGene/L will fit into about 2,500 square feet and use approximately 1.5 MW.