PS3GRID.NET: Building a distributed supercomputer using Cell processors Gianni De Fabritiis, Computational Biochemistry and Biophysics Laboratory (GRIB), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB)
[email protected] Molecular simulations (MS) methods will mature in the next few years to be able to simulate temporal scales of biological interests, changing drastically its importance in biological discovery. Gianni De Fabritiis, Uniiversity Pompeu Fabra 2 Why not now? . MD: Newton Equation . Characteristic scales . Timescale: 10E-15 s . Lengthscale: 10E-10 m . Application scales (biology) . Micro-milli seconds . 10-100 nm . Current resolution: . Nanoseconds . 10 nm Helical dimer (PDB: 1JNO) Lipids not shown Gianni De Fabritiis, Uniiversity Pompeu Fabra 3 Where are we going? Source: NVIDIA Gianni De Fabritiis, Uniiversity Pompeu Fabra 4 Accelerator processors: A new challenging era for computational science We are at a crucial critical point in . Data-memory the evolution of microprocessors: Single core => multi-core . Every CPU maker (IBM, INTEL, AMD, NVIDIA) is working on Memory heavily multi-core chips handling bottleneck hundreds of threads. A different memory architecture is needed => IBM Cell processor, GPUs Computation-cpus Gianni De Fabritiis, Uniiversity Pompeu Fabra 5 Cell Processor . 9 cores (1 PPE + 8 SPEs) . Only 80$ per chip . 230 Gflops in single precision . 8 SPE cores are specialized for number crunching with local memory access. Altivec-like, memory alignment, async DMA, mailboxes, signals, memory mapped (16 SPEs in shared mem) Gianni De Fabritiis, Uniiversity Pompeu Fabra 6 Sony-Toshiba-IBM Cell Processor . Available: IBM blades (roadrunner, 16,000 Cell) and PlayStation3 . Software barriers: . Codes do not automatically run faster .