ISC'12

June 17-21, 2012

Hamburg, Germany

Contribution Details

 
Name: Algorithms & Analysis
(9) Improving Atomistic & Molecular Simulations Performance on Parallel Machines with a Hierarchical Mapping Strategy
 
Time: Monday, June 18, 2012
3:00 PM - 8:30 PM
 
Room:   Hall H, #911
CCH - Congress Center Hamburg
 
Speakers:   Christiane Pousa Ribeiro, University of Zurich
 
Abstract:   The study of how atoms and molecules behave is important in the conception of novel materials or to better understand existing ones. CP2K is a real-world parallel application that is used to perform atomistic and molecular simulation. It implements state-of-art methods, such as ab-initio DFT and Hartree-Fock, that allows it to produce efficient and accurate simulations. The parallelism in CP2K is obtained through the use of a hybrid model, in which message passing (MPI) and shared memory models (OpenMP and CUDA) are combined to exploit current large scale parallel machines. Such parallel machines are assembled with hundreds or even thousands of compute nodes interconnected by an efficient network. These networks usually have a wide diameter and a limited bisection bandwidth. Additionally, the compute nodes rely on multi-core architecture with a Non Uniform Memory Access design and cores sharing several resources. Therefore, to obtain high efficiency, it is crucial to take into account the machine topology to reduce the overhead of memory accesses and network communication. In this context, to allow CP2K to fully exploit the power of current machines, we introduce a hierarchical mapping strategy that reduces both memory and communication costs perceived by CP2k. The proposed strategy places together processes and threads that communicates more, avoiding longer latencies and lower bandwidths. The goal is to automatically combine information extracted from CP2K with the machine topology to apply process mapping among the compute nodes and process affinity within each one of them.  
  • Tutorial Pass
  • HPC in Asia Workshop Pass
  • Conference Pass
  • Conference Pass or Exhibition Pass
    Satellite Event marked with * requires separate pass
  • Morning & Afternoon Coffee Breaks
    Midday Lunch Break
Program may be subject to changes.