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StreamMD Molecular Dynamics. Eric Darve. MD of water molecules. Cutoff is used to truncate electrostatic potential Gridding technique: water molecules are grouped in clusters of size r cutoff . Problem: what data structure do we use to store this array of clusters?.

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md of water molecules
MD of water molecules
  • Cutoff is used to truncate electrostatic potential
  • Gridding technique: water molecules are grouped in clusters of size rcutoff.
  • Problem: what data structure do we use to store this array of clusters?
slide3
Option: 3D array of streams.
  • Needs to be updated at each time step (or every 10 time steps) to account for molecules that enter or leave a cluster.
  • Q: how do I move data from one stream to another?
  • Q: how does the compiler take care of the load balancing?
  • Data locality defined by geometric distance between clusters, i.e.If two clusters are neighbors, they should be physically located in neighbor processors.
current implementation
Current implementation
  • After position has been updated:
    • Loop over all clusters C[i][j][k]:
      • We push in C[i][j][k] if water molcl is in same cluster.
      • We push in Ctmp otherwise.
    • Ctmp is then concatenated in a large stream Mol which contains all the molecules which have exited their cell.
    • Kernel is exec. to push molecules in Mol to C[][][].
md of proteins
MD of proteins
  • Three possible types of potentials:Bond stretch: two atoms and 1 bond.Bond angle: three atoms and 2 bonds.Torsion angle: four atoms and 3 bonds.
  • Typical organization of the computation:loop over bond stretch, bond angle and torsion potentials.
  • Brook needs some information to map the data in an efficient manner.
slide6
Information is static: connectivity between atoms does not change throughout the run.
  • However the information is not accessible to the compiler: run-time information.
  • Protein backbone: sequence of amino-acids. Typically 10-20 atoms each.
  • User can provide following information: for each atom, give residue number.
slide7
“Distance” between two data can then be defined as the difference between residue number.
  • Run-time optimization approach:all atoms with same residue number are on the same processor.2 processors with nearby residue numbers should be physically close to each other.
load balancing
Load balancing
  • Typical size of protein: 10 residues for test proteins to hundreds for real life problem.
  • Size is relatively small but computationally very expensive.Well optimized load balancing and distribution of data is critical.
  • Example: Duan and Kollman ’98. 36-residue protein + 3000 water molecules.1/2 billion time steps: four months on 256-processor computer. Complete fold would have required: x 10, x 100.
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