MDoC: A molecular dynamics application framework for the QCDOC supercomputer.

摘要

We present the first molecular dynamics application package, called MDoC, for the QCDOC supercomputer designed, superficially, for QCD (quantum chromodynamics) applications. Due to the high complexity and uniqueness of the hardware architecture particularly the network, other molecular simulation packages will require major development to take advantage of QCDOC features. MDoC is custom designed, to fully exploit such unique architectural advances.; Typical bio-molecular systems have thousands, possibly millions, of atoms with timescales at microseconds to milliseconds. Simulating them requires a substantial amount of computational power that can be provided by using supercomputers. The most time consuming calculation for simulating bio-molecules is that of the electrostatic interactions, commonly handled through the use of the Ewald algorithm. We also address other algorithms necessary for molecular simulations, specifically, constant temperature and pressure algorithms using the Melchionna-modified Nose-Hoover method. We discuss an efficient all-gather method for QCDOC. Since QCDOC does not have a network specific algorithm for global communication like the tree network on BlueGene/L, we present one specifically for handling the long range electrostatic interactions. We demonstrate the usability of QCDOC to for non-QCD applications. Due to the fast communication network and the flexibility of the PowerPC processor, molecular dynamics simulations are capable of 70% parallel efficiency when using 1024 processors for a protein with approximately 30,000 atoms including solvents.