W. Smith and T. R. Forester. Parallel macromolecular simulations and the replicated data strategy: I. The computation of atomic forces. Comp. Phys. Comm., 79:52--62, 1994.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....of this F matrix to different processors. 3 Replicated Data Method The most commonly used technique for parallelizing MD simulations of molecular systems is known as the replicated data (RD) method [24] Numerous parallel algorithms and simulations have been developed based on this approach [5, 8, 9, 16, 17, 18, 22, 25]. Typically, each processor is assigned a subset of atoms and updates their positions and velocities for the duration of the simulation, regardless of where they move in the physical domain. To explain the method, we first define x and f as vectors of length N which store the position and total ....

....faster on the Paragon, the two sets of RD timings (filled and open squares) are similar. Both curves show a marked roll off in parallel efficiency above 64 128 processors due to the poor scaling of the expand and fold operations. This is typical of the results reported in references [8, 9, 16, 17, 18, 22, 25] for RD implementations of other macromolecular codes such as CHARMM, AMBER, and GROMOS on a variety of parallel machines. Parallel efficiencies as low as 10 15 on a few dozens to hundreds of processors are reported and in some cases the overall speed up is even reduced as more processors are ....

W. Smith and T. R. Forester. Parallel macromolecular simulations and the replicated data strategy: I. The computation of atomic forces. Comp. Phys. Comm., 79:52--62, 1994.

....[13, 33] and is beyond the scope of this paper. The most commonly used technique for parallelizing short range MD simulations of molecular systems is known as the replicated data (RD) method [31] Numerous parallel algorithms and simulations have been developed based on this approach [7, 11, 12, 18, 21, 23, 29, 32]. Typically, each processor stores a copy of all the atom positions in the simulation. It uses this vector of information to compute non bonded forces for the subset of atoms assigned to it. The bonded force computation can be simply parallelized in this scheme, since each processor can compute ....

....is called a fold operation [4, 16, 25] and scales optimally as N , the volume of data in the force vector f . We note that the fold operation is less costly than a global sum operation where each processor ends up with the total force on all N atoms, as is done in the RD algorithms discussed in [12, 21, 23, 32]. A global sum operation typically scales as N log 2 (P ) and so on 256 processors is 8 times more expensive than a fold. The N=P forces resulting from the fold are used to update atom positions and velocities in step (4) Finally, in step (5) the new atom positions in x z are shared among all P ....

[Article contains additional citation context not shown here]

W. Smith and T. R. Forester. Parallel macromolecular simulations and the replicated data strategy: I. The computation of atomic forces. Comp. Phys. Comm., 79:52--62, 1994.

....resort is parallelisation. Over the last 10 15 years, a vast number of parallel MD simulation algorithms 1 A first release will be made available to the public in spring 1999. have been presented and some of them have been implemented and are available as more or less ready to use packages ([7, 8, 11, 2]) Almost all of them concentrate on the parallel simulation of biopolymers and very few (e.g. 8] also explicitly target at synthetic polymers. This is difficult to understand and regrettable. Synthetic polymers are increasingly penetrating all aspects of modern life and there is a huge demand ....

....A first release will be made available to the public in spring 1999. have been presented and some of them have been implemented and are available as more or less ready to use packages ( 7, 8, 11, 2] Almost all of them concentrate on the parallel simulation of biopolymers and very few (e.g. [8]) also explicitly target at synthetic polymers. This is difficult to understand and regrettable. Synthetic polymers are increasingly penetrating all aspects of modern life and there is a huge demand for compute intensive theoretical investigations of polymer models and real world polymers. As ....

[Article contains additional citation context not shown here]

W. Smith and T. R. Forester. Parallel macromolecular simulations and the replicated data strategy. Computer Physics Communications, 79:63--77, 1994. Package DL-POLY http://gserv1.dl.ac.uk/TCSC/Software/DL POLY/main.html.

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC