Message Passing Implementation

Berendsen, Van der Spoel, D. Van Drunen, R. GROMACS A message-passing parallel molecular dynamics implementation. Comput. Phys. Comm. 91 (1995) 43-56. 

Two implementation decisions could be made immediately. First, DPMTA is based on the PVM message-passing library [11] and therefore it was necessary to base NAMD on PVM as well. All communication done by NAMD, however, would use an intermediate interface to allow communications to be easily retargeted to MPI [12] or other standards, and to simplify later implementation of communication optimizations such as combining messages destined for the same processor. Second, after much debate C++ was selected... 

The major task undertaken as a part of the code development efforts during the past year was implementation of the Message Passing Interface (MPI) such that the code could be run on parallel computers. This is a very important step, as the intensity of the planned simulations makes it impossible to generate the results using only a single processor. 

MPICH2 is an implementation of the Message-Passing Interface (MPI). It is available on the World Wide Web at http //www.mcs.anl.gov/mpi/mpich2. 

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