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Running NAMD

NAMD runs on a variety of serial and parallel platforms. While it is trivial to launch a serial program, a parallel program depends on a platform-specific library such as MPI to launch copies of itself on other nodes and to provide access to a high performance network such as Myrinet or InfiniBand if one is available.

For typical workstations (Windows, Linux, Mac OS X, or other Unix) with only ethernet networking (hopefully gigabit), NAMD uses the Charm++ native communications layer and the program charmrun to launch namd2 processes for parallel runs (either exclusively on the local machine with the ++local option or on other hosts as specified by a nodelist file). The namd2 binaries for these platforms can also be run directly (known as standalone mode) for single process runs.



Subsections

http://www.ks.uiuc.edu/Research/namd/