Replica-exchange MD on a single node / SMP workstation

From: Zachary Ulissi (
Date: Fri Nov 09 2012 - 17:57:26 CST

I've been trying to get the mpi-based replica exchange example to work on a
workstation for testing (4 processor, 64 core SMP). I have mpich2 set up,
have compiled the MPI version of NAMD2.9, and namd/charmm sees the machine
as a single 64-way SMP node.

When I run the replica exchange example for alanin, it does a hard-check in
the patched charm++ code to make sure the number of nodes is greater than
the number of replicas and then stops (since 1node<8replicas), even if I
specify multiple processes for mpirun.

Is there a reason why you need a complete node per replica simulation? If
not, is it possible to run multiple replicas on a single node with multiple
processes? Am I missing something obvious?


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