Re: Running fulldirect in parallel

From: Aron Broom (
Date: Sun Oct 07 2012 - 15:14:10 CDT

can you set the cutoff value very high? I've done some implicit solvent
and particularly vacuum simulations in NAMD where I essentially wanted full
electrostatics, and so just set "cutoff 999". For efficiency you also want
to turn "switching off", and use "staticAtomAssignment yes". Maybe I'm
missing something important about fullDirect though, does it do a different
kind of electrostatic calculation?


On Sun, Oct 7, 2012 at 4:08 PM, Tom Coles <> wrote:

> I was trying to use the fulldirect method and found that it only works in
> serial mode; there is an error every time I try to run it in parallel. I
> know that fulldirect is very slow and inefficient, but I need to do a
> simulation of a non-periodic system.
> Anyway, I looked at the source code and noticed that the doWork method in
> ComputeFullDirect.C calls the sendMessage method in Communicate.C for all
> PEs and not just PE 0, but sendMessage gives an error for any non-zero PE.
> sendMessage accepted any PE in NAMD2.5b1 and earlier, so fulldirect worked
> in parallel until that time. However, it was changed to only accept PE 0
> for NAMD2.5 and later. I would like to try to make it work in parallel
> again, so I was wondering why there was a problem with non-zero PEs in
> Communicate.C and if there is recommended alternative way of performing the
> communication required by fulldirect?
> Thanks for any help,
> Tom Coles

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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