Re: Running fulldirect in parallel

From: Aron Broom (
Date: Sun Oct 07 2012 - 15:43:54 CDT

oh I see.

Yes, the staticAtomAssingment will help a bit with performance, since you
don't need to be checking partners and such, but I have no idea how to get
around the VDW problem.


On Sun, Oct 7, 2012 at 4:21 PM, Tom Coles <> wrote:

> Thanks for the fast reply. I wasn’t aware of staticAtomAssignment
> before, but I will try it now.****
> ** **
> I have been setting the cutoff high, but I was hoping to make things
> faster with fullDirect because simply using a large cutoff has the
> following issues:****
> **1) ** L-J calculations also occur all the way out to the large
> cut-off, wasting some computational time.****
> **2) **I would like to use fullElectFrequency to evaluate long-range
> electrostatics at a larger timestep. I know that nonBondedFreq can be used
> to evaluate L-J and electrostatics at a larger timestep, but the long-range
> part can be safely evaluated at an even larger timestep and I was hoping to
> take advantage of that.
> ****
> Tom****
> ** **
> *From:* Aron Broom []
> *Sent:* 07 October 2012 16:14
> *To:* Tom Coles
> *Cc:*
> *Subject:* Re: namd-l: Running fulldirect in parallel****
> ** **
> 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?
> ~Aron****
> 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--f46d04428210d3e50404cb7e299a--

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:39 CST