REMD across gpus

From: Massimiliano Porrini (
Date: Sun May 08 2011 - 06:02:19 CDT

Dear all,

I am attempting to run replica exchange MD across my three GPUs
(two Teslas C2070 and one GTX 470).

I am using the example files for the deca-alanine folding and I have set a number of replica equal to 30 and have added the
flags "+devices 0,1,2" and "+idlepoll" in the fold_alanin.conf file, as
you can see:

  set spawn_namd_command [list spawn_namd_simple "[file join
$namd_bin_dir namd2] +devices 0,1,2 +idlepoll +netpoll"]

I was expecting to have 10 replicas per GPU, but unfortunately I did not.
Indeed, when I checked which and how many GPUs are actually being used
(via the command
nvidia-smi -a) I see that only the first typed GPU is used, in the
above case the number 0 (GTX480).
Alike if I typed "+devices 1,2" the script will use only the number 1
(i.e. one Tesla C2070).

Any hint/suggestion would be really appreciated.

At this point, another (most likely daft) question came up to me:

Is possible to run an "hybrid" simulation across GPU and CPU cores?
I mean: would NAMD be able to run a REMD simulation with e.g. 32
replica, where 8 replica are run
using the CPU, 8 using the GTX, 8 on the Tesla and the last 8 on the only left Tesla?

Thanks a lot in advance.

All the best,

> --
> Dr Massimiliano Porrini
> P. E. Barran Research Group
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
> Tel +44-(0)131-650-5229
> E-mails :
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:05 CST