REMD across gpus

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Mon May 09 2011 - 09:28:51 CDT

Dear all,

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

They are all inside my GPU workstation, hence I have one node with three GPUs.

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 thought to have 10 replicas per GPU, but unfortunately I did not.
Apparently the above modifications are not enough.

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,
MP

>
> --
> 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 : M.Porrini_at_ed.ac.uk
>              mozz76_at_gmail.com
>              maxp_at_iesl.forth.gr
>
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>

-- 
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 : M.Porrini_at_ed.ac.uk
             mozz76_at_gmail.com
             maxp_at_iesl.forth.gr

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:54 CST