Re: REMD across gpus

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 10 2011 - 15:05:06 CDT

On Mon, May 9, 2011 at 10:28 AM, Massimiliano Porrini
<M.Porrini_at_ed.ac.uk> wrote:
> 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

the problem is the devices flag. you will have to alternate between
"+devices 0" " +devices 1" and "+devices 2" to have the jobs scattered
across the GPUs.

also, if you want to do hybrid (cpu/gpu) you'd have to have two sets
of namd binaries (with and without GPU support) and figure out how
many CPU cores you have to use to have a runtime comparable to
one CPU core plus GPU.

i'd rather get time on a simple cluster and forget about this mess.

axel.

> 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
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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