From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Tue May 10 2011 - 15:29:36 CDT
Dear Axel,
Thanks for the useful reply.
Only one clarification:
Your word "mess" was referred only to the hybrid (gpu/cpu) simulation
or also to the REMD across multiple GPUs ?
I mean, is REMD across GPUs easily doable?
Thanks again,
MP
PS: by the way I am already running REMD on our cluster, but it is
"slightly" slow.
2011/5/10 Axel Kohlmeyer <akohlmey_at_gmail.com>:
> 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.
>
>
-- 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
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