From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Mar 31 2014 - 02:41:24 CDT
>From what you say, I can only conclude that we failed to set the correct
flags on that IBM cluster (which is largely unbalances as to the GPU/CPU
ratio).
Could you please reveal details on the hardware / flags / size of the
system that might help me to find the correct conditions on the IBM
iDataPlex DX360M3? In particular, for a T-REMD on a peptide of ca 500
atoms under GB conditions, do GPUs really help? Or are you carrying out
T-REMD in a water peridic box, where, because of the much larger size of
the system, certainly GPUs could help?
thanks
francesco pietra
On Mon, Mar 31, 2014 at 7:39 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> Hmm O_o ??
>
>
>
> I’m running REMD without problems over our four Dual-GPU-Nodes with NAMD
> 2.10 NB from many months ago. Why should this be a problem?
>
>
>
> Norman Geist.
>
>
>
> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
> Auftrag von *Francesco Pietra
> *Gesendet:* Samstag, 29. März 2014 08:29
> *An:* NAMD
> *Betreff:* namd-l: remd across gpus
>
>
>
> Hello:
>
>
>
> On Tue, May 10, 2011 at 4:29 PM, Massimiliano Porrini
> <M.Porrini_at_ed.ac.uk<M.Porrini_at_ed.ac.uk?Subject=Re:%20%20REMD%20across%20gpus>>
> wrote:
> *> 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 ? *
>
> mostly.
>
> *> I mean, is REMD across GPUs easily doable? *
>
> i don't know. as far as i know, the NAMD implementation
> is entirely based on Tcl script code using a socket interface.
> that is an elegant way of implementing REMD without having
> the rewrite the executable. i did something similar a while ago
> in python using pypar and HOOMD and it was fun to see it
> work, but somehow a bit unsatisfactory.
>
> i know of other codes that have such features and other
> multi-replica method implemented on a lower level and
> they appear to me more elegant to use. that may be
> the price to pay.
>
> cheers,
> axel.
>
>
>
> translated into the present, we found it difficult to run t-remd across
> cpu/gpus with either namd2.9 or namd2.10 (remd hard cored into the latter).
> For example, on IBM DX360M3. Difficult, means that it failed in our hands--089e015365e6a5d73f04f5e22d56--
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