Hi Ross:
Does any AMBER/GPU benchmark exist about T-REMD? I am carrying out T-REMD
with NAMD on a 41 aa peptide in periodic water box on a BlueGene/Q 128
nodes (4024 processors) 32 replicas. However, I would also like to carry
out T-REMD "at home" on a single node. NAMD requires multiple physical
nodes and has problems - as far as I could understand - in restarting with
harmonic forces applied to a part of the system (harmonic forces that are
absolutely needed in my project ). Of course I will limit "at home" T-REMD
to simpler systems, like under GB conditions and/or smaller peptides.
At present I am at ivy-bridge/two GTX680 PCIExpress 3.0, i.e., devised for
a code, like NAMD, that shifts from GPU to CPU at any step. I am at
AMBER10, so that I need upgrading that too.
For reason of budget, I intend to assemble "at home" the computer for
AMBER, using for last components, which usually is no big loss. Also, I
exchange the older with the new parts with my dealer, which also keeps the
prices lower.
Thanks
francesco pietra
On Mon, Feb 10, 2014 at 7:10 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Divi,
>
> You might want to take a look at the recommended hardware on this page:
>
> http://ambermd.org/gpus/recommended_hardware.htm#hardware
>
> Note if you only plan on having 2 or less GPUs in a box then you only need
> single CPU. Dual socket boards are expensive and only needed if you want 3
> or more GPUs in the same box. What you have right now seems very expensive
> to me especially for home built.
>
> Also note that the GTX-Titan is now end of line so you may not be able to
> get hold of one. There is a replacement called the GTX-Titan Black Edition
> - announcement coming in just over a week. I don't have specs for you
> right now but it is likely to be priced similar to the GTX-Titan but quite
> a bit faster. That said we haven't had any to actually test and validate
> either so I'd say if you buy one within the first month or so of their
> release be vary wary since we've seen issues in the past with brand new
> kit and it can take a few months to iron the bugs out.
>
> So if you are cautious you might want to consider GTX-780 GPUs instead for
> the time being.
>
> So to summarize, dual socket is overkill (for <3 GPUs) unless you plan on
> doing lots of CPU runs on this machine. GPU AMBEr operates independently
> of the CPU so you don't ned to buy high bin parts (it will make no
> difference to performance). So you only need to go for expensive CPUs if
> you have lots of CPU only jobs to run.
>
> All the best
> Ross
>
>
>
>
> On 2/10/14, 3:36 AM, "Ved Prakash" <ved.bakli.gmail.com> wrote:
>
> >Dear Divi,
> >
> >Thanks for your previous email. I looked through various web resources and
> >finally came up with the following configuration for the computing system
> >(please see the attachment for further details). Please let me know if
> >everything is OK. The overall price for the system is somewhere around
> >$3300, which is perfectly fine with us. :)
> >
> > Part
> >
> >Specification
> >
> >Processor
> >
> >AMD Opteron 6320 2.8GHz, 8-Core (two)
> >
> >RAM
> >
> >32GB (4 x 8GB)
> >
> >Hard drive
> >
> >Seagate 2TB (two) (RAID 1)
> >
> >Graphics card
> >
> >ZOTAC NVIDIA GeForce GTX TITAN 6GB GDDR5
> >
> >
> >--
> >Best wishes
> >--
> >Ved Prakash
> >Research Scholar
> >Dr. Yamuna Krishnan's Lab
> >National Centre for Biological Sciences
> >Tata Institute of Fundamental Research
> >GKVK, Bellary Road,
> >Bangalore 560065, India
> >
> >Phone: 09632160081
> >
> >
> >website: http://www.niser.ac.in/wiki/index.php/Ved_Prakash
> >
> >
> >On Sat, Jan 25, 2014 at 11:44 PM, Divi/GMAIL <dvenkatlu.gmail.com> wrote:
> >
> >> Hi Ved:
> >> I am not sure you can get a high end system for 3K. but you can get a
> >> decent GPU workstation.
> >> My suggestion is to get a workstation that is dual processor
> >>(hexacore or
> >> quad-core, depending on prices in India) system with motherboard that
> >> supports dual PCIE-3 lanes (X16/X16).
> >> You can get two GTX-780 cards to go with the system and 16 or 32GB
> >> memory.
> >> These cards are about Rs. 50,000 in India. Make sure you get 1200
> >>Watts
> >> Gold certified Power supply from the Vendor (if you are not building
> >> yourself).
> >>
> >> My personal choice is not to buy Gaussian that in my opinion is
> >>waste of
> >> money given your budget limit. Rather, you can get NWCHEM or GAMESS
> >>free.
> >> Both codes would do almost everything that GAUSSIAN does. I have NWCHEM
> >> and
> >> GAUSSIAN in my lab. Unix friendly students use NWCHEM and GUI driven
> >> click-and-submit students like GAUSSIAN (on Windows). Both programs get
> >>the
> >> job done.
> >>
> >> I built myself several GPU workstations in my lab including GTX780
> >>and
> >> TITAN's for anywhere from USD2500 to 3200. They are running perfect
> >>24/7
> >> for the past one year.
> >>
> >> Hope it helps, Feel free to shoot an email if you have more
> >>questions.
> >>
> >> Divi
> >>
> >> -----Original Message-----
> >> From: Ved Prakash
> >> Sent: Saturday, January 25, 2014 11:14 AM
> >> To: amber.ambermd.org
> >> Subject: [AMBER] enquiry regarding latest Amber
> >>
> >> Hi,
> >>
> >> We are planning to buy a high end computing system for carrying out MD
> >> simulations on molecular systems as large as a few hundred atoms (mostly
> >> nucleic acids with small organic fluorophores covalently attached to
> >>them).
> >> Apart from this, we also plan to carry out DFT level calculations on
> >> similar molecular systems (mostly biological molecules) using
> >>"Gaussian".
> >>
> >> It would be great if you can help us out with the best version of Amber
> >>and
> >> the optimized system configuration (for example processor, RAM, etc.)
> >>for
> >> carrying out such calculations. Our budget for the computing system
> >> (excluding software) is around USD 3,000.
> >> --
> >> Best wishes
> >> --
> >> Ved Prakash
> >> Research Scholar
> >> Dr. Yamuna Krishnan's Lab
> >> National Centre for Biological Sciences
> >> Tata Institute of Fundamental Research
> >> GKVK, Bellary Road,
> >> Bangalore 560065, India
> >>
> >> Phone: 09632160081
> >>
> >>
> >> website: http://www.niser.ac.in/wiki/index.php/Ved_Prakash
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
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> >>
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Received on Tue Feb 11 2014 - 07:00:02 PST
