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
>> _______________________________________________
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>>
>>
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Received on Mon Feb 10 2014 - 10:30:03 PST
