Re: Help building a desktop for namd

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 14 2011 - 08:37:20 CDT

On Thu, Apr 14, 2011 at 1:07 AM, Jeffrey Potoff
<jpotoff_at_chem1.eng.wayne.edu> wrote:
> For $6,500 each, I was able to build 4-way 2.3 GHz 8 core Opteron machines
> with 64 GB of ram.  I started with a Supermicro barebone AS-2042G-6RF.
>
> http://www.newegg.com/Product/Product.aspx?Item=N82E16816101321
>
> And added CPUs
>
> http://www.newegg.com/Product/Product.aspx?Item=N82E16819105265
>
> and RAM.  The nice thing about the Supermicro barebones is that the come
> with the heat sinks, so all you need to do is drop in the CPUs and ram, and
> you are ready to go.
>
> I went with 2U instead of the 1U because it was all I could get at the time.
>  If I was doing it now, I'd probably go with the 1U to save $500 a node.
>  You might save some money by going with less ram, but you will still need a
> lot of sticks because the board needs to be populated in multiples of 4.
>  These things are very loud.  I would not want to work in the same office
> with one under full load.  Hide it in a closet and you should be ok.
>
> You will have a hard time finding a typical "PC" type setup for this because
> the 4-way motherboards have a unique form factor and are larger than EATX.
>  Last summer I was looking for a chassis to fit such a board and gave up.
>  Much easier to go with the motherboard/chassis combo.

jeff,

this is very good advice. it is not only easier, you were saving
yourself a lot of trouble.

saving money is important to a lot of people, but if you
trying too hard to save, you will be losing more than you
can save. in my experience, saving money at all costs
simply doesn't pay. you have to go with substandard
hardware and then one has to factor in that even an
experienced person does not work perfectly, so the more
manual steps the assembly of a machine requires, the
higher the chances that something is not perfect and
that can in the worst case lead to broken hardware
and a complete loss of all money.

most "PC" hardware is spec'd to be used at most
a few hours each day. you have to factor this in when
running a production machine.

cheers,
    axel.

>
> Regards,
>    Jeff
>
>
> On 4/13/2011 6:06 PM, Gianluca Interlandi wrote:
>>
>> Hi Salvador,
>>
>> Just a thought:
>>
>>
>> http://www.newegg.com/Product/Product.aspx?Item=N82E16859105793&cm_re=opteron-_-59-105-793-_-Product
>>
>> An example of a 4x 12-core opteron node.
>>
>> So far, I have not been able to find a "classic" PC built with 4x 12-core
>> opteron. Does it exist? I was able to find a motherboard which supports a 4x
>> 12-core:
>>
>> http://www.newegg.com/Product/Product.aspx?Item=N82E16813151219
>>
>> but can you mount it in a tower case?
>>
>> Gianluca
>>
>> On Wed, 13 Apr 2011, Salvador H-V wrote:
>>
>>> Hi all,
>>>
>>> Thanks a lot to all of you people who share their experience with me.
>>>
>>> I found your comments and ideas very useful!
>>>
>>> I think we have a very good starting point. Of course, I will be checking
>>> the mail
>>> list for new ideas.
>>>
>>> Kind regards,
>>>
>>> Salvador Herrera Velarde
>>>
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>                    +1 (206) 685 4435
>>                    http://artemide.bioeng.washington.edu/
>>
>> Postdoc at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
>
> --
> ======================================================================
> Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
> Associate Professor                       Wayne State University
>
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr                     Phone:(313)577-9357
>
> Detroit, MI 48202                         Fax:  (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>
>

-- 
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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