Re: running NAMD on Amazon EC2?

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 14 2013 - 14:53:56 CST

On Thu, Feb 14, 2013 at 9:48 PM, Cloud Computing
<cloudbiocomputing_at_gmail.com> wrote:
> Ajasja,
>
> I'd be very interested to learn how you built your own cluster on AWS. Did
> you use any customer apps from AWS or build your own system to create
> clusters of virtual machines? We only need to build a small size cluster,
> ~50 virtual cores should be able to do the jobs.

then why don't you get a machine with 4 16-core AMD opterons?
you can run it like a workstation. and they tend to be affordable.
am certain that this is easier to set up that any of this cloudy stuff.

axel.

>
> Thanks,
> Jaycee
>
>
> On Thu, Feb 14, 2013 at 12:39 AM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
>> wrote:
>
>> Hi,
>>
>> Last time I checked (3 years ago) it was much cheaper to build your own. I
>> had a lot of fun building my own 10k€ cluster. If you throw in some GPUs
>> you can get impressive performance. My only regret is that I could really
>> use the two/three months I spend for this now (toward the end of my PHD).
>>
>> For example 3 months of a Quadruple Extra Large GPU costs ~4500$ for
>> which you can buy your own (and it will last at least a year).
>>
>> Regards,
>> Ajasja
>>
>>
>> On 14 February 2013 08:30, Norman Geist <norman.geist_at_uni-greifswald.de>wrote:
>>
>>> Hi,****
>>>
>>> ** **
>>>
>>> Just for my interest, wouldn’t it be more comfortable to spend the money
>>> in some own hardware, where you can have physical access? Distributing
>>> computations to any cloud network sounds unreliable and complicated.
>>> Additionally, why not get an account for a high performance computing
>>> centre? This AWS stuff don’t seem to be meant for “long time full load”
>>> usage.****
>>>
>>> ** **
>>>
>>> But 1st of all, what are you going to do with namd. How big will your
>>> systems be. If we know some detail, we can better advice you. Maybe some
>>> local GPUs will do the job for you.****
>>>
>>> ** **
>>>
>>> Norman Geist.****
>>>
>>> ** **
>>>
>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *Cloud Computing
>>> *Gesendet:* Mittwoch, 13. Februar 2013 23:05
>>> *An:* namd-l_at_ks.uiuc.edu
>>> *Betreff:* namd-l: running NAMD on Amazon EC2?****
>>>
>>> ** **
>>>
>>> Dear all,****
>>>
>>> ** **
>>>
>>> Does anyone have experience running NAMD on Amazon web service? I created
>>> an Amazon machine image for NAMD on single node setting (you can locate it
>>> by searching for namd in AWS public ami) , but it'd be nice to learn how to
>>> run NAMD jobs on a cluster setting on AWS. So if anyone has relevant
>>> experience or interests and would like to share, let's have a discussion

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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