Re: running NAMD on Amazon EC2?

From: Cloud Computing (cloudbiocomputing_at_gmail.com)
Date: Thu Feb 14 2013 - 14:38:38 CST

We're a small lab doing drug discovery,and just need to run a few molecular
dynamics trajectories to relax and refine the 3-D target structure, and we
have no plan to purchase clusters for dedicated large-scale computationally
intensive jobs simply because we don't have this need. Getting an account
at a national supercomputing center will have to submit a proposal and go
through a lengthy process, since most of our MD jobs will be small, we
don't think it's necessary or worth the effort. Amazon web service seems
convenient, as long as you have a lab credit card you're ready to go. My
only problem meanwhile is it's easy to run NAMD on a single node with a
maximum of 8 cores, but spinning up a large cluster for parallel computing
seems to require some extra work.

Jaycee

On Wed, Feb 13, 2013 at 11:30 PM, 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.
> ****
>
> ** **
>
> Jaycee Chan****
>
> Research Scientist at UW****
>

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