I believe you can gt a compute OS on a 120GB solid state that costs about
70 quid. that's good value for money IMO. :)
On 5 June 2013 10:55, Jan-Philip Gehrcke <jgehrcke.googlemail.com> wrote:
> Hello, see below.
>
> On 06/05/2013 11:38 AM, Josh Berryman wrote:
> > Hello AMBER Devs & Users:
> >
> > I am speccing out a new compute lab for MSc students to use as a
> > sandbox-type facility to learn simulations. Of course I will use it
> myself
> > as my personal minicluster when the students are not around.
> >
> > Does anyone want to comment on this rough spec which I have drawn up?
> Can
> > anyone post the documentation for any similar setup of their own?
> >
> > ***********
> >
> > 8 workstation machines, each as:
> >
> > * 1 Tesla C2075 or similar GPU (worth bothering with for pmemd?)*
>
> What do you mean with 'worth bothering'? Make yourself familiar with the
> advantages Amber takes of modern GPU hardware, and then decide yourself
> depending on your needs. If the plan is to run mostly MD with Amber on
> this cluster, then you could consider focussing entirely on GPU hardware
> (more GPU, less CPU, could also consider AMD buying AMD).
>
> The point is: you can have much more performance per money with GPUs
> than with running on CPUs only.
>
> >
> > 16 cores (Intel are promising a die shrink this summer: should I wait
> for
> > this next gen, 'Haswell'?)
>
> Waiting not required, you could always wait for the next generation. The
> CPU specifics strongly depend on whether you want to focus on GPU
> hardware or not:
>
> If not, take something really fast. But be aware that especially with
> Intel price it not proportional to performance. Check the benchmarks.
>
> If yes, take something really cheap :-)
>
> >
> > 4 GB ram
>
> This is not enough. Even an office workstation these days should have 8
> GB of RAM. And you should definitely consider buying at least 12-24 GB,
> because, if I understood correctly, these workstations will also be used
> as graphical workstations. Sometimes you want to be able to load huge MD
> trajectory data into RAM....
>
> >
> > 200 GB HDD for OS, scratch & swap (maybe use a solid-state drive?)
>
> SSDs are awesome, of course, but if you are short in money, I'd rather
> invest in RAM than in SSDs.
>
> >
> > 1 monitor, 24" or so. Pref low power use for these (twisted nematic,
> > but without IPS, such as Dell P2412-H).
>
> Buy larger screens. You don't have fun these days with just 24 inches
> :-) Look up the price differences, they are not significant compared on
> what you plan to spend anyway...
>
> >
> > ************
> >
> > 1 x GB ethernet switch
> >
> > 1 x 10TB NAS-NFS for home directories
> >
> > 1 x 20TB NAS-NFS to backup the first one
>
> Discussing backup strategies would be way too off-topic here, I just
> hope that you are experienced here or have someone experienced at hand.
>
> Cheers,
>
> Jan-Philip
>
> > *************
> >
> > Josh Berryman
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Wed Jun 05 2013 - 15:00:02 PDT
