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
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Received on Wed Jun 05 2013 - 03:00:04 PDT
