VMD-L Mailing List

From: Johannes von Langen (langen_at_imb-jena.de)
Date: Mon Jul 22 2002 - 05:26:19 CDT

Dear Zhanwu,

I'm using quite a few intel based Linux machines for dynamic-simulation
using Amber6, maybe this will help you:

All my machines are Dual Athlon boxes with MP1500+ to MP1900+ CPUs -
Using mpich or LAM/MPI scaling up to two Prozessors works very nice, but
using more CPUs on one job is a hard task, as normal networks are to
slow.
I connected two Dual MP1900+ boxes via Gigabit directly (a Gigabit-Hub
would have been to expensive), and like this, scaling up to 4 CPUs is
pretty much allright.

My boards are all Tyan Tiger with 512MB to 1GB RAM (although they say,
you need registered RAM, normal RAM works as well on my machnines - but
of course no guarantee for that).

Heat can be a difficult task to solve - I allways leave my boxes on one
side open (thou pretty noisy).

Normal harddrives (IDE) perform sufficient.

The price for one box (2xMP1600+ 512MB RAM 40GB Harddrive) was approx.
1.500 Euro halv a year ago (with a cheap grafic-card).

They had all been build up at a local hardware shop.

If you want to process large trajectories using vmd - make sure, your
swap space is large enough!
My experiences with trajecotries are, that you should have at least 1.5
times the amount of RAM than the size of your trajectory, if you plan
to jump around within the trajectory - just for movie-production or
looking through it works fine with less RAM.

yours Johannes

"Liu, Zhanwu" wrote:
>
> Dear VMD-L,
>
> We plan to buy a intel based Linux machine to do processing of
> large trajectory files(~ 1 Giga), could you give me some suggestion
> about the configuration of the computer, and whether there is
> such computer from any manufacture?
>
> Thanks a lot!
>
> Yours Zhanwu
>
> ---------------------------
> Zhanwu Liu, Ph.D.
> Department of Anesthesiology
> University of Pittsburgh 

-- 
Johannes von Langen                       langen_at_imb-jena.de
Institut fuer Molekulare Biotechnologie   
Beutenbergstrasse 11, Jena                Tel.: +49-3641-65-6213
Postfach 100 813, D-07708 Jena, Germany   Fax:  +49-3641-65-6210