Subject: Summary of "How to build PC clusters for MD simulation"

From: "Keisuke Ishida" <[email-masked]>
Date: Fri, 31 Mar 2000 02:06:49 +0900

Thank you very much for many replies to my question that is
"I want to build PC cluster for MD simulation.
Please let me know how to build PC cluster
and which MD programs can I get for parallel computers."

I know that many people have interested in this field and
I have received some e-mails for summary of replies to my question.
So I will summarize many replies as follows:

********************
>Li Guo Hui wrote:
as i known, molsim.chem.uva.nl is the very useful homepage for what you
want, when you begin to build culster,could you tell
me some details about your cluster ?

********************
>Vincent wrote:
you will probably use Linux as operating system... (or else you should).
you then might want to take a look at the Boewulf Project on clustering
computing with Linux.
Also, look at this page (from the UCLA computing center) for other details
on
high performance computing:
http://www.ats.ucla.edu/at/hpc/topics_in_hpc/default.htm
Also, here's a nice documentation about Linux clustering:
http://metalab.unc.edu/mdw/HOWTO/Beowulf-HOWTO.html
Hope this will help you.

********************
>Dr O. Parchment wrote:
A posting that you made to the CCL mailing list regarding PC clusters
for MD has been forwarded to the Beowulf mailing list. I have been involved
with the construction of 2 PC clusters, which are capable of running MD
codes.
The first was a small 8 cpu cluster
http://www.soton.ac.uk/~chemphys/jessex/beowulf.html
and latterly a 19 node machine http://www.soton.ac.uk/~oz which I have
run MD codes on both of these pages have information on the hardware &
software
used. If you need any further help I would be pleased to give what help I
can.

********************
>Huub van Dam wrote:
If you want to know how to build a PC cluster I suggest you start by looking
at
the Beowulf homepage:
    http://www.beowulf.org/
this leads to some information on the issues involved and there are pointers
to
other sites building the same class of systems.

********************
>Jose C. Corchado wrote:
We are planning to do the same thing: a PC cluster that will be mostly
dedicated to MD calculations.

As for the cluster, I have found some information on the beowulf project
web page and the links included there. I have also found a few web pages
where custom-build clusters are sold (hardware and software). As for MD
programs, I know that the program "moldy", which is availabe at CPC, can
work on parallel computers.

Some web pages are:
http://www.beowulf.org
http://www.extremelinux.org
They are plenty of links to tutorials and other web pages where you can
get more info.

Some companies selling clusters are:
http://www.xtreme-machines.com/
http://www.microway.com
http://www.plogic.com/
http://www.kachinatech.com/

********************
>Antonio Luiz Oliveira de Noronha wrote:
Look for Beowulf cluster project or Extreme Linux project.
The Beowulf is the project from NASA about pc clusters.

In the inthernet there are some HOWTO's about beowulf clusters, specially
in the linux documantation project.

You just need to downlowd the HOWTO's ( general one ) and when you unzip
him, you will find the HOWTO about beowulf and intranet.

About the program, a good one could be AMBER, but this depends about what
is your project.

********************
>NELSON HENRIQUE MORGON wrote
in this site you will find useful informations:
http://molsim.chem.uva.nl/cluster/

********************
>Dr. David van der Spoel wrote
The GROMACS software will work fine on PC clusters
http://md.chem.rug.nl/~gmx
however you have to invest in networking, do get Gigabit ethernet or
something like that.

Scaling information on a simple cluster can be found at
http://zorn.bmc.uu.se/~spoel/gmxscaling.html
The best I got was slightly more than 75% scaling for an 8 processor
cluster.

********************
>Armel Le Bail wrote
There is a brand new one here, with detailed
explanations and pictures :
http://weblotus.univ-lemans.fr/w3lotus/index.html

********************
>Alex Ninaber wrote
'just' a beowulf PC cluster is a pretty bad idea for doing MD code. Unless
you are going to run lots of small MD jobs with a slightly different
starting structure, a PC cluster connected with ethernet is going to be
pointless. MD code, especially if you want to use Ewald or PME, scales
notoriously bad with the number of processors. Dual Intels connected with
Myrined or some other type of fast interconnect appears to be ok. Alphas
with the Quadrics interconnect is pretty good if you have some money to
burn. For Intels, expect the interconnect to be close to the price of a
single Intel box.

As for good MD programs:

Amber
Gromacs
Charm
Gromos

All run on clusters. We have had excellent results with the free
Gromacs. Factor 2 compared to Amber running with PME on a 6 node SGI
Origin. We expect to see the same thing on Alpha computers.

If anyone is interested in having more information on this topic, we
specialise in optimising the cluster computer environment for the specific
software applications.

********************

Thanks,

Keisuke Ishida
Chemistry Laboratory, Taiho Pharmaceutical Co.,Ltd.
Hanno 357-8527 Japan
TEL. +81-429-72-8900
FAX. +81-429-72-8913
E-mail. [email-masked]