RE: Amber/Gentoo linux

From: Ross Walker <>
Date: Sun 11 Aug 2002 22:32:37 +0100

Dear Jianhui

> I will try to rephase my question again. From what I can get from the
> internet search, amber guys mostly use RedHat or SUSE linux.
> A computer
> (linux) guy told me that Gentoo is optimised for cluster and
> could give
> me significant performance gain over other linux
> distribution. Is he is
> right, how come I never hear that amber guys use Gentoo linux?

I doubt this would make a huge difference, it may be easier to set up
and include more cluster based tools but I doubt it would make a huge
difference to overall performance. If you compile your own kernel in
RedHat then it will be optimised for the cpu you select. Also, if you
compile amber on your working machine then it too (depending on what
compile time options you choose) will also be optimised for your cpu.
Hence I don't see where Gentoo would make a huge difference to the
performance. It may indeed be quicker than a stock "out of the box"
RedHat distribution but with careful setting up RedHat ought to be just
as fast.
> If you are running amber under Gentoo linux, could you give me a line
> and say "Hey, it is better"? (or perhaps not so different
> with Redhat?)

I run Amber with RedHat linux in a cluster environment, I have run both
single channel 100MBPs, Dual Channel 100MBps, Myrinet 2000 and Scali
with both MPICH and LAM MPI (Note, I found RedHat's default installed
LAM MPI to be about 15 % faster than MPICH) and it works perfectly and
the performance appears to be fine. I tried Suse a while back and it
made no difference to the performance. Thus my advice to you is to use
whatever distribution you are comfortable with. I use RedHat as I grew
up with RedHat, I know all the config file formats, tools etc. RedHat is
also a very popular "flavour" of Linux and so help is easily available
on the web and RPMs exist for most packages. However, if you have people
working with you who familiar with Gentoo then by all means use this

I hope this helps.

Ps. This is just my personal opinion so no 'this is better than that'
flames please :-)

All the best

|\oss Walker

| Imperial College of Science, Technology & Medicine |
| Department of Chemistry | Theoretical Division |
| Tel:- +44 20 759(45851) |
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Received on Sun Aug 11 2002 - 14:32:37 PDT
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