[gmx-users] Re: comparison of gromacs in CENTOS and UBUNTU

[Alexandre Suman de Araujo]

Obviously the HD space has nothing to do with GMX performance (unless it is
full, of course), but the use of Ubuntu precompiled packages can affect
drastically the GMX performance, especially if you are also using pre-compiled
MPI library package.

An important rule when you are interested in High Performance 
Computing: Compile
ALL your softwares (the last REALLY stable version) using GOOD 
compilers (GCC is
fine, but if you have access to Intel or Portland ones is better).

This rule is highly recommended ALSO to your linux kernel.

Never leave the important and easy work of compile your important 
programs with
unknown people!

Cheers


-- 
**************************************************************
Alexandre Suman de Araujo                                    *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto        *
Universidade de São Paulo                                    *
Dep. de Física e Química                                     *
Grupo de Física Biológica     * e-mail: asaraujo at fcfrp.usp.br*
Av. do Café, s/n°             * e-mail: ale.suman at gmail.com  *
CEP: 14040-903                * Phone: +55 (16) 3602-4172    *
Ribeirão Preto, SP, Brasil    * Phone: +55 (16) 3602-4222    *
**************************************************************



Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
> I don't see how hard disk space of the OS has anything to do with the 
> speed of Gromacs.  Are the machines you refer to identical in terms 
> of hardware (CPU, RAM, etc) as well as the compilers used to install 
> the software?
>
> I have installed Gromacs under several different OS - Mac, Ubuntu 
> Linux, Yellowdog Linux, and Fedora Linux.  The only real speed 
> difference comes from the hardware.
>
> -Justin
>
> Laercio Pol Fachin wrote:
>> Hi!
>>  In a UBUNTU installation in dual boot (with Windows, in my case), 
>> GROMACS is approximatedely twice slower than in a installation in an 
>> entire HD.
>>  If you need to install Linux in dual boot, maybe CentOS is a better choice.
>>  Best regards,
>> Laércio Pol-Fachin
>>
>> --- Em *ter, 21/7/09, gmx-users-request at gromacs.org 
>> /<gmx-users-request at gromacs.org>/* escreveu:
>>
>>
>>        1. comparison of gromacs in CENTOS and UBUNTU (jagannath mondal)
>>
>>     Date: Tue, 21 Jul 2009 22:49:12 +0530 (IST)
>>     From: jagannath mondal <jmondal2004 at yahoo.co.in
>>     <http://br.mc515.mail.yahoo.com/mc/compose?to=jmondal2004@yahoo.co.in>>
>>     Subject: [gmx-users] comparison of gromacs in CENTOS and UBUNTU
>>     To: gmx-users at gromacs.org
>>     <http://br.mc515.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
>>     Message-ID: <410193.9922.qm at web7906.mail.in.yahoo.com
>>     
>> <http://br.mc515.mail.yahoo.com/mc/compose?to=410193.9922.qm@web7906.mail.in.yahoo.com>>
>>     Content-Type: text/plain; charset="iso-8859-1"
>>
>>     Hi,   I was planning to install one of the linux distributions :
>>     CENTOS or UBUNTU in our xeon 8-core processor.  Can any one suggest
>>     which one will be better for Gromacs as far as installation and
>>     performance is concerned?ThanksJagannath
>>
>>
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>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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