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

[Jim Kress]

 > you do compile and experiment suitably. For GROMACS, a 
> straight configure && make install is rather unlikely to be 
> suitable, these days.

Why?

Jim

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
> Sent: Wednesday, July 22, 2009 3:45 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Re: comparison of gromacs in CENTOS 
> and UBUNTU
> 
> Alexandre Suman de Araujo wrote:
> > 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!
> 
> Caveat that you need to be reasonably competent at compiling 
> software at least for your machine and those pieces of 
> software in order to be assured you're not doing a worse job 
> then those maligned nameless people. Acquiring the necessary 
> expertise is something of a hit-and-miss process, and so I 
> would leave things like MPI and FFTW libraries and kernels 
> alone to the supervision of people who think they know about 
> them. Perhaps one could try some different versions of 
> libraries to find the best one, or make some inquiries about 
> the experience of the person who compiled the library to help judge.
> 
> Then also, consult the available documentation for the things 
> you do compile and experiment suitably. For GROMACS, a 
> straight configure && make install is rather unlikely to be 
> suitable, these days.
> 
> Mark
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