[gmx-users] Re: stepsize too small: help to solve problem in GROMACS installation

Mark Abraham mark.abraham at anu.edu.au
Thu May 27 09:28:48 CEST 2010

----- Original Message -----
From: Anna Marabotti <anna.marabotti at isa.cnr.it>
Date: Thursday, May 27, 2010 16:55
Subject: [gmx-users] Re: stepsize too small: help to solve problem in	GROMACS installation
To: gmx-users at gromacs.org

> Dear Justin, dear all,
> sorry for not having seen the warning before asking the question about
> compilers (just a little justification, however: the warning 
> appears only on
> the Download page, not on the Installation page; I went directly 
> to the
> installation page and I did not notice it).

> The only other possibility we have is to try compiling GROMACS 
> with gcc-442
> compiler. This time I checked more carefully (at least, I hope 
> so!) on the
> site and it seems to me that no problems are reported. For your 
> experience,is it a good choice or we can expect other problems? 
> In this last case, what
> do you suggest as the best compiler for Gromacs?

GROMACS performance is pretty insensitive to compiler version so long as you are using assembly-language inner loops (e.g. always true by default on x86). Most of the compute time is spent there, so most of the rest is irrelevant.

The main side issue is the FFT performance for PME. Make sure you're using either vendor FFT libraries, or suitably well-compiled FFTW. Even there, FFTW with gcc -O5 (making sure the SSE(n) optimization is used) was only a hair behind icc+mkl in some tests I did a year ago.


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