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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 22 09:44:45 CEST 2009

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.


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