[gmx-users] Wrong LJ energies on Apple Mac OS X with Myrinet

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 28 23:48:09 CEST 2006

Goran Krilov wrote:
> Hi,
> I have an  issue with GROMACS on Apple PPC that I am trying to
> resolve. Careful analysis of our data has shown that one particular
> term of the energy function (LJ short range) gives a different result,
> depending on which version of GROMACS we use.
> Namely, if I use the binary precompiled by GROMACS developers on  darwin 
> 8.2.0,
> I get the result 9.99750e+03. However if I use the binaries built  with the
> Myrinet MX and Apple 4.0 compiler on 8.3.0, that were built by us
>  we get  1.00229e+04 for the same term. That is a significant
> difference. Especially so, because all the other energy terms are  
> exactly the
> same for the two versions.
> Moreover, when we use GROMACS 3.3 and GROMACS 3.2.1 on Linux, we get
> 9.99750e+03. Also, independent calculation with a different package  
> gives us .99750e+03. In all cases we used the same input and data  
> files, and outputs
> are identical except for the difference in the energy term noted.
> So it would seem our Myrinet built GROMACS gives the wrong answer.  Any 
> ideas what
> could be going on?

A difficult problem, although there is only one deviation. You say you 
have myrinet stuff linked in, but do you use it in this case? If this is 
not a parallel simulation, then the myrinet library will not affect the 
results. If this is a parallel simulation you could try to use the tcp 
communication, if this gives the right results your myrinet library 
might be faulty, although it seems very unlikely. I would  rather 
suspect the compiler. But first things first: if you can provide a tpr 
file that works in 3.2.1 and that produces the right values in 3.2.1 we 
can test it. Please file a bugzilla in that case.

> Thanks!
> Regards,
> ------------------------------------------------------------------------ 
> ----
> Dr. Goran Krilov                    Tel. (617) 552-8927
> Assistant Professor               Fax (617) 552-2705
> Department of Chemistry     E-mail: goran.krilov at bc.edu
> Boston College
> Merkert Center, 2609 Beacon St
> Chestnut Hill, MA 02467
> ------------------------------------------------------------------------ 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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