[gmx-users] Version error running mdrun

[David van der Spoel]

On Mon, 2005-03-21 at 12:57 +0100, Jordi Camps wrote:
> Hello
> 
> The warnings occur with the .tpb files. They are also #processors dependent:
> with 2 processors I get 2 warnings and the simulation finish. With 1
> processor I get lot of warnings and a fatal error (the one that you saw).
> And with 4 processors I get a lot of warnings too and the fatal error.
OK,

does this system run on another machine? (Pentium or something like
that)? It could be a problem in your simulation.
> 
> -- 
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> c/. Jordi Girona 1-3              
> Modul C6-E201                     Tel.  : 934 011 650
> E-08034 Barcelona                 Fax   : 934 017 014
> Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu
> 
> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> nombre de David van der Spoel
> Enviado el: lunes, 21 de marzo de 2005 9:02
> Para: Discussion list for GROMACS users
> Asunto: RE: [gmx-users] Version error running mdrun
> 
> 
> On Sun, 2005-03-20 at 23:03 +0100, Jordi Camps wrote:
> > Hello,
> > 
> > The hardware is new for us, but gromacs I think that other users has 
> > gromacs running on this processor with other Oses (MacOSX). Either way 
> > the computer is not in production phase yet, and IBM technicians are 
> > working on the setup. This means that the software installed is 
> > minimum and gromacs is not part of the basic installation.
> OK, have them see over the installation of rpc/nfs/xdr libraries.
> 
> 
> > About the test in other machines, you are right. The files generated 
> > (.tpr) are different between another Linux (2.4 kernel) and my 
> > cluster. My .tpr file does not run on any mdrun, but the .tpr file 
> > generated outside my cluster works in and outside of my cluster. So 
> > the problem is in writing the file for sure. Maybe reading too, 
> > because the simulation fails after so many warnings like this and the 
> > error:
> > 	Step 3013, time 6.026 (ps)  LINCS WARNING
> 
> Does this happen with the tpb files as well?
> 
-- 
David.
________________________________________________________________________
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://xray.bmc.uu.se/~spoel
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