[gmx-users] Version error running mdrun

Jordi Camps jcamps at lsi.upc.edu
Mon Mar 21 12:57:38 CET 2005


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.

Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
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 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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