[gmx-users] Version error running mdrun

[Jordi Camps]

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.
I check the executables used with "which mdrun" and the result is my own
executable. If I do not set up the PATH variable with the gromacs folder
this test returns nothing.

My system has a 64bit OS:
	$ uname -a
	Linux login1 2.6.5-7.111-pseries64 #1 SMP Wed Oct 13 15:45:13 UTC
2004 ppc64 ppc64 ppc64 GNU/Linux

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
	relative constraint deviation after LINCS:
	max inf (between atoms 284 and 285) rms inf
	bonds that rotated more than 30 degrees:
	 atom 1 atom 2  angle  previous, current, constraint length
	    284    285   90.0  7405077.5000      inf      0.1000
	    284    286   90.0  4839638.0000      inf      0.1000
	    289    290   90.0    0.1000      inf      0.1000
	    295    296   90.0  717.9312      inf      0.1000
	    295    297   90.0  478.8020      inf      0.1000
	Fatal error: ci = -2147483648 should be in 0 .. 1319 [FILE nsgrid.c,
LINE 218]

But I don't want to take care for this error right now.

Thanks a lot for your help!

-- 
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: domingo, 20 de marzo de 2005 21:32
Para: Discussion list for GROMACS users
Asunto: RE: [gmx-users] Version error running mdrun


On Sun, 2005-03-20 at 21:13 +0100, Jordi Camps wrote:
> Hello!
> 
> I gave a try to you advise to use .tpb file format, and it worked! But 
> the question is: why the .tpr format is not recognized???
Does your system have a 64bit OS? There could be an incompatibility with
libraries that is only noted at run time. 
 
The tpb file is not portable (in contrast to the tpr format), so regard 
it as a workaround only. 

You could also try to read a tpr file from your cluster on a PC, and vice
versa, such that we know whether the problem is in reading files, writing
them, or both.
> > 
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

-- 
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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