[gmx-users] invalid number of nodes

[Carsten Kutzner]

Hi Rebeca,

Lines 69/70 of 3.3 include/types/simple.h reads

/* Max number of nodes 	*/
#define MAXNODES	256	

This obviously needs to be set to a higher value.
There is also a MAXNODES parameter in CVS src/gmxlib/tpxio.c,
which I guess also needs to be set to the same value if
you want to use 3.3 grompp together with CVS mdrun.

Good luck!

Carsten


Rebeca García Fandiño wrote:
> Hello,
> 
> I want to simulate a membrane+proteína system  (more than 700.000 atoms) 
> with Gromacs 4 and I would like to use 512 proc.
> 
> I am creating the mdp file with Gromacs 3, since I have read in the wiki 
> that it was a good way to include the number or processors ins the mdp 
> file for the new version.
> 
>  
> 
> For grompp with Gromacs 3.3 I amincluding this options in the input mdp 
> file:
> 
>  
> 
> fourierspacing           = 0.12
> 
> fourier_nx               = 1024
> 
> fourier_ny               = 1024
> 
> fourier_nz               = 0
> 
>  
> 
> but when I execute:
> 
>  
> 
> grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o 
> equilibrado2.tpr -n index.ndx -np 512
> 
>  
> 
> I receive this error:
> 
>  
> 
> -------------------------------------------------------
> 
> Program grompp, VERSION 3.3.3
> 
> Source code file: grompp.c, line: 1021
> 
>  
> 
> Fatal error:
> 
> invalid number of nodes 512
> 
>  
> 
> -------------------------------------------------------
> 
>  
> 
> When I had tried the same with 256 proc, using fourier_nx= 
> fourier_ny=512, the correspondent error did not appear.
> 
> Is there a limit of processors in Gromacs for grompp or which could be 
> the problem?
> 
>  
> 
> Thank you very much for your help in advance,
> 
>  
> 
> Rebeca García Fandiño
> 
> Parc Cientific of Barcelona
> 
> 
> ------------------------------------------------------------------------
> ¿Todavía no conoces El Duelo? Descúbrelo y reta a tus contactos de 
> Messenger El Duelo <http://www.vivelive.com/duelo>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php