[gmx-users] RE: problems with parallel mdrun

singh singh at biophysik.chemie.uni-dortmund.de
Mon Aug 13 14:52:38 CEST 2007

Dear Mark and Carsten,
Thanks for the reply
Manually setting the grid dimensions works but I have a doubt

Since I am using  walls in my simulations with wall_ewald_zfac =3
Will it be more appropriate to use

Or to leave Fourier_nz=52 and grompp will extend it ?
The other suggested approach doesn't work as grompp from Gromacs 3.3.1  does
not recognize the wall options of mdp files and gives errors. so it seems
that back compatibility will not be there specially when using new features
in mdp files.

With Regards
Gurpreet Singh 

University of Dortmund
Department of Chemistry
Physical Chemistry I  -  Biophysical Chemistry
Otto-Hahn Str. 6
D-44227 Dortmund
Office:   C1-06 room 176
Phone:  +49 231 755 3916
Fax:     +49 231 755 3901
-----Original Message-----
From: Mark Abraham [mailto:Mark.Abraham at anu.edu.au] 
Sent: Thursday, August 09, 2007 10:02 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problems with parallel mdrun

Carsten Kutzner wrote:
> Mark Abraham wrote:
>> Gurpreet Singh wrote:
>>> I get the following errors while using paralled version of mdrun
>>> with openmpi.
>>> mpirun -np 4 mdrun_d_mpi -np 4 -v -deffnm EQUI1
>>> *****
>>> Program mdrun_d_mpi, VERSION 3.3.99_development_20070720
>>> Source code file: gmx_parallel_3dfft.c, line: 90
>>> Fatal error:
>>> nx (50) and ny (50) must be divisible by the number of nodes (4).
>>> *******
>>> I am using a cubic box of 5nm and grid spacing is 0.1. The simulations
>>> runs fine if i use 5 nodes
>>> I am using a machines with 2 dual xeon processors so -np 4 is more
>>> appropriate for my sytems.
>>>  Is there any way to use -np 4  without changing the gridspacing or
>>> box size?
>> No. I'm guessing your .mdp file is trying to specify nx/ny/nz, rather
>> than the grid spacing. If you specify the latter, grompp will take care
>> of this issue so that you get the largest allowable spacing smaller than
>>  (or equal to) the requested grid spacing.
> Hi,
> in the current CVS version of grompp you cannot use the -np switch
> anymore. You will have to comment out the 'fourierspacing = 0.1' line
> and set
> fourier_nx               = 52
> fourier_ny               = 52
> fourier_nz               = 52
> in order to get a tpr file that you can run on 4 processors.
> Alternatively, stick to the original mpd settings but use the 3.3.1
> version of grompp with -np 4. These tpr files are read by CVS gromacs.

Aha, that explains it. Gurpreet, don't bother with the testing procedure 
I just outlined. Try one of Carsten's suggestions.


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